sign in sign up
<<
Home , Berchemiella, Epiphyas, Eteobalea, Matthew Hurles, McIlwain, Peruvian plantcutter

APPENDIX II –CURRICULA VITAE

ROL E NAME (e.g., ICI leader, co-investigator, project manager, etc.) Peter Freeman Executive Director

John Chenery Director of Media and Communications

Jesse Ausubel Member, Board of Directors

Ivar Myklebust Member, Board of Directors Rocky Skeef Member, Board of Directors Steve O’Brien Chair, Science Advisory Board David Haussler Member, Science Advisory Board Paul Thompson Member, Science Advisory Board John McPerson Chair, Technology Development Advisory Group Jay Shendure Member, Technology Development Advisory Group Barton Slatko Member, Technology Development Advisory Group Baoli Zhu Member, Technology Development Advisory Group Christian Brochmann Vice-chair, WG2.4

Greg Singer Chair, WG5.1 Peter Phillips Chair, WG6.2 David Castle Chair, WG6.5 Richard Gold Chair, WG6.3 David Secko Chair, WG6.4 Tania Bubela Chair, WG6.1 Andrew Mitchell Australia representative on the SSC Andrew Lowe Australia alternate on the SSC

Thomas Valqui Peru representative on the SSC Gisella Orjeda Peru alternate on the SSC

98 PETER FREEMAN BA, PHD, FIBD

120 Stuart Street, Guelph, Ontario, CANADA N1E 4S8 Phone (W): +1 519 824 4120 Cell: +1 519 731 2163 Email: [email protected]

PROFILE Experienced science-based (PhD qualified) executive director, with a track record of successfully co- ordinating large multi-institutional research projects, networks and consortia in , proteomics, stem cell research and population health. Strong financial management, strategic planning and project management skills gained in R&D and operations roles in the international malting and brewing industry Superior mentoring, facilitating, technical writing and editing skills used to develop successful interdisciplinary funding proposals. Fully proficient in information /communication technologies and their use in knowledge translation and public outreach activities.

EMPLOYMENT HISTORY

UNIVERISTY OF GUELPH Institute of Ontario EXECUTIVE DIRECTOR, International Barcode of life Project (iBOL) July 2010 – present iBOL’s primary mission is the construction of a DNA-based identification system for all ,and the application of this new tool to better manage, discover and protect global biodiversity.

Reporting to the Scientific Director and responsible to the Board of the iBOL Corporation, the Executive Director coordinates administrative and operational activities for accomplishment of the goals of the International Barcode of life Project

UNIVERSITY OF CALGARY, FACULTY OF MEDICINE Department of Community Health Sciences

EXECUTIVE DIRECTOR, Calgary Institute for Population and Public Health July 2009 – June 2010 The Calgary Institute for Population and Public Health (CIPPH) is a partnership between the University of Calgary and Alberta Health Services. The CIPPH aims to improve health care delivery and population health through a shared research agenda and knowledge transfer and exchange among medical, veterinary and clinical researchers, social scientists and policy-makers.Current activities include:

Developing the Institute’s governance and management framework and inaugural strategic plan Mapping membership demographics and research / knowledge advancement interests Designing and delivering inaugural planning workshop to establish research themes and programs Establishing geographic and virtual collaborative nodes and relationships with key stakeholders Overseeing fundraising activities

99 Peter Freeman - Page 2

UNIVERSITY OF CALGARY, FACULTY OF MEDICINE Department of Community Health Sciences

RESEARCH DEVELOPMENT MANAGER, Population Health Intervention Research Centre February 2008 – June 2009

The Population Health Intervention Research Centre (PHIRC) was established in 2004 with initial funding of $2.4M from the Canadian Institutes of Health Research (CIHR).

Co-ordinated development of the governance and strategic planning processes which led to the establishment of PHIRC as a research centre within the emerging Calgary Institute for Population and Public Health (CIPPH).

EU FRAMEWORK 6: EUROSTEMCELL PROJECT MANAGER (based at University of Edinburgh), 2004-2008

With a 4-year budget of €12M, EuroStemCell was among the largest EU ‘Framework 6’ Programmes, integrating the efforts of 27 leading stem cell research groups (>100 scientists) in 13 academic centres and three biotechnology SMEs across 8 European countries. The role of the Project Manager was to provide day to day management and oversight of the project, supporting the (Scientific) Co-ordinator, Board of Directors and participating researchers in achieving project objectives and strategically positioning the consortium for success in future funding calls. Specific responsibilities included financial management; contractual and administrative co-ordination with participating institutions; organizing and providing secretariat support for scientific meetings, summer schools and workshops; writing, editing and submitting reports and funding proposals; liaison with the EU in Brussels; intellectual property management; overseeing training, communications and public outreach programs.

Over the 4 year lifespan of the project, the consortium

Provided over 100 Deliverables (major project outputs) to the European Commission and published more than 120 scientific papers in leading international peer-review journals.

Generated and collated resources, including antibody reagents and microarray data, which are accessible through the European Stem Cell Database, StemDB, developed by the consortium.

Filed 20 patent applications, several of which have been licensed for biopharmaceutical exploitation by SME partners.

Initiated three successful applications to EU ‘Framework 7’ calls, each funded at a level of €12M. o EuroSyStem: www.eurosystemproject.eu o NeuroStemcell: www.neurostemcell.org/ o OptiStem: www.optistem.org

At the end of the project reconfigured the EuroStemCell website, www.eurostemcell.org , which attracts 15,000 visitors per annum, to serve as an ongoing web portal for European stem cell research.

ALBERTA NETWORK FOR PROTEOMICS INNOVATION (ANPI) EXECUTIVE DIRECTOR (based at University of Calgary), 2002-2004

ANPI, a partnership between the Universities of Alberta, Calgary and Lethbridge, was established with $16 million in federal and provincial funding, directed to establishing technology platforms to support proteomics research and capacity building at the three universities. Platforms included Mass Spectrometry, NMR, Microarray, Mouse Genomics and Bioinformatics facilities.

100 Peter Freeman - Page 3

Responsible for day-to-day financial management and reporting, working with researchers and finance managers at participating institutions to ensure accountability to funders. Supported the CEO and Board of Directors in implementing ANPI’s strategic initiatives, providing leadership and stakeholder accountability within Alberta’s proteomics research community, and establishing a base for longer term provincial and federal support of functional genomics technology platforms.

CONAGRA MALT VICE-PRESIDENT, TECHNICAL SERVICES (BASED IN TORONTO AND CALGARY ) 1993-2002 DIRECTOR, RESEARCH & DEVELOPMENT (BASED IN CALGARY ) 1991-1993

ConAgra Malt is today part of North American Malt, which annually produces approximately one million tonnes of malt and generates revenues in excess of $400M from 14 in Canada, USA, UK and Australia. The company is a leader in its industry, serving many of the world’s largest brewers and distillers.

Managed a group of thirty-two staff engaged in research and development, quality assurance and sales support, with coordination responsibilities for group R&D and technical services functions in Canada, USA, UK and Australia, and for joint venture partnerships in Argentina and Uruguay. Developed and implemented Key Account Management processes across the group’s independently operated trading companies, utilizing cross-functional and cross-geographic teams in a matrix management structure to increase global market share by an estimated $3 million per annum. Spearheaded the successful development, scale-up and installation of new "at-line" product analysis technologies, combined with a laboratory information management system (LIMS) to streamline analytical facilities in Canada and USA.

MORAY FIRTH MALTINGS PLC, ARBROATH, SCOTLAND TECHNICAL MANAGER, 1984-1991

Managed a group of twelve staff engaged in research and development, quality assurance and sales support

BEAMISH & CRAWFORD BREWERY LTD., CORK, IRELAND BREWER / SHIFT MANAGER, 1982-1984

Technical and supervisory responsibility for brewing and packaging operations

MINCH NORTON MALTING, DUBLIN, IRELAND LABORATORY MANAGER, 1974-1978

Managed a group of six staff engaged in quality assurance.

PROFESSIONAL SERVICE

BREWING AND MALTING BARLEY RESEARCH INSTITUTE (BMBRI), WINNIPEG INTERIM MANAGING DIRECTOR (part time secondment), 1999-2000

Led the strategic planning process, revising and updating the organisation's mission and mandate to fund and support pre-competitive research in malting and brewing, and recruiting a new CEO.

101 Peter Freeman - Page 4

PROFESSIONAL ASSOCIATIONS

Advisory Board, Scottish Stem Cell Network, 2007-2008 Treasurer, Institute of Brewing and Distilling (Scottish Section), 2005 – 2007 Board of Directors, American Society of Brewing Chemists, 1995 – 1996 Board of Directors, American Malting Barley Association, 1996 – 1999 Editor-in-Chief, Journal of the American Society of Brewing Chemists, 1996 – 2000 EDUCATION

HERIOT-WATT UNIVERSITY, EDINBURGH, SCOTLAND

Ph.D. (Physiological Aspects of Enzymic Modification in Malting Barley), 1982

Post-graduate Diploma in Brewing and Distilling, with Distinction, 1979.

TRINITY COLLEGE, DUBLIN, IRELAND

B.A., Natural Sciences (Chemistry, ), 1974

AWARDS AND DISTINCTIONS

1979: Brewers’ Association of Scotland Prize, and Brewers’ Society (UK) Scholarship to undertake PhD studies

1990: Fellowship, Institute of Brewing and Distilling (IBD) “Fellowship is the highest membership grade of the IBD. Fellows are nominated and will be distinguished IBD members with substantial experience and responsibility in the field of brewing, fermentation, distilling and associated activities. Fellows may use the post-nominals FIBD”

PUBLICATIONS AND PRESENTATIONS

Freeman, P.L. Current research trends in genomics, proteomics and bioinformatics, and their relevance to malting barley (2003) Presented at the 3rd Canadian Barley Symposium, Red Deer, Alberta, June 19-20. Available: http://www1.agric.gov.ab.ca/$department/deptdocs.nsf/all/fcd7438?opendocument

Freeman, P.L. (Book Chapter) Barley and Malting (1999) in The Practical Brewer, Master Brewers’ Association of the Americas.

Garden, S.W. and Freeman, P.L. Applications of near-infrared spectroscopy in malting: Calibrations for analysis of green malt (1998) Journal of the American Society of Brewing Chemists, 56 (4), pp. 159-163

Wheeler, J.W., Freeman, P.L., Jones, D.K. Selection and application of chemometric techniques in near infrared evaluation of barley malts (1996) Near Infrared Spectroscopy: The Future Waves , pp. 232-235. A. M. C. Davies and P. Williams, eds. NIR Publications, Chichester, UK

102 Peter Freeman - Page 5

Freeman, P.L. Objectives for specialized malting techniques (1994) European Brewery Convention, Monograph XXIII, pp. 165-179 Fachverlag Hans-Carl, Nuremberg, Germany

Freeman, P.L., Churchill, K., Wheeler, J.W., Ruan, R., Fulcher, G. and Armstrong, E. The structural of barley and malt quality (1994) Proc. Fourth Aviemore Conference on Malting, Brewing and Distilling , pp. 25-32 I. Campbell and F.G. Priest, eds. Institute of Brewing and Distilling, London

Freeman, P.L. and Rehmanji, M. The homogeneity of commercial malts in relation to processing conditions (1992) Technical Quarterly, Master Brewers’ Association of the Americas, 29 (2), pp. 57-59

Brown, A.T. and Freeman, P.L. The use of alternative laboratory mashing and filtration techniques in malt quality control (1991) Proc. Conv. Inst. Brew (Central & Southern Africa Section), Victoria Falls, (3), pp. 66-71

Freeman, P.L. and Palmer, G.H The influence of the pericarp and testa on the direct passage of gibberellic acid into the aleurone of normal and abraded barleys (1984) Journal of the Institute of Brewing, 90 (2), pp. 95-105

Freeman, P.L. and Palmer, G.H The structure of the pericarp and testa of barley (1984) Journal of the Institute of Brewing, 90 (2), pp. 88-94

103 John Chenery 28 Rusholme Park Crescent 416-532-8218 Toronto, ON M6J 2C9 416-452-6016 (cell) Canada [email protected]

PROFILE

o Communications and public relations specialist with outstanding record of achievement in public, private, non-governmental and academic sectors. o Extensive experience across the full spectrum of communications activities – media, public and stakeholder relations, strategic advice and issues management, speech writing, preparation of promotional materials and other printed, web and electronic content. o Skilled and creative writer/editor with a background in journalism on four continents.

EXPERIENCE

2009-present International Barcode of Life Project – University of Guelph Director of Media and Communications o Developed comprehensive communications strategy for world’s largest biodiversity genomics initiative. o Executing this strategy with full range of communications products including media campaigns, website redevelopment, online networking, print and multi- media materials, merchandise and events. o Write and edit media releases and initiate other media opportunities resulting in regular coverage of iBOL project and DNA barcoding in international and national press, magazines and television. o Oversaw complete overhaul of project’s web presence, including main website as well as YouTube and various social networking platforms. o Created quarterly newsletter, the Barcode Bulletin.

1998-2009 Bingera Associates - Toronto Principal o Planned and executed communications strategies for private sector, government, international and non-governmental organizations including Canadian Council for Public-Private Partnerships, Environment Canada, Public Service Alliance of Canada, Canadian Centre for Pollution Prevention, International Institute for Sustainable Development, among others. o Wrote and edited media releases, speeches, op-eds, case studies and other materials for public and private sector clients. o Achieved regular media placement in national press, television. o Wrote freelance magazine articles. o Managed UNU Update, online news magazine of United Nations University.

2006-2007 Green Party of Canada - Ottawa Director of Communications o Directed all external and internal communications activities, including media relations, issues management, website content and integrated internet-based communications, public relations and compilation and production of newsletters, brochures, policy documents, merchandise and other materials.

104 – 2 – November 12, 2010

o Worked with party leadership to identify messaging goals, priorities, strategies and tactics. o Worked closely with Leader to achieve maximum communications value from her interactions with media and other messaging strategies.

1997-98 The Earth Council – San José, Costa Rica Director of Communications o Developed and directed communications strategy for international environment and sustainable development organization based in Costa Rica. o Led international team that delivered press conferences, media events, press kits and releases and other promotional materials to announce and publicize programs and projects. o Directed compilation, translation, editing and production of all English, Spanish and French technical and non-technical publications and documents including books, newsletters, reports, brochures and other publicity materials, strategy documents, project briefs and proposals. o Maintained communications with international network of journalists tracking international development issues.

1996-97 Central America Media Services – San José, Costa Rica Founder and Director o Founded media relations and marketing consultancy. o Internet consultant for Interamerican Institute for Cooperation on Agriculture.

1994-96 Costa Rica Today – San José, Costa Rica Editor

1988-93 Mail Newspapers plc – London, UK Senior Commissioning Editor

1985-87 Various National Newspapers – London UK Journalist (writer and sub-editor)

1984 The Sun – Sydney, Australia National Columnist

1980-83 The Sydney Morning Herald Ltd – New York, USA Foreign Correspondent

1979-80 The Sun – Sydney, Australia Financial Journalist

EDUCATION Bachelor of Economics (1978) – University of Queensland

105 Jesse Huntley Ausubel http://phe.rockefeller.edu

Areas of interest: environmental science & technology, industrial , diffusive processes, academic & research enterprise, science & diplomacy

Current Positions: The Rockefeller University, Director, Program for the Human Environment, and senior research associate (1993-); fellow in science and public policy (1989-1993) Alfred P. Sloan Foundation, Vice President (2009-), program director (1994-2009), responsible for basic scientific research and for history of science & technology Woods Hole Oceanographic Institution, Adjunct Scientist (1995-), guest investigator (1990- 1994) Resources for the Future, University Fellow (1994-)

Prior Positions: Carnegie Commission on Science, Technology, and Government, director of studies (1989- 1993) National Academy of Engineering, director of programs (1983-1989) National Research Council, Board on Atmospheric Sciences & Climate, study director (1981- 83) International Institute for Applied Systems Analysis (IIASA), Resources and Environment Area, research scholar and leader, Climate Task (1979-1981) National Academy of Sciences, Climate Research Board, resident (Sloan) fellow (1977-79)

Concurrent part-time positions: The Rockefeller University, assistant to the executive vice president (1984-1988) National Science Board, Committee on International Science, consultant & sec'y (1983- 1985)

Major contributions: Organized 1st UN World Climate Conference (Geneva, 1979); helped formulate and start US and World Climate Programs and International Geosphere-Biosphere (Global Change) Program; improved projections of climate-changing emissions from human activities and understanding of environmental and societal consequences of climate change; helped invent and apply a new vocabulary for studying interactions of technology and environment: dematerialization, decarbonization, and industrial ecology; quantified potentials for technology to spare land for nature and reduce environmental burdens; initiated and help lead worldwide Census of Marine Life; catalyzed development of short DNA sequences (Barcoding) for species identification and international Barcode of Life Initiative for biodiversity management and research; founding chairman of on-line Encyclopedia of Life to create a webpage for every species; initiated Deep Carbon Observatory to examine reservoirs & fluxes of carbon and origins of hydrocarbons & life

Publications: Author or editor of more than 140 books, articles, and reports including The Liberation of the Environment (Daedalus 125(3), 1996), Technology and Environment (National Academy, Washington DC 1989), and Changing Climate (National Academy, Washington DC, 1983)

106 Software: Managed development of package for analysis of logistic wavelets, Loglet Lab (release 2.0 2003 http://phe.rockefeller.edu/LogletLab), and simulation game of US university, Virtual U., released 7/2000 (http://www.virtual-u.org); helped found & launch “Serious Games” movement.

Selected memberships, and advisory & consulting activities: Net Assessment Summer Study, Office of the Secretary of Defense, Co-Chair, 2009 International Barcode of Life (iBOL) project, Board of Directors, 2009- Encyclopedia of Life project, Steering Committee, Founding Chair (2006-2008), member (2008-) Ocean Exploration Working Group, advisory to Nat’l Oceanic & Atmospheric Admin. (2006-) European Distributed Institute of , Scientific Advisory Council (2006-) U.S. Ocean Research & Resources Advisory Panel (2003-7), appointed by Secretary of Navy Canadian Centre for Marine Biodiversity Advisory Board (2001-) President's Panel on Ocean Exploration (2000-2001), appointed by President Clinton Richard Lounsbery Foundation, Board of Trustees (1998-) Electric Power Research Institute, Adv. Council (1998-2006), Board of Directors (2006-2010) Oppenheimer Asset Management investment funds, board member (1998-) Council on Foreign Relations, member (1992-); Committee on Studies (1997-2009); director, Energy & Foreign Policy group (1995-1996); chair, Global Forests study group (1999-2000); Martha’s Vineyard Conservation Society, Board of Directors (1995-) U.S. Environmental Protection Agency, Science Advisory Board, exec. committee (1994-1996) Cohn Forum on Biomedical Affairs, Rockefeller U., org’g (1993-), chair (1997-2007) White House Ministerial Conference on Global Change, 1990, impacts work group, vice-chair National Science Foundation, Directorate of Scientific, Technological, and International Affairs, Advisory Board (1990-1992) National Academy of Sciences/Academy of Engineering, Greenhouse Warming Panel (1989-92) U.S. National Climate Program Office, Intergov’l Panel on Climate Change, reviewer (1988-92) American Academy of Arts & Sciences, US Committee for IIASA (1988-1994) Scientific Committee on Problems of the Environment (SCOPE), climate project (1981-1985) UN Environment Programme/World Meteorological Organization, World Climate Programme, consultant and advisor (1979-1982) Columbia Univ., income & product accounts for the oceans project, research ass't (1976-1977)

Honors: Doctorate, honoris causa, Dalhousie University, 2009; Blue Frontier/Peter Benchley award for ocean science, 2010; Partnership for Observation of the Global Oceans award, 2008

107 Professional Societies: American Association for the Advancement of Science, American Meteorological Society, New York Academy of Sciences, Sigma Xi (Scientific Research Society), Society of American Foresters, International Society for Industrial Ecology

Editorial boards: Journal of Industrial Ecology (1996-); International Journal of Environment & Pollution (1992-); Technological Forecasting and Social Change (1987-2008); Climatic Change (1985-1998)

Media, outreach, application:  Broadcast appearances on radio and TV; Op-Eds, features for dailies, weeklies; coverage in NY Times & other print media in US and abroad; >10,000 monthly unique visitors to PHE website  Activities with US Congress, Federal agencies, numerous international agencies  Frequent contact with industry practitioners in electric power, transport, natural resources, and other sectors; Merrill-Lynch Core “decarbonization” portfolio based on our ideas

Education: Columbia University, 1977, Master of International Affairs & Master of Business Administration Honors: Beta Gamma Sigma, International Fellow; foci: operations research, resource economics Harvard College, 1974, BA with honors Other higher education: College de France, Paris, history, 1973; CIDOC, Mexico, history, 1972 Secondary school: Collegiate School, New York, 1969, numerous honors in math & science

Languages: Italian, French, Spanish; lesser skill in German

Interests: Writing (authored plays, stories, translations from Italian); cities; baseball; Leonardo Cosmos Club, Washington DC, member b. 9/27/51

Addresses: Program for the Human Environment, Box 234, The Rockefeller University, 1230 York Avenue, NY NY 10065-6399; 212-327-7917, [email protected]

Alfred P. Sloan Foundation, 630 5th Ave., New York NY 10111-0242; 212-649-1650

108 Appendix 5

Ivar Myklebust Cand.scient

Director of the Norwegian Biodiversity Information Centre

Erling Skakkes gate 47 7491 Trondheim Norway

Phone: + 47 73 59 21 51/Fax: + 47 73 59 22 40/ mobile: + 47 95 13 31 31

e-mail: [email protected]

109 Curriculum Vitae

Scientific degree: Master of science (cand.scient), zoology, University of Trondheim. 30.04.92.

Title on the : "Accumulation of cadmium in willow ptarmigan(Lagopus lagopus ) at Dovrefjell." (in norwegian).

Employment record:

01.01.05- d.d. Director, Norwegian Biodiversity Information Center 01.09.01- 31.12.04. Head of Department, Directorate for Nature Management 01.01.98-31.08.01 Senior Advicer, Directorate for Nature Management 01.01.93 - 31.12.97 Senior executive officer, Directorate for Nature Management 01.06.92-31.12.92: Research assistent, Norwegian institute for nature research

Particularly relevant working experience:

Keywords: environmental monitoring, biodiversity, management, nature conservation i) International activities:

- Arctic monitoring and assessment programme - The joint Norwegian-Russian commission on environmental protection - Different working groups under the Nordic Council of Ministers - The Global Biodiversity Information Facility (GBIF), member of the Norwegian delegation GBIF Governing Board ( ongoing activity) ii) Other activities of particular interest:

- Development of the national strategy for biodiversity monitoring - Development of the national programme for biodiversity monitoring - Administrator of the «Programme for monitoring terrestrial ecosystems». - Establishing the Norwegian Boidiversity Information Centre (established 01.01.2005). - Head of the Steering Committee for the Norwegian Taxonomy Initative

110

Publications:

Pedersen, H.C., Nygård, T., Myklebust, I. & Sæther, M. 1991. Metallbelastninger i lirype. - NINA Oppdragsmelding 71: 1-18.

Kålås, J.A., Pedersen, H.C., Lierhagen, S., Myklebust, I., Nygård, T. & Steinnes, E. 1991. High levels of cadmium in Norwegian willow ptarmigan. I: Farmer, J.G.(red), Heavy metals in the environment, 1: 212-215. Cep Consultants Ltd., Edinburgh, UK.

Pedersen, H.C., Myklebust, I., Nygård, T. & Sæther, M. 1992. Akkumulering og effekter av kadmium i lirype. - NINA Oppdragsmelding 152: 1-27.

Myklebust, I. 1992. Akkumulering av kadmium i lirype (Lagopus lagopus ) på Dovrefjell. Hovedfagsoppgave i zoologi, Universitetet i Trondheim, AVH, Zoologisk institutt.

Kålås, J.A. & Myklebust, I. 1993. Metaller i hjortedyr i Norge. - NINA Utredning 58

Myklebust, I., Nybø, S., Kålås, J.A. & Pedersen, H.C.1993. Cadmium accumulation in willow ptarmigan (Lagopus l. lagopus ) and rock ptarmigan (L. mutus ) in Central Norway. Sci. Total Environ.134 suppl.: 135-138

Pedersen, H.C. & Myklebust, I. 1993. Age-dependent accumulation of cadmium and zinc in the liver and kidneys of Norwegian willow ptarmigan. Bull. Environ. Contam. Toxicol. 51: 381-388.

Barikmo, J., Myklebust, I. & Olsen, K.V. 1997. Keeping an eye on nature: Example of integrated monitoring. In: Brune, D., Chapman, D.V., Gwynne, M.D. & Pacyna, J.M. (eds). The global environment. Science, technology and management. VCH Weinheim.

Løbersli, E. & Myklebust, I. 1998. Overvåking av miljøgifter i naturen. Ottar nr. 1-98: 38-45.

Myklebust, I. & Pedersen, H.C. 1999. Accumulation and distribution of cadmium in willow ptarmigan Lagopus l. Lagopus. Ecotoxicology 8: 457-465.

111 Appendix 4

Rocky Skeef 1. CONTACT Physical address National Research Foundation (NRF) Meiring Naude Rd Brummeria NRF Private Box PO Box 2600 Pretoria, 0001 South Africa Phone & e-mail Tel : +27 12 481 4129 Cell: +27 83 390 7126 E-mail: [email protected]

2. EDUCATION (Earliest to latest)

University of the Western Cape:

1977 - 80 Completed BSc covering Physics, Botany, Zoology, Biology, Chemistry, Mathematics, Physiology (major) and Biochemistry (major).

University of Natal, Pietermaritzburg:

1981 Registered as a non-degree-purpose (NDP) student to obtain Chemistry II, a pre-requisite to Biochemistry Hons. Also repeated Biochemistry II to improve symbol.

1982 Completed BSc (Hons) in Biochemistry. Title of main research project was “The Effect of Dietary Leucine on the Immune Response, Growth & Feeding of Chickens”.

1983-84 Completed MSc in Biochemistry. Title of thesis was “Dietary Zinc and Cyclic Adenosine-monophosphate as Factors in Cell Proliferation”.

Rhodes University, Grahamstown:

Appendix 4 - iBOL_Summary CV_Rocky Skeef_Sep10.doc 112 1985-87 Completed research for PhD in Biochemistry, supervised by Prof JR Duncan. Thesis entitled “Zinc Inhibition of : Its relevance to Cancer Cells & Possible Mechanism of Action” certified in January 1989.

3. RECENT EMPLOYMENT HISTORY (Latest to earliest)

4.1 2004 (November) – CURRENT

Employer National Research Foundation (NRF). A statutory science council responsible for supporting and promoting science research through funding, human resources development and provision of facilities, to facilitate knowledge creation and innovation (visit www.nrf.ac.za).

Position Executive Director: New Business Development (NBD). A corporate position originally reporting to the President/CEO & currently reporting to the Group Executive – Finance & Business Systems. Main purpose of position is to grow the NRF’s financial resources through:  Facilitating access to & leverage of local & international sources of funding for research  Promoting the NRF as “agency of choice” for research & innovation promotion & support  Developing & securing a strong, positive corporate image of the NRF

Key Performance Areas: Note – As an outcome of recent restructure in rolling out the current NRF Strategic Plan (NRF Vision 2015), the functional areas included in this directorate have evolved to exclude International Relations (effective Sep 08) and Corporate Communication (effective Apr 09)

 Leading the development and roll-out of NRF’s Growth Strategy whose target is to grow NRF revenue to R4billion by 2015 to enable delivery of “NRF Vision 2015”.  Growing knowledge of NRF on funding opportunities (local and international) to pursue its mandate  Establishing new programmes or projects relevant to the business of NRF and locating these within the appropriate operation of the NRF.  Leveraging funding from foreign institutions.

Appendix 4 - iBOL_Summary CV_Rocky Skeef_Sep10.doc 113  Managing the implementation of bi-national and inter- institutional (NRF to foreign counterpart) science & technology (S&T) cooperation agreements.  Leading development of strategy for NRF’s “Focus on Africa” priority and roll-out of this strategy, coordinating efforts with that of government.  Securing SA membership to select S&T bodies and facilitate use of membership privileges by the science community.  Developing corporate policies & standards relating to this function & facilitating compliance across the NRF  Ensuring an efficient, reliable, user-friendly and integrated communication infrastructure.  Establishing & maintaining effective & efficient policies & practice for enhancing the flow of relevant information between NRF & its stakeholders (internal & external).  Doing all that is necessary to portray a single, unified corporate image of the NRF internally & externally.  Interacting with various stakeholders, aimed at raising the profile of the NRF.  Managing finances.  Leading & managing human resources.  Monitoring performance, ensuring compliance to various policies & contracts & reporting accordingly.

Position Statistics:  Scope of the directorate was/is: Government Relations; Industry Relations; International Relations; Corporate Communications; & Branding.  Directorate of 16 positions including 4 managers reporting to the Director.  Directly responsible for a budget that has ranged between +/- R70M to R6M, sometimes indirectly impacting on additional +/- R30M.

Appendix 4 - iBOL_Summary CV_Rocky Skeef_Sep10.doc 114

December 22, 2010 CURRICULUM VITAE

Name: Stephen James O'Brien

Address: Laboratory of Genomic Diversity National Cancer Institute Building 560, Room 21-105 Frederick, Maryland 21702-1201 Telephone: 301/846-1296 FAX: 301/846-1686

Email: [email protected] WEB http://home.ncifcrf.gov/ccr/lgd/

Citizenship: United States

Marital Status: Married, 1968; two children

Education:

1962- Graduated from Good Counsel High School, Wheaton, MD 1965- Summer School, Georgetown University, Washington, D.C. 1966- B.S.; St. Francis College, Loretto, PA; major: Biology; minor: Chemistry 1971- Ph.D.; Cornell University, Major Field:

Brief Chronology of Employment:

1997 – Date Sylvio Conte Senior Biomedical Research Service Fellow-NIH 1986 – Date Chief, Laboratory of Genomic Diversity, National Cancer Institute, NIH, Frederick, MD 1983 – 1985 Acting Chief, Laboratory of Viral Carcinogenesis, National Cancer Institute, NIH, Frederick, MD 1980 - Date Chief, Section of Genetics, Laboratory of Viral Carcinogenesis, National Cancer Institute, NIH, Frederick, MD 1978 - 1980 Research Geneticist, Laboratory of Viral Carcinogenesis, National Cancer Institute, NIH, Frederick, MD. Chief - G.J. Todaro 1973 - 1978 Staff Fellow, Laboratory of Viral Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD. Research area - cell genetics, oncogenetics, tumor virology and immunology 1972 - 1973 NIH Postdoctoral Fellow, National Cancer Institute, NIH, Bethesda, MD. Supervisor, Charles W. Boone; research area - somatic cell genetics and development 1971 - 1972 Postdoctoral Fellow, genetics-biochemistry, Gerontology Research Center, Baltimore; Supervisor, Bertram Sacktor; research area - genetic control of bioenergetics.

1 115 Adjunct University Appointments

1974 - Date Adjunct Professor of Genetics, George Washington University 1979 - Date Adjunct Graduate Advisor, Dept. of Biology, American University 1982 - Date Adjunct Professor, Dept. of Zoology, University of Maryland 1982 - Date Adjunct Professor, Dept. of Biology, Johns Hopkins University 1982 - Date Adjunct Graduate Advisor, Dept. of Biology, Hood College 1994 - Date Adjunct Professor, Dept. of Pathology, Colorado State University 1994 - Date Adjunct Professor,, Dept. of Biology, George Mason University 1996 - Date Adjunct Professor, Dept. of Biology, Peking University 2004 –Date Adjunct Professor, Harvard School of Public Health 1996 - Date Director, AGA/ Smithsonian NOAHS Center Short Course: Recent Advances in Conservation Genetics, CRC - Front Royal, VA

Graduate Students Supervised:

M.S. Degrees M. Catherine Rice M.S. George Washington University, 1979 Thesis: An examination of the extent of genetic variation in laboratory outbred mice and wild mouse populations.

Cheryl A. Winkler M.S. University of Maryland, 1981 Thesis: Preliminary characterization of the major histocompatibility complex in Felis catus.

Andrea Newman M.S. Hood College, 1983 Thesis: Estimating the extent of biochemical genetic variation in eight species of the Felidae.

Eric J. Berman M.S. George Washington University, 1984 Thesis: Assignment of four new genes in the domestic cat by somatic cell hybridization.

Dianne N. Janczewski M.S. George Mason University, 1989 Thesis: Estimate of genetic distance of orangutan (Pongo pygmaeus) subspecies based on isozyme and two-dimensional electrophoresis.

Nuria Vazquez Salat M.S Hood College 2004 Thesis: Molecular evolution of the CCR cluster in domestic cats and other mammal species

Valerie Beason M.S. Hood College, 2004 Thesis: Genetic variation, subspecies identification and conservation of the clouded leopard (Neofelis nebulosa)

2 116 Ph.D. Degrees Completed Roger H. Reeves Ph.D. University of Maryland, 1983 Thesis: Characterization of a family of endogenous feline retroviral sequences

Cheryl A. Winkler Ph.D. University of Maryland, 1986 Thesis: The serological definition of the feline major histocompatibility complex, FLA, in the domestic cat, Felis catus.

Dennis A. Gilbert Ph.D. The Johns Hopkins University, 1990 Thesis: Application of DNA fingerprinting to measure the genetic structure of populations.

Dianne N. Janczewski University of Maryland, 1992 Subject: Phylogenetic radiation of the great cats, Panthera, as estimated by DNA sequence analysis of mitochondrial genes.

Sriyanie Miththapala University of Florida, 1993 Subject: Molecular definition of subspecies differentiation in the Old World leopard, Panthera pardus.

Jose Lopez George Mason University, 1995 Subject: Molecular organization of an historic transposition and amplification of mitochondrial DNA segments to nuclear genes in the Felidae.

Melanie Culver University of Maryland, 1998 Subject: Molecular genetic variation, population structure and natural history of free ranging pumas, Puma concolor.

Olga Uphyrkina University of Novosibirsk, 2002 Subject: Molecular genetic population structure of the leopard, Panthera pardus.

Eduardo Eizirik University of Maryland, 2002 Subject: Molecular evolution of melanism in the Felidae (Mammalia, Carnivora)

Shu Jin Luo University of Minnesota, 2006 Subject: Comparative Phylogeography of sympatric wild cats: Implications for biogeography and conservation in Asian biodiversity hotspots

Ann Schmidt-Kuntzel George Washington University, 2007 Subject Genetic origins of coat color in Felis silvestris catus. . Meredith Brown Michigan State University, 2007 Subject: Molecular genetic characterization of emerging viral infections and determinants of pathogenicity in free-ranging felid populations 3 117

Ph.D. Degrees Pending Carlos Driscoll Oxford University Subject: On the origins of cat domestication in the Wildcat, Felis silvestris

4 118 Editorial Appointments:

1975-1978 Editor, ISOZYME BULLETIN 1980-Date Editor, GENETIC MAPS, Cold Spring Harbor Publications 1987-1991 Associate Editor - Chief Subject Editor - comparative gene mapping, GENOMICS, Academic Press. 1987-2007 Chief Editor, Journal of Heredity, American Genetics Association 1990-Date Associate Editor, MAMMALIAN GENOME Associate Editor, MOLECULAR PHYLOGENETICS AND EVOLUTION 1993 Guest Editor, CURRENT BIOLOGY, Molecular Evolution Issue 1994 COSMOS Journal Advisory Board 1995 Guest Editor, CURRENT BIOLOGY, Genomes and Evolution Issue

Boards of Trustees/Directors:

American Type Culture Collection Cheetah Conservation Fund American Genetic Association Bioethics - Johns Hopkins University Family Investigation of Nephropathy and Diabetes (FIND) study NOAHS Center, Smithsonian Institution International BarCode of Life, Chair Sci Advis Board Bejijbg Genomics Institute

Societies:

1966 - Date American Association for the Advancement of Science 1966 - Date Genetics Society of America 1970 - Date American Society of Naturalists 1976 - Date Tissue Culture Association 1976 - Date American Genetics Association 1979 - Date New York Academy of Science 1984 - Date American Association of Zoological Parks and Aquariums

Research Interests:

Human genetics, Comparative Genomics, Genetic Epidemiology, Molecular Evolution, HIV, FIV, AIDS, Virology, Bio-informatics , Forensic genetics, Conservation.

Honors, Administrative Appointments and Other Special Recognitions:

1966-1971 NIH genetics traineeship 1971-1973 NIH postdoctoral fellowship 1972-1978 Co-Chairman and founder, Mid-Atlantic Drosophila Society 1975-1976 Elected council representative, NCI Assembly of Scientists 1977-1978 President, NCI Assembly of Scientists 1979-Date Elected New York Academy of Science 1979-Date Member, International Committee on Comparative Gene Mapping 1982-Date Appointed Research Fellow of Smithsonian Institution, Washington, D.C. 1983-Date Elected Board of Trustees, American Type Culture Association, Rockville, MD 1984-Date Appointed, Executive Board, American Type Culture Collection, Rockville, MD 1984-Date Elected Board of Directors, American Genetics Association (AGA) 1985 National Geographic Society Research Award (for study of genetics and reproduction of East African cheetah) 1985-Date Appointed, Chairman, Long Range Planning Committee, AGA 5 119 1985-Date Founder and Co-Director, NOAHS (New Opportunities in Health Sciences) Center for Wildlife Sciences, Smithsonian Institution 1985-Date Member, Cat Specialist Group, International Union for Conservation of Nature, I.U.C.N., Geneva 1986 Recipient World Wildlife Fund Research Award (for study of genetic structure of relict populations of giant pandas) 1986-Date Member, Captive Breeding Specialist Group, Species Survival Commission, I.U.C.N., Geneva 1986-Date Advisor, Special Survival Plan-Cheetah, American Zoological Association 1987-Date Secretary-Treasurer, Board of Trustees, American Type Culture Collection 1987-Date Chairman, International Committee on Comparative Gene Mapping 1987-Date Elected member Cosmos Club, Washington, D.C. 1988 Explorer's Club Annual Dinner Principal Lecture Award in Commemoration of the 100th Anniversary of the National Geographic Society. 1988-Date Elected Fellow Explorer's Club, New York, N.Y. 1994-Date Elected Fellow of the American Academy of Arts and Sciences. 1994 Distinguished Alumnus in Natural Sciences, St. Francis College, Loretto, PA 1997 Visiting Fellow, Merton College, Oxford University, Oxford 1998-Date Elected Fellow, American Association for the Advancement of Science 1998 Oscar W. Schlam Lectureship Award School of Veterinary medicine University of California Davis 1998-2004 Andrew Dixon White Professor-at-Large, Cornell University 2006 Chairman Board of Trustees Cheetah Conservation Fund 2006 Annual Citation Award for Outstanding Research in AIDS Cancer and Public Health; University of St Petersburg, St Petersburg, Russia 2006 Institutution of the Stephen J.O’Brien Award for Outstanding Paper Published by American Genetic Association 2009 Honorary Doctarate Degree in Veterinary Medicine conferred by the College of Veterinary Medicine, University of Zurich, Switzerland

Veterinary Research Honors:

1988 Explorer's Club Annual Dinner Principal Lecture Award in Commemoration of the 100th Anniversary of the National Geographic Society.

1998 Oscar W. Schlam Lectureship Award School of Veterinary Medicine University of California Davis

1998-2004 Andrew Dixon White Professor-at-Large, College of Veterinary Medicine Cornell University, Ithaca

2009 Honorary Doctarate Degree in Veterinary Medicine conferred by the College of Veterinary Medicine, University of Zurich, Switzerland

Isabella Photos.lnk

6 120

Financial Aspects Stephen J. O’Brien

I Laboratory of Genomic Diversity: Budget – Gross (NCI)

FY2001 $7,016,429 FY2002 $7,510,784 FY2003 $8,828,256 FY2004 $8,935,243 FY2005 $9,120,307 FY2006 $9,025,516 FY2007 $9,219,830

II Outside Grants and Contracts

Granting Co-PI Date Total Title Of Grant Agency Analysis of Circulatory Protein Extracts For NIAAA 1988/1993 $630,000

Susceptibility to HIV

Identification Of Genetic Variation In Candidate HIV NIH Dean 1990 $161,000 Restriction Genes

Characterization Of MDR Genes From Simple NCI Dean 1992 $150,000 Eukaryotes

Molecular Genetic Analysis Of FL Panthers USFWS 1992 $4,000

Molecular Genetic Approach To Taxonomic & AAZPA 1992 $80,852 Phylogenetic Relationships In South American Felids & Asian Small Cats

Development and Detection of Polymorphisms in Canine Health 1995 $50,000 Comparative Mapping Anchor Loci Type I Markers by Foundation PCR-based Methods in Candids /AKC

Molecular Genetic Analyses Of The FL Panther FL Game & 1996 10,000 Fresh Water Fish Comm Development of Genetic Databases and Standard Health Robert Winn Lyons 1996 $15,000 Evaluations For Pedigreed Domestic Cat Breeds. Foundation

Construction of the Purina Cat-BAC Library For Gene Ralston Purina Lyons 1997 $50,000 Hunting in Felines

Identification of Genetic Risk Factors For Prostate NIH Office of Smith 1998 $100,000 Cancer In African Americans Minority Health

Development of Genetic Databases And Standard Health Robert Winn 1998 $5,000 Evaluations For Pedigreed Domestic Cat Breeds Foundation

7 121 Granting Co-PI Date Total Title Of Grant Agency Department of Justice Interagency Agreement DOJ/NCI Raymond 2000 $265,570

Characterization of Polymorphic Microsatellite Loci For Wildlife Johnson 2000 $5,000 Use in the Conservation and Management of Lynx Conservation Species Society

The Role of Infectious Diseases in the Conservation of Madrid 2000 $4,000 the Endangered Iberian

An Integrated (Coding Gene and Microsatellite Marker) Morris Animal Johnson 2002 $287,000 Radiation Hybrid Map of the Alpaca Foundation

Molecular Genetics of African Elephants: Systematics, US Fish & Roca 2002 $100,000 Biogeography, and Conservation Wildlife Service

African American Admixture Mapping Applied to NCMHD Smith 2003 $471,447 Prostate Cancer Gene Discovery

A Global Study of the Molecular Genetics of Pangolins, National Johnson 2003 $17,500 the Scaly Anteaters Geographic Society African American Admixture Mapping Applied to NCMHD 2003 $471,446 Prostate Cancer Gene (MALD)

The Family Investigation of Nephropathy and Diabetes Institute of 2003 $2,657,21 Study of African, Hispanic, Native and European Diabetes and 0 Americans (FIND) Digestive and Kidney Diseases A Full Genome Scan of the for AIDS NIAID 2003 $3,000,00 Restriction Genes (ARG) 0

Nestle Purina Nestle Purina Raymond 2004/2005 $54,000

Molecular Analysis of Schizophrenia Genes NIMH Dean 2004/2006 $374,212

ABC Transporters and Genetic Disease Office of Rare Dean 2004/2006 $40,000 Diseases MGE Special Study NIDDK Winkler 2004 $66,000 p Feline Conference Office of Rare 2005 $25,000 Diseases MALD Meeting Office of Rare Smith 2005 $20,000 Diseases ABCC6 Gene PXE Foundation Dean 2006 $2,500

Role of HLA and KIR Genes in Severity of Lung Cystic Fibrosis Carrington 2005 $40,000 Disease in Cystic Fibrosis Foundation Host Genetics of HIV-1 Subtype C Infection, NIAID RO1 Myron 2007 $2,100,00 Progression and treatment in Africa Essex 0 Harvard U.

8 122 Granting Co-PI Date Total Title Of Grant Agency A 1000K SNP /CNV/Haplotype based-Genome Wide NIH-Office of Winkler, 2008 $2,700,00 Association (GWA) scan for AIDS Restriction Genes AIDS Research Smith 0 (ARGs)

BOOKS

O’Brien, S.J.: Tears of the Cheetah and Other Tales from the Genetic Frontier, St. Martin’s Press, New York, 2003, pp 273.

EDITED VOLUMES

1. O’Brien, S.J., Menninger, J. C and Nash, W. G.: An Atlas of Mammalian Genomes. John Wiley & Sons Publishers, New York, NY, 2006.

2. O'Brien, S.J. (Ed.): Isozyme Bulletin, 1976, Vol. 9, pp. 1-79.

3. O'Brien, S.J. (Ed.): Isozyme Bulletin, 1977, Vol. 10, pp. 1-90.

4. O'Brien, S.J. (Ed.): Isozyme Bulletin, 1978, Vol. 11, pp. 1-68.

5. O'Brien, S.J. (Ed.): Genetic Maps, 1980, Vol. 1, pp. 1-28

6. O'Brien, S.J. (Ed.): Genetic Maps, 1982, Vol. 2, pp. 1-406.

7. O'Brien, S.J. (Ed.): Genetic Maps, 1984. Cold Spring Harbor Laboratory Press, New York, Vol. 3, 1984, 584 pp.

8. O'Brien, S.J. (Ed.): Genetic Maps, 1987. Cold Spring Harbor Laboratory Press, New York, Vol. 4, 842 pp.

9. Clegg, M. T., and O'Brien, S.J. (Eds.): Molecular Evolution, 1990, Vol. 122, Proceedings of a UCLA Colloquium, UCLA Symposia on Molecular and Cellular Biology, Lake Tahoe, CA, Wiley- Liss, New York, N.Y., pp. 1-322.

10. O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes. Fifth Edition. 1990. Cold Spring Harbor Laboratory Press, New York, Unabridged 1104 pp.

11. O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes. Fifth Edition. 1990. Cold Spring Harbor Laboratory Press, New York. Published in six volumes: Book 1 Viruses 186 pp Book 2 , Protozoa, and Algae 138 pp Book 3 Lower Eukaryotes 206 pp Book 4 Nonhuman Vertebrates 180 pp Book 5 Human Maps 262 pp Book 6 152 pp

12. O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes. Sixth Edition. 1993. Cold Spring Harbor Laboratory Press, New York. Unabridged 1617 pp.

9 123

13. O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes. Sixth Edition. 1993. Cold Harbor Laboratory Press, New York. Published in six volumes: Book 1 Viruses 205 pp Book 2 Bacteria, Protozoa, and Algae 181 pp Book 3 Lower Eukaryotes 318 pp Book 4 Nonhuman Vertebrates 342 pp Book 5 Human Maps 310 pp Book 6 Plants 261 pp

14. O'Brien, S.J. and Clegg, M. T. (Eds.): Genes and Genomes. Curr. Opin. Genet. Devel. 3: 835-998, 1993.

15. Hartl, D. L., Kafatos, F., and O'Brien, S.J. (Eds.): Genomes and Evolution. Curr. Opin. Genet. Devel. 5: 705-847, 1995.

16. O’Brien, S.J. and Fraser, C. M. Genomes and Evolution. Curr. Opin. Genet. Devel. 15: 569-665, 2005

10 124 SCIENTIFIC ARTICLES

1. O'Brien, S.J. and MacIntyre, R. J.: An analysis of gene enzyme variability in natural populations of Drosophila melanogaster and D. simulans. Am. Nat. 103: 97 113, 1969.

2. O'Brien, S.J. and MacIntyre, R. J.: Empirical demonstration of a transient linkage disequilibrium in Drosophila. Nature 230: 335 336, 1971.

3. O'Brien, S.J. and MacIntyre, R. J.: A biochemical genetic map of the Drosophila genome. Drosophila Info. Serv. 46: 89 93, 1971.

4. O'Brien, S.J. and MacIntyre, R. J.: α glycerophosphate cycle in Drosophila melanogaster. I. Biochemical and developmental aspects. Biochem. Genet. 7: 141-161, 1972.

5. O'Brien, S.J. and MacIntyre, R. J.: The α glycerophosphate cycle in D. melanogaster. II. Genetic aspects. Genetics 71: 127 138, 1972.

6. O'Brien, S.J. and MacIntyre, R. J.: The α glycerophosphate cycle in D. melanogaster. III. The effect of "null" at α Gphd 1 locus on viability. Am. Nat. 106: 967 971, 1972.

7. O'Brien, S.J.: On estimating functional gene number in eukaryotes. Nature New Biol. 242: 52 54, 1973.

8. O'Brien, S.J.: Comparative analysis of malate dehydrogenase of Drosophila melanogaster. Biochem. Genet. 10: 191 205, 1973.

9. O'Brien, S.J. and Gethmann, R. C.: Segmental aneuploidy as a probe for structural genes in Drosophila: Mitochondrial membrane enzymes. Genetics 75: 155 167, 1973.

10. O'Brien, S.J. and Shimada, Y.: The α glycerophosphate cycle in Drosophila melanogaster. IV. Metabolic, ultrastructural, and adaptive consequences of α Gphd 1 "null" mutations. J. Cell Biol. 63: 864 882, 1974.

11. O'Brien, S.J., Boone, C. W., Simonson, J. M., and Austin, F.: The paired label assay for cell surface antigens. Tissue Cult. Assoc. Manual 2: 423 427, 1975.

12. O'Brien, S.J.: Biochemical mutants of Drosophila melanogaster. In: King, R. C. (Ed.) Handbook of Genetics, Vol. III. New York, Plenum, 1975, pp. 669 678.

13. O'Brien, S.J., Kleiner, G., Kern, J., and Reynolds, J.: Zymogram phenotypes of widely used cell lines from various animal species. Isozyme Bull. 9: 20 27, 1976.

14. O'Brien, S.J.: Bvr 1, a restriction locus of a type C RNA virus in the feline cellular genome: Identification, location, and phenotypic characterization in cat x mouse somatic cell hybrids. Proc. Natl. Acad. Sci. USA 73: 4618-4622, 1976.

15. O'Brien, S.J., Simonson, J. M., and Boone, C. W.: Expression of virus structural proteins on murine cell surfaces in association with the production of murine leukaemia virus. J. Gen. Virol. 33: 355 360, 1976.

16. O'Brien, S.J.: Isozymes and allozymes as genetic footprints of cultured cells. In Petricianni, J. (Ed.): Proceedings of the FDA Conference on Cell Substrates for Vaccine Production, 1976, pp. 46n 59n.

11 125

17. MacIntyre, R. J. and O'Brien, S.J.: Interacting gene enzyme systems in Drosophila. Ann. Rev. Genet. 10: 281 318, 1976.

18. O'Brien, S.J., Kleiner, G., Olson, R., and Shannon, J.: Enzyme polymorphisms as genetic signatures in human cell cultures. Science 195: 1345 1348, 1977.

19. O'Brien, S.J. and Boone, C. W.: Expression of feline leukemia virus antigens on cat lymphoma cells: Kinetics of biosynthesis. J. Gen. Virol. 35: 511 523, 1977.

20. Lemons, R. S., O'Brien, S.J., and Sherr, C.J.: A new genetic locus, Bevi, on human 6 which controls the replication of baboon type C virus in human cells. Cell 12:251-262, 1977.

21. O'Brien, S.J. and MacIntyre, R. J.: Genetics and biochemistry of enzymes and specific proteins of Drosophila. In Wright, T. R. F. and Ashburner, M. (Eds.): Genetics and Biology of Drosophila, Vol IIa. New York, Academic, 1977, pp. 395 551.

22. O'Brien, S.J., Simonson, J. M., and Davis, S.: Deposition of retrovirus associated antigens (p30 and gp70) on cell membranes of feline and murine leukemia virus infected cells. J. Gen. Virol. 38: 483 496, 1978.

23. O'Brien, S.J. and Simonson, J. M.: Bvr 1: A restriction locus of a type C RNA virus in the feline cellular genome: Pleiotropic restriction of endogenous BALB virus in cat X mouse somatic cell hybrids. J. Exp. Med. 147: 219-232, 1978.

24. Lemons, R. S., O'Brien, S.J., and Sherr, C. J.: The Bevi locus (chromosome 6) encodes a post- penetrational cellular function required for baboon endogenous virus replication in human cells. Cytogenet. Cell Genet. 22: 255-259, 1978.

25. Lemons, R. S., Nash, W. G., O'Brien, S.J., Benveniste, R. E., and Sherr, C. J.: A gene (Bevi) on human chromosome 6 is an integration site for baboon type C DNA provirus in human cells. Cell 14: 995-1005, 1978.

26. Engel, L. W., Young, N. A., Tralka, T. S., Lippman, M. E., O'Brien, S.J., and Joyce, M. J.: Establishment and characterization of three new continuous cell lines derived from human breast carcinomas. Cancer Res. 38:3352-3364, 1978.

27. Kucera, L. S., Simonson, J. M., O'Brien, S.J., and Coon, H.: On the Lucke tumor origin of LT 1 cells. J. Natl. Cancer Inst. 60: 493-495, 1978.

28. O'Brien, S.J. and Rice, M. C.: Genetic aspects of carcinogenesis and carcinogen testing in outbred Swiss mice. J. Toxicol. Environ. Health 5:69-81, 1979.

29. Noguchi, P., Wallace, R., Johnson, J., Earley, E. M., O'Brien, S.J., Ferrone, S., Pellegrino, M. A., Milstein, J., Needy, C., Browne, W., and Petriceianni, J.: Characterization of the WIDR: A human colon carcinoma cell line. In Vitro 15: 401-408, 1979.

30. Surti, U., Szulman, A. E., and O'Brien, S.J.: Complete (classic) hydatidiform mole with 46,XY karyotype of paternal origin. Hum. Genet. 51: 153-155, 1979.

31. O'Brien, S.J. and Rice, M. C.: Specific genetic loci as targets of carcinogens and tumor promoters in mammals. J. Environ. Pathol. Toxicol. 2: 1055-1068, 1979.

12 126 32. Gail, M. H., , G. H., Mante, N., and O'Brien, S.J.: A solution to the generalized birthday problem with application to allozyme screenings for cell culture contamination. J. Appl. Prob. 16:242-251, 1979.

33. Gardner, M. B., Rasheed, S., Pal, B. K., Estes, J. D., and O'Brien, S.J.: Akvr 1, a dominant MuLV restriction gene segregates in leukemia prone wild mice. In Yohn, D. S., Lapin, B. A., and Blakeslee, J. R. (Eds.): Comparative Leukemia Research. New York, Elsevier/North Holland, 1979, pp. 149-150.

34. Pearson, P. L., Roderick, T. H., Davisson, M. T., Garver, J. J., Warburton, D., Lalley, P. A., and O'Brien, S.J.: Report of the committee on comparative gene mapping. Cytogenet. Cell Genet. 25: 82-95, 1979.

35. Rice, M. C. and O'Brien, S.J.: Genetic variance of laboratory outbred Swiss mice. Nature 283: 157-161, 1980.

36. Gardner, M. B., Rasheed, S., Pal, B. K., Estes, J. D., and O'Brien, S.J.: Akvr 1, a dominant murine leukemia virus restriction gene is polymorphic in leukemia prone wild mice. Proc. Natl. Acad. Sci. USA 77:531-535, 1980.

37. O'Brien, S.J., Shannon, J. E., and Gail, M. H.: A molecular approach to the identification and individualization of human and animal cells in culture: Isozyme and allozyme genetic signatures. In Vitro 16: 119 135, 1980.

38. Rice, M. C., Gardner, M. B., and O'Brien, S.J.: Genetic diversity in leukemia-prone feral house mice infected with murine leukemia virus. Biochem. Genet. 8: 915 928, 1980.

39. Nelson Rees, W. A., Hunter, L., Darlington, G. J., and O'Brien, S.J.: Characteristics of HeLa strains: Permanent vs. variable features. Cytogenet. Cell Genet. 27: 216 231, 1980.

40. O'Brien, S.J.: The extent and character of biochemical genetic variation in the domestic cat (Felis catus). J. Hered. 71: 2 8, 1980.

41. O'Brien, S.J., Gail, M. H., and Levin, D. L.: Correlative genetic variation in natural populations of cats, mice and men. Nature 288: 580 583, 1980.

42. Gardner, M. B., Rasheed, S., Pal, B. K., Estes, J. D., Berman, E., and O'Brien, S.J.: Genetic analysis of Akvr 1 relative to other murine retrovirus restriction loci. In Baltimore, D., Huang, A. S., and Fox, C. F. (Eds.): Proceedings of ICN UCLA Symposium on Animal Virology. 1980, pp. 223 232.

43. O'Brien, S.J., Nash, W. G., Simonson, J. M., and Berman, E. J.: Establishment of a biochemical genetic map of the domestic cat (Felis catus). In Hardy, W. D., Essex, M., and McClelland, A. J. (Eds.): Feline Leukemia Virus. New York, Elsevier/North Holland, 1980, pp. 401 412.

44. O'Brien, S.J. and Nash, W. G.: Somatic cell genetic analysis of enzyme structural genes of the domestic cat (Felis catus). Carnivore Genet. 4: 81 88, 1980.

45. Harris, N. L., Gang, D. L., Quay, S. C., Poppema, S., Nelson Rees, W. A., and O'Brien, S.J.: Contamination of Hodgkin's disease cell cultures. Nature 289: 228-230, 1981.

46. O'Brien, S.J., Simonson, J. M., Grabowski, M. W., and Barile, M. F.: Analysis of multiple isoenzyme expression among twenty two species of Mycoplasma and Acholeplasma. J.

13 127 Bacteriol. 146: 222 232, 1981.

47. O'Brien, S.J., Nash, W. G., Benveniste, R. E., Wildt, D. E., and Bush, M. E.: Palaeontological and molecular views of panda phylogeny. Nature 319: 428, 1986.

48. O'Brien, S.J. and Nash, W. G.: Genetic mapping in mammals: Chromosome map of the domestic cat. Science 216: 257 265, 1982.

49. O'Brien, S.J.: Plausible alternatives to bottlenecks to explain reduced genetic diversity. Trends Ecol. Evol. 4: 176-178, 1989.

50. Anagnou, N. P., Antonarakis, S. E., O'Brien, S.J., and Nienhuis, A. W.: A novel form of human polymorphism involving the hDHFR-psi 1 pseudogene identifies three RFLPs. Nucleic Acids Res. 15: 5501, 1987.

51. O'Brien, S.J., Moore, J. L., Martin, M. A., and Womack, J. E.: Evidence for the horizontal acquisition of murine AKR virogenes by recent horizontal infection of the germ line. J. Exp. Med. 155: 1120 1123, 1982.

52. O'Brien, S.J. and Barile, M. F.: Isozyme resolution in mycoplasmas. In Razin, S. and Tully, J. G. (Eds.): Methods of Mycoplasmology, Vol. I. New York, Academic, 1982, pp. 391 396.

53. O'Brien, S.J., Nash, W. G., Winkler, C. A., and Reeves, R. H.: Genetic analysis in the domestic cat as an animal model for inborn errors, cancer and evolution. Prog. Clin. Biol. Res. 94: 67-90, 1982.

54. O'Brien, S.J., Simonson, J. M., and Eichelberger, M. A.: Genetic analysis of hybrid cells using isozyme markers as monitors of chromosome segregation. In Shay, J. W. (Ed.): Techniques in Somatic Cell Genetics. New York, Plenum, 1982, pp. 513 524.

55. Pearson, P. L., Roderick, T. H., Davisson, M. T., Lalley, P. A., and O'Brien, S.J.: Report of the committee on comparative mapping. Oslo Conference (1981): Sixth International Workshop on Human Gene Mapping. Cytogenet. Cell Genet. 32: 208 220, 1982.

56. Nash, W. G. and O'Brien, S.J.: Conserved regions of homologous G banded between orders in mammalian evolution: Carnivores and primates. Proc. Natl. Acad. Sci. USA 79: 6631 6635, 1982.

57. O'Brien, S.J. and Johnson, P. A.: An abridged human gene map including oncogenes, neoplasia- related loci and biochemical loci whose homologous counterparts have been assigned in other mammalian species. In O'Brien, S.J. (Ed.): Genetic Maps, Vol. 4. New York, Cold Spring Harbor Laboratory, 1987, pp. 598-604.

58. O'Brien, S.J.: Genetic map of the domestic cat, Felis catus. In O'Brien, S.J. (Ed.): Genetic Maps, Vol. 4. New York, Cold Spring Harbor Laboratory, 1987, pp. 482-485.

59. O'Brien, S.J., Nash, W. G., Winkler, C. A., Simonson, J. M., and Lemons, R. S.: Control of integration of baboon endogenous virus in human chromosomes by the BEVI locus. In Yohn, D. S. and Blakeslee, R. J. (Eds.): Comparative Leukemia Research. New York, Elsevier/North Holland, 1981, pp. 399 400.

60. O'Brien, S.J., Wildt, D. E., Simonson, J. M., Brand, D. J., Ebedes, H., van Dyk, A., Meltzer, D., Simmons, L. G., and Bush, M.: On the extent of genetic variation of the African cheetah,

14 128 Acinonyx jubatus. In Fowler, M. (Ed.): Proceedings of the American Association of Zoo Veterinarians, 1981, pp. 74 77.

61. Seibert, K., Shafie, S. M., Tricke, T. J., Whang Peng, J. J., O'Brien, S.J., Toney, J. H., Huff, K. K., and Lippman, M. E.: Clonal variation of MCF 7 breast cancer cells in vivo and in athymic nude mice. Cancer Res. 43: 2223 2239, 1983.

62. Surti, U., Szulman, A. E., and O'Brien, S.J.: Dispermic origin and clinical outcome of three complete hydatidiform moles with 46,XY karyotype. J. Obstet. Gynecol. 144: 84 87, 1982.

63. O'Brien, S.J., Wildt, D. E., Goldman, D., Merril, C. R., and Bush, M.: The cheetah is depauperate in genetic variation. Science 221: 459 462, 1983.

64. Wildt, D. E., Bush, M., Howard, J. G., O'Brien, S.J., Meltzer, D., van Dyk, A., Ebedes, H., and Brand, D. J.: Unique seminal quality in the South African cheetah and a comparative evaluation in the domestic cat. Biol. Reprod. 29:1019 1025, 1983.

65. O'Brien, S.J., Simonson, J. M., Razine, S., and Barile, M. F.: On the distribution and characteristics of isozyme expression in Mycoplasma, Acholeplasma, and Ureaplasma species. Yale J. Biol. Med. 56: 701 708, 1983.

66. O'Brien, S.J., Bonner, T. I., Cohen, M., O'Connell, C., and Nash, W. G.: Mapping of an endogenous retroviral sequence to human chromosome 18. Nature 303: 74 77, 1983.

67. O'Brien, S.J., Nash, W. G., Goodwin, J. L., Lowy, D. R., and Chang, E. H.: Dispersion of the ras family of transforming genes to four different chromosomes in man. Nature 302:839-842, 1983.

68. O'Brien, S.J., Berman, E. J., Estes, J. D., and Gardner, M. B.: Murine retroviral restriction genes Fv 4 and Akvr 1 are alleles of a single locus. J. Virol. 47: 649 651, 1983.

69. Barile, M. F., Grabowski, M. W., Stephens, E. B., O'Brien, S.J., Simonson, J. M., Izumikawa, K., Chandler, D. K. F., Taylor Robinson, D., and Tully, J. G.: Mycoplasma hominis tissue cell interactions: A review with new observations on phenotypic and genotypic properties. Sex Transm Dis 10: 345 354, 1983.

70. Reeves, R. H. and O'Brien, S.J.: Molecular genetic characterization of the RD 114 gene family of endogenous feline retroviral sequences. J Virol 52:164-171, 1984.

71. Reeves, R. H., Nash, W. G., and O'Brien, S.J.: Genetic mapping of endogenous RD 114 retroviral sequences of domestic cats. J Virol 56:303-306, 1985.

72. Bonner, T., O'Brien, S.J., Nash, W. G., Rapp, U. R., Morton, C. C., and Leder, P.: The human homologs of the raf (mil) oncogene are located on human chromosomes 3 and 4. Science 223:71- 74, 1984.

73. Wayne, R. and O'Brien, S.J.: Empirical demonstration that structural gene and morphometric variation of mandible traits are uncoupled between mouse strains. J. Mammal. 67:441-449, 1986.

74. Seigel, L. J., Harper, M. E., Wong Staal, F., Gallo, R. C., Nash, W. G., and O'Brien, S.J.: Gene for T cell growth factor: Location on human chromosome 4q and feline chromosome B1. Science 223: 175 178, 1984.

75. Roderick, T. H., Lalley, P. A., Davisson, M. T., O'Brien, S.J., Womack, J. E., Creau Goldberg,

15 129 N., Echard, G., and Moore, K. L.: Report of the committee on comparative mapping. Cytogenet. Cell Genet. 37: 312 339, 1984.

76. O'Brien, S.J., Reeves, R. H., Simonson, J. M., Eichelberger, M. A., and Nash, W. G.: Parallels of genomic organization and endogenous retrovirus organization in cat and man. Develop. Genet. 4: 341 354, 1984.

77. O'Brien, S.J., Nash, W. G., Bauer, R., Chang, E. H., and Seigel, L. J.: Trends in chromosomal and oncogene evolution in vertebrates. In Patterson, M. K. (Ed.): Uses and Standardization of Vertebrate Cell Cultures. In Vitro Monograph No. 5. Gaithersburg, Tissue Culture Association, 1984, pp. 204 214.

78. Seigel, L. J., Nash, W. G., Manzari, V., Wong Staal, F., Gallo, R. C., and O'Brien, S.J.: A genetic analysis of human T-cell leukemia virus integration in HUT 102 and the localization of the structural gene for T cell growth factor to chromosome 4. In Gallo, R. C. and Essex, M. (Eds): Human T-Cell Leukemia/Lymphoma Viruses. New York, Cold Spring Harbor Laboratory, 1984, pp. 167 180.

79. O'Brien, S.J., Goldman, D., Knight, J., Moore, H. D., Wildt, D. E., Bush, M., Montali, R. J., and Kleiman, D.: Giant panda paternity. Science 223: 1127 1129, 1984.

80. Anagnou, N. P., O'Brien, S.J., Shimada, T., Nash, W. G., Chen, M., and Nienhius, A. W.: Chromosomal organization of the human dihydrofolate reductase genes: Dispersion, selective amplification and a novel form of polymorphism. Proc. Natl. Acad. Sci. USA 81: 5170 5174, 1984.

81. O'Brien, S.J., Roelke, M. E., Marker, L., Newman, A., Winkler, C. A., Meltzer, D., Colly, L., Evermann, J. F., Bush, M., and Wildt, D. E.: Genetic basis for species vulnerability in the cheetah. Science 227: 1428 1434, 1985.

82. Newman, A., Bush, M., Wildt, D. E., van Dam, D., Frankehuis, M., Simmons, L., Phillips, L., and O'Brien, S.J.: Biochemical genetic variation in eight endangered feline species. J. Mammal. 66: 256 267, 1985.

83. Stephens, J. C., Chipperfield, M. A., and O'Brien, S.J.: An abridged human gene map. In O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes, Sixth Edition. New York, Cold Spring Harbor Laboratory, 1993, pp. 5.209-5.239

84. O'Brien, S.J., Seuanez, H. N., and Womack, J. E.: On the evolution of genome organization in mammals. In: MacIntyre, R. J. (Ed.) Molecular Evolutionary Genetics (Monographs in Evolutionary Biology Series). New York, Plenum, 1985, pp. 519 589.

85. Burk, R. D., Szabo, P., O'Brien, S.J., Nash, W. G., Yu, L., and Smith, K. D.: Organization and chromosomal specificity of autosomal homologs of human repeated DNA. Chromosoma 92: 225 233, 1985.

86. O'Connell, C., O'Brien, S.J., Nash, W. G., and Cohen, M.: ERV3, a full length human endogenous provirus: Chromosomal localization and evolutionary relationship. J. Virol. 138: 225 234, 1984.

87. Wayne, R. K., Modi, W. S., and O'Brien, S.J.: Morphological variability in the cheetah (Acinonyx jubatus), a genetically uniform species. Evolution 40: 78 85, 1986.

16 130 88. Collier, G. E. and O'Brien, S.J.: A molecular phylogeny of the Felidae: Immunological distance. Evolution 39: 473 487, 1985.

89. Longo, D. L., Gelmann, E. P., Cossman, J., Young, R. A., Gallo, R. C., O'Brien, S.J., and Matis, L. A.: Isolation of HTLV transformed B lymphocyte clone from a patient with HTLV associated adult T cell leukaemia. Nature 310: 505 506, 1984.

90. O'Brien, S.J.: Genetic and reproductive approaches to an endangered species, the giant panda. In Wagner, R. O. (Ed.): Proceedings of the Association of Zoological Parks and Aquariums. Miami, AAZPA, 1984, pp. 169 180.

91. O'Brien, S.J., Benveniste, R. E., Nash, W. G., Simonson, J. M., Eichelberger, M. A., Wildt, D. E., and Bush, M.: Constructing a molecular phylogeny of the giant panda, Ailuropoda melanoleuca. In Klos, H. G. and Fradrich, H. (Eds.): Proceedings International Symposium on Giant Panda, 1984, Vol. 10. Berlin, Bongo, 1985, pp. 175-182.

92. O'Brien, S.J., Nash, W. G., Wildt, D. E., Bush, M. E., and Benveniste, R. E.: A molecular solution to the riddle of the giant panda's phylogeny. Nature 317: 140-144, 1985.

93. Brownell, E., O'Brien, S.J., Nash, W. G., and Rice, N.: Genetic characterization of human c rel sequences. Mol. Cell. Biol. 5: 2826-2831, 1985.

94. Goldman, D., Goldin, L. G., Rathnagiri, P., O'Brien, S.J., Egeland, J. A., and Merril, C. R.: Twenty seven protein polymorphisms by two dimensional electrophoresis of serum erythrocytes and fibroblasts in two pedigrees. Am. J. Hum. Genet. 37: 898-911, 1985.

95. Surti, U., Szulman, A. E., Wagner, K., Leppert, M., White, R., and O'Brien, S.J.: Tetraploid partial hyatidiform moles: Two cases with a triple paternal contribution and a 92,XXXY karyotype. Hum. Genet. 72: 15-21, 1986.

96. Wayne, R. K., Forman, L., Newman, A. K., Simonson, J. M., and O'Brien, S.J.: Genetic monitors of captive zoological populations: Morphological and electrophoretic assays. Zoo Biol. 5: 215- 232, 1986.

97. Goldman, D., Giri, P.R., and O'Brien, S.J.: A molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis. Proc. Natl. Acad. Sci. USA 84: 3307- 3311, 1987.

98. Forman, L., Kleiman, D. G., Bush, M. R., Dietz, J. M., Ballou, J. D., Phillips, L. G., Dietz, J. L., Coimbra Filho, A. F., and O'Brien, S.J.: Genetic variation within and among lion tamarins. Am. J. Phys. Anthropol. 71: 1-11, 1986.

99. Nienhuis, A. W., Bunn, H. F., Turner, P. H., Gopal, T. V., Nash, W. G., O'Brien, S.J., and Sherr, C. J.: Expression of the human c fms proto oncogene in hematopoietic cells and its deletion in the 5q- syndrome. Cell 42: 421 428, 1985.

100. Watson, D. K., Smith, M. J., Kozak, C., Reeves, R., Gearhart, J., Nunn, M. F., Nash, W., Fowle, J. R., III, Duesberg, P., Papas, T. S., and O'Brien, S.J.: Conserved chromosomal positions of dual domains of the ets proto oncogene in cats, mice and man. Proc. Natl. Acad. Sci. USA 83: 1792 1796, 1986.

101. Watson, D. K., McWilliams Smith, M. J., Nunn, M. F., Duesberg, P. H., O'Brien, S.J., and Papas, T. S.: The ets sequence from the transforming gene of avian erythroblastosis virus, E26, has

17 131 unique domains on human chromosomes 11 and 21: Both loci are transcriptionally active. Proc. Natl. Acad. Sci. USA 82: 7294 7298, 1985.

102. Brownell, E., Kozak, C. A., Fowle, J. R. 3rd, Modi, W. S., Rice, N. R., and O'Brien, S.J.: Comparative genetic mapping of cellular rel sequences in man, mouse, and the domestic cat. Am. J. Hum. Genet. 39: 194-202, 1986.

103. Berman, E. J., Nash, W. G., Seuanez, H. N., and O'Brien, S.J.: Chromosomal mapping of enzyme loci in the domestic cat: GSR to C2, ADA and ITPA to A3, and LDHA ACP2 to D1. Cytogenet Cell Genet 41: 114-120, 1986.

104. Seigel, L. J., Nash, W. G., Poiesz, B. J., Moore, J. L., and O'Brien, S.J.: Dynamic and nonspecific dispersal of human T-cell leukemia/lymphoma virus type I integration in cultured lymphoma cells. Virology 154: 67-75, 1986.

105. Seigel, L. J., Ratner, L., Josephs, S. F., Derse, D., Feinberg, M. B., Reyes, G. R., O'Brien, S.J., and Wong Staal, F.: Transactivation induced by human T lymphotropic virus type III (HTLV III) maps to a viral sequence encoding 58 amino acids and lacks tissue specificity. Virology 148: 226-231, 1986.

106. Steele, P. E., Martin, M. A., Rabson, A. B., Bryan, T., and O'Brien, S.J.: Amplification and chromosomal dispersion of human endogenous retroviral sequences. J Virol 59: 545-550, 1986.

107. O'Brien, S.J.: Genetic analysis in mammals: Past, present, and future. Basic Life Sci. 37: 139- 149, 1986.

108. O'Brien, S.J., Wildt, D. E., and Bush, M.: The cheetah in genetic peril. Sci. Am. 254: 84-92, 1986.

109. Papas, T. S., Watson, D. K., Sacchi, N., O'Brien, S.J., and Ascione, R.: The mammalian ets genes: Two unique chromosomal locations in cat, mice and man and novel translocated position in human leukemias. In Hagenbeck, A. and Lowenberg, B. (Eds.): Minimal Residual Disease in Acute Leukemia: 1986. Boston, Martinus Nijhoff/Dodrecht, 1986, pp. 23-42.

110. Wildt, D. E., Schiewe, M. C., Schmidt, P. M., Goodrowe, K. L., Howard, J. G., Phillips, L. G., O'Brien, S.J., and Bush, M.: Developing animal model systems for embryo technologies in rare and endangered wildlife. Theriogenology 25: 33 51, 1986.

111. O'Brien, S.J., Haskins, M. E., Winkler, C. A., Nash, W. G., and Patterson, D. F.: Chromosomal mapping of beta globin and albino loci in the domestic cat: A conserved mammalian chromosome group. J. Hered. 77: 374-378, 1986.

112. O'Brien, S.J.: Molecular genetics in the domestic cat and its relatives. Trends Genet. 2:137-142, 1986.

113. O'Brien, S.J., Collier, G. E., Benveniste, R. E., Nash, W. G., Newman, A. K., Simonson, J. M., Eichelberger, M. A., Seal, U. S., Bush, M., and Wildt, D. E.: Setting the molecular clock in Felidae: The great cats, Panthera. In Tilson, R. L. and Seal, U. S. (Eds.): Tigers of the World: The Biology, Biopolitics, Management and Conservation of an Endangered Species. Park Ridge, New Jersey, Noyes Publications, 1987, pp. 10-27.

114. O'Brien, S.J., Wildt, D. E., Bush, M., Caro, T. M., FitzGibbon, C., Aggundey, I., and Leakey, R. E.: East African cheetahs: Evidence for two population bottlenecks? Proc. Natl. Acad. Sci. USA

18 132 84: 508-511, 1987.

115. Goldman, D., Rathna Giri, P., and O'Brien, S.J.: Molecular genetic-distance estimates among the Ursidae as indicated by one- and two-dimensional protein electrophoresis. Evolution 43: 282- 295, 1989.

116. Park, M., Dean, M., Cooper, C. S., Schmidt, M., O'Brien, S.J., Blair, D. G., and Vande Woude, G. F.: Mechanism of met oncogene activation. Cell 45: 895-904, 1986.

117. Jaye, M., Howk, R., Burgess, W., Ricca, G. A., Chiu, I. M., Ravera, M. W., O'Brien, S.J., Modi, W. S., Maciag, T., and Drohan, W. N.: Human endothelial cell growth factor: Cloning, nucleotide sequence, and chromosome localization. Science 233: 541-545, 1986.

118. Schuchman, E. H., O'Brien, S.J., and Desnick, R. J.: Assignment of the feline alpha-L- iduronidase gene to chromosome D4. Genomics 4: 442-444, 1989.

119. Papas, T. S., Watson, D. K., Sacchi, N., O'Brien, S.J., and Ascione, R.: The cellular ets genes: Molecular biology and clinical implications in human leukemias. Cancer Invest. 4: 555-574, 1986.

120. Watson, D. K., Sacchi, N., McWilliams Smith, M. J., O'Brien, S.J., and Papas, T. S.: The avian and mammalian ets genes: Molecular characterization, chromosome mapping, and implication in human leukemia. Anticancer Res. 6: 631-636, 1986.

121. Papas, T. S., Watson, D. K., Sacchi, N., O'Brien, S., and Ascione, R.: The cellular ets genes: Molecular probes in human neoplasia. Haematologica 72(Suppl): 6-18, 1987.

122. Wayne, R. K., Nash, W. G., and O'Brien, S.J.: Chromosomal evolution of the Canidae: I. Species with high diploid numbers. Cytogenet. Cell Genet. 44: 123-133, 1987.

123. Wayne, R. K., Nash, W. G., and O'Brien, S.J.: Chromosomal evolution of the Canidae: II. Divergence from the primitive carnivore karyotype. Cytogenet. Cell Genet. 44: 134-141, 1987.

124. Hentze, M. W., Keim, S., Papadopoulos, P., O'Brien, S.J., Modi, W. S., Drysdale, J., Leonard, W. J., Harford, J. B., and Klausner, R. D.: Cloning, characterization, expression, and chromosomal localization of a human ferritin heavy-chain gene. Proc. Natl. Acad. Sci. USA 83: 7226-7230, 1986.

125. Anagnou, N. P., Antonarakis, S. E., O'Brien, S.J., Modi, W. S., and Nienhuis, A. W.: Chromosomal localization and racial distribution of the polymorphic human dihydrofolate reductase pseudogene (DHFRP1). Am. J. Hum. Genet. 42: 345-352, 1988.

126. Papas, T. S., Watson, D. K., Sacchi, N., O'Brien, S.J., and Ascione, R.: Molecular evolution of ets genes from avians to mammals and their cytogenetic localization to regions involved in leukemia. Gene Amplif Anal. 4: 207-238, 1986.

127. Wildt, D. E., O'Brien, S.J., Howard, J. G., Caro, T. M., Roelke, M. E., Brown, J. L., and Bush, M.: Similarity in ejaculate-endocrine characteristics in captive versus free-ranging cheetahs of two subspecies. Biol. Reprod. 36: 351-360, 1987.

128. O'Brien, S.J., Martenson, J. S., Packer, C., Herbst, L., de Vos, V., Joslin, P., Ott-Joslin, J., Wildt, D. E., and Bush, M.: Biochemical genetic variation in geographic isolates of African and Asiatic lions. Natl. Geo. Res. 3: 114-124, 1987.

19 133

129. O'Brien, S.J., Joslin, P., Smith, G. L., III, Wolfe, R., Schaffer, N., Heath, E., Ott-Joslin, J., Rawal, P. P., Bhattacherjee, K. K., and Martenson, J. S.: Evidence for African origins of founders of the Asiatic lion species survival plan. Zoo Biol. 6: 99-116, 1987.

130. Modi, W. S., Nash, W. G., Ferrari, A. C., and O'Brien, S.J.: Cytogenetic methodologies for gene mapping and comparative analyses in mammalian cell culture systems. Gene Anal. Tech. 4: 75- 85, 1987.

131. Wayne, R. K., Benveniste, R. E., Janczewski, D. N., and O'Brien, S.J.: Molecular and biochemical evolution of the Carnivora. In Gittleman, J. L. (Ed.): Carnivore Behavior, Ecology and Evolution. New York, Cornell University, 1989, pp. 465-494.

132. Kinzler, K. W., Bigner, S. H., Bigner, D. D., Trent, J. M., Law, M. L., O'Brien, S.J., Wong, A. J., and Vogelstein, B.: Identification of an amplified highly expressed gene in a human glioma. Science 236: 70-73, 1987.

133. Epstein, N. D., Karlsson, S., O'Brien, S., Modi, W., Moulton, A., and Nienhuis, A. W.: A new moderately repetitive DNA sequence family of novel organization. Nucleic Acids Res. 15: 2327- 2341, 1987.

134. Wildt, D. E., Bush, M., Goodrowe, K. L., Packer, C. Pusey, A. E., Brown, J. L., Joslin, P., and O'Brien, S.J.: Reproductive and genetic consequences of founding isolated lion populations. Nature 329: 328-331, 1987.

135. Modi, W. S., Wayne, R. K., and O'Brien, S.J.: Analysis of fluctuating asymmetry in cheetahs. Evolution 41: 227-228, 1987.

136. Wayne, R. K. and O'Brien, S.J.: Allozyme divergence within the Canidae. Syst. Zool. 36: 339- 355, 1987.

137. Nash, W. G. and O'Brien, S.J.: A comparative chromosome banding analysis of the Ursidae and their relationship to other Carnivores. Cytogenet. Cell Genet. 45: 206-212, 1987.

138. Killen, P. D., Francomano, C. A., Yamada, Y., Modi, W. S., and O'Brien, S.J.: Partial structure of the human alpha 2(IV) collagen chain and chromosomal localization of the gene (COL4A2). Hum. Genet. 77: 318-324, 1987.

139. O'Brien, S.J. and Knight, J. A.: The future of the giant panda. Nature 325: 758-759, 1987.

140. O'Brien, S.J.: The ancestry of the giant panda. Sci. Am. 257: 102-107, 1987.

141. O'Brien, S.J., Martenson, J. S., Eichelberger, M. A., Thorne, E. T., and Wright, F. W.: Genetic variation and molecular systematics of the black-footed ferret. In Seal, U. S., Thorne, E. T., Bogan, M. A., and Anderson, S. H. (Eds.): Conservation Biology and the Black-Footed Ferret. New Haven, Yale University, 1989, pp. 21-23.

142. Yuhki, N. and O'Brien, S.J.: Molecular characterization and genetic mapping of class I and class II MHC genes of the domestic cat. Immunogenetics 27: 414-425, 1988.

143. Marker, L. and O'Brien, S.J.: Captive breeding of the cheetah (Acinonyx jubatus) in North American Zoos (1871-1985). Zoo Biol. 8: 3-16, 1989.

20 134 144. Kamholz, J., Spielman, R., Gogolin, K., Modi, W., O'Brien, S., and Lazzarini, R.: The human myelin-basic-protein gene: Chromosomal localization and RFLP analysis. Am. J. Hum. Genet. 40: 365-373, 1987.

145. el Awady, M. K., Kaplan, J. B., O'Brien, S.J., and Burk, R. D.: Molecular analysis of integrated human papillomavirus 16 sequences in the cervical cancer cell line SiHa. Virology 159: 389- 398, 1987.

146. Le Beau, M. M., Epstein, N. D., O'Brien, S.J., Nienhuis, A. W., Yang, Y.-C., Clark, S. C., and Rowley, J. D.: The interleukin 3 gene is located on human chromosome 5 and is deleted in myeloid leukemias with a deletion of 5q. Proc. Natl. Acad. Sci. USA 84: 5913-5917, 1987.

147. Jaye, M., Modi, W. S., Ricca, G. A., Mudd, R., Chiu, I.-M., O'Brien, S.J., and Drohan, W. N.: Isolation of a cDNA clone for the human laminin-B1 chain and its gene localization. Am. J. Hum. Genet. 41: 605-615, 1987.

148. Dean, M., Kozak, C., Robbins, J., Callahan, R., O'Brien, S., and Vande Woude, G. F.: Chromosomal localization of the met proto-oncogene in the mouse and cat genome. Genomics 1:167-173, 1987.

149. Graninger, W. B., Goldman, P. L., Morton, C. C., O'Brien, S.J., and Korsmeyer, S.J.: The kappa deleting element: Germline and rearranged, duplicated and dispersed forms. J Exp Med 167:488-501, 1988.

150. Modi, W. S. and O'Brien, S.J.: Quantitative cladistic analyses of chromosomal banding data among species in three orders of mammals: Hominoid primates, felids and arvicolid rodents. In Gustafson, J. P. and Appels, R. (Eds.): Chromosome Structure and Function. New York, Plenum, 1988, pp. 215-242.

151. Goodrowe, K. L., Wall, R. J., O'Brien, S.J., Schmidt, P. M., and Wildt, D. E.: Developmental competence of domestic cat follicular oocytes after fertilization in vitro. Biol. Reprod. 39:355- 372, 1988.

152. Lalley, P. A., O'Brien, S.J., Creau-Goldberg, N., Davisson, M. T., Roderick, T. H., Echard, G., Womack, J. E., Graves, J. M., Doolittle, D. P., and Guidi, J. N.: Report of the committee on comparative mapping. Human Gene Mapping 9. Cytogenet. Cell Genet. 46:367-389, 1987.

153. Gilbert, D. A., O'Brien, J. S. and O'Brien, S.J.: Chromosomal mapping of lysosomal enzyme structural genes in the domestic cat. Genomics 2: 329-336, 1988.

154. Modi, W. S., Masuda, A., Yamada, M., Oppenheim, J. J., Matsushima, K., and O'Brien, S.J.: Chromosomal localization of the human interleukin 1alpha (IL-1 alpha) gene. Genomics 2: 310- 314, 1988.

155. O'Brien, S.J. and Evermann, J. F.: Interactive influence of infectious disease and genetic diversity in natural populations. Trends Ecol. Evol. 3: 254-259, 1988.

156. Yuhki, N., Heidecker, G. F., and O'Brien, S.J.: Characterization of MHC cDNA clones in the domestic cat: Diversity and evolution of class I genes. J. Immunol. 142: 3676-3682, 1989.

157. Fanning, T. G., Modi, W. S., Wayne, R. K., and O'Brien, S.J.: Evolution of heterochromatin- associated satellite DNA loci in felids and canids (Carnivora). Cytogenet. Cell Genet. 48: 214- 219, 1988.

21 135

158. Modi, W. S., Fanning, T. G., Wayne, R. K., and O'Brien, S.J.: Chromosomal localization of satellite DNA sequences among 22 species of felids and canids (Carnivora). Cytogenet. Cell Genet. 48: 208-213, 1988.

159. Ruppert, J. M., Kinzler, K. W., Wong, A.J., Bigner, S. H., Kao, F. T., Law, M. L., Seuanez, H., O'Brien, S.J., and Vogelstein, B.: The GLI-Kruppel family of human genes. Mol. Cell. Biol. 8: 3104-3113, 1988.

160. Rao, V. N., Modi, W., Drabkin, H. D., Patterson, D., O'Brien, S.J., Papas, T.S., and Reddy, P.: The human erg gene maps to chromosome 21, band q22: relationship to the 8; 21 translocation of acute myelogenous leukemia. Oncogene 3: 497-500, 1988.

161. O'Brien, S.J., Seuanez, H. N., and Womack, J.E.: Mammalian genome organization: An evolutionary view. In Campbell, A. (Ed.): Annual Review of Genetics, Vol. 22. Palo Alto, Annual Reviews Inc., 1988, pp. 323-351.

162a. O'Brien, S.J.: Molecular biology and evolutionary theory: The giant panda's closest relatives. In Hecht, M. K. (Ed.): Evolutionary Biology at the Crossroads: A Symposium at Queens College. New York, Queens College, 1989, pp. 89-116.

162b. O'Brien, S.J., Benveniste, R. E., Nash, W. G., Martenson, J. S., Eichelberger, M. A., Wildt, D. E., Bush, M., Wayne, R. K., and Goldman, D.: Molecular biology and evolutionary theory: The giant panda's closest relatives. In Warren, L. and Koprowski, H. (Eds.): New Perspectives on Evolution, New York, Wiley-Liss, 1991, pp. 225-250.

163. Westerman, M., Janczewski, D.N., and O'Brien, S.J.: DNA-DNA hybridization studies and marsupial phylogeny. Aust. J. Zool. 37: 315-323, 1990.

164. Wayne, R. K., Meyer, A., Lehman, N., Van Valkenburgh, B., Kat, P. W., Fuller, T. K., Girman, D., and O'Brien, S.J.: Large sequence divergence among mitochondrial DNA genotypes within populations of eastern African black-backed jackals. Proc. Natl. Acad. Sci. USA 87: 1772-1776, 1990.

165. Weissman, A. M., Hou, D., Orloff, D. G., Modi, W. S., Seuanez, H., O'Brien, S.J., and Klausner, R. D.: Molecular cloning and chromosomal localization of the human T-cell receptor zeta chain: Distinction from the molecular CD3 complex. Proc. Natl. Acad. Sci. USA 85: 9709-9713, 1988.

166. Winkler, C., Schultz, A., Cevario, S., and O'Brien, S.J.: Genetic characterization of FLA, the cat major histocompatibility complex. Proc. Natl. Acad. Sci. USA 86: 943-947, 1989.

167. Wayne, R. K., Van Valkenburgh, B., Kat, P. W., Fuller, T. K., Johnson, W. E., and O'Brien, S.J.: Genetic and morphological divergence among sympatric canids. J. Hered. 80: 447-454, 1989.

168. Miyake, Y., O'Brien, S.J., and Kaneda, Y.: Regional localization of rDNA gene on pig chromosome 10 by in situ hybridization. Nippon Juigaku Zasshi 50: 341-345, 1988.

169. Evermann, J. F., Heeney, J. L., Roelke, M. E., McKeirnan, A. J., and O'Brien, S.J.: Biological and pathological consequences of feline infectious peritonitis virus infection in the cheetah. Arch. Virol. 102: 155-171, 1988.

170. O'Brien, S.J. and Graves, J. A. M.: Geneticists converge on divergent mammals: An overview of comparative mammalian genetics. Aust. J. Zool. 37: 147-154, 1990.

22 136

171. Giri, P.R., Krug, J. F., Kozak, C., Moretti, T., O'Brien, S.J., Seuanez, H. N., and Goldman, D.: Cloning and comparative mapping of a human class III (chi) alcohol dehydrogenase cDNA. Biochem. Biophys. Res. Commun. 164: 453-460, 1989.

172. O'Brien, S.J.: Barbara Kuhn. J. Hered. 79:491, 1988.

173. Rojko, J. L., Kociba, G. J., Abkowitz, J. L., Hamilton, K. L., Hardy, W. D. Jr., Ihle, J. N., and O'Brien, S.J.: Feline lymphomas: Immunological and cytochemical characterization. Cancer Res. 49:345-351, 1989.

174. Evermann, J. F., Heeney, J. L., McKeirnan, A. J., and O'Brien, S.J.: Comparative features of a coronavirus isolated from a cheetah with feline infectious peritonitis. Virus Res. 13:15-27, 1989.

175. Heeney J. L., Evermann, J. F., McKeirnan, A. J., Marker-Kraus, L., Roelke, M. E., Bush, M., Wildt, D. E., Meltzer, D. G., Colly, L., Lucas, J., Manton, V. J., Caro, T., O'Brien, S.J.: Prevalence and implications of feline coronavirus infections of captive and free-anging cheetahs (Acinonyx jubatus). J. Virol. 64: 1964-1972, 1990.

176. Gilbert, D. A., Reid, Y. A., Gail, M. H., Pee, D., White, C., Hay, R. J., and O'Brien, S.J.: Application of DNA fingerprints for cell-line individualization. Am. J. Hum. Genet. 47: 499- 514, 1990.

177. Modi, W. S., Levine, M. A., Seuanez, H. N., Dean, M., and O'Brien, S.J.: The human chromogranin A gene: Chromosome assignment and RFLP analysis. Am J Hum Genet 45:814- 818, 1989.

178. Lalley, P. A., Davisson, M. T., Graves, J. A. M., O'Brien, S.J., Roderick, T. H., Doolittle, D. P., and Hillyard, A. L.: Report of the committee on comparative mapping. Human Gene Mapping 9.5: Update to the Ninth International Workshop on Human Gene Mapping. Cytogenet. Cell Genet. 49:227-235, 1988.

179. Yuhki, N. and O'Brien, S.J.: DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history. Proc. Natl. Acad. Sci. USA 87: 836-840, 1990.

180. Mann, D.L., O’Brien, S.J., Gilbert, D.A., Reid, Y., Popovic, M., Read-Connole, E., Gallo, R. C., and Gazdar, A. F.: Origin of the HIV-susceptible human CD4+ cell line H9. AIDS Res. Hum. Retroviruses 5: 253-255, 1989.

181. McGuire, E. A., Hockett, R. D., Pollock, K. M., Bartholdi, M. F., O'Brien, S.J., and Korsmeyer, S.J.: The t(11;14) (p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts including Ttg-1, a gene encoding a potential zinc finger protein. Mol. Cell. Biol. 9: 2124-2132, 1989.

182. Anagnou, N. P., Economou-Pachnis, A., O'Brien, S.J., Modi, W. S., Nienhuis, A. W., and Tsichlis, P. N.: The human homolog of the Moloney leukemia virus integration 2 locus (MLV12) maps to band p14 of chromosome 5. Genomics 5: 354-358, 1989.

183. Sack, G. H., Jr., Talbot, C. C., Seuanez, H., and O'Brien, S.J.: Molecular analysis of the human serum amyloid A (SAA) gene family. Scand. J. Immunol. 29: 113-119, 1989.

184. Gardner, M. B., Kozak, C., and O'Brien, S.J.: The Lake Casitas wild mouse: Evolving genetic resistance to retroviral disease. Trends Genet. 7: 22-27, 1991.

23 137

185. Mock, B., Kozak, C., Seldin, M. F., Ruff, N., D'Hoostelaere, L., Szpirer, C., Seuanez, H., O'Brien, S., and Banner, S.: A glutaminase (Gls) gene maps to mouse chromosome 1, rat chromosome 9 and human chromosome 2. Genomics 5: 291-297, 1989.

186. Hentze, M. W., Seuanez, H. N., O'Brien, S.J., Harford, J. B., and Klausner, R. D.: Chromosomal localization of nucleic acid-binding proteins by affinity mapping: Assignment of the IRE-binding protein gene to human chromosome 9. Nucleic Acids Res. 17:6103-6108, 1989.

187. Johnston, L. A., O'Brien, S.J., and Wildt, D. E.: In vitro maturation and fertilization of domestic cat follicular oocytes. Gamete Res. 24: 343-356, 1989.

188. Reeves, R. H., Gearhart, J. D., Hecht, N. B., Yelick, P., Johnson, P., and O'Brien S.J.: Mapping of PRM-1 to human chromosome 16 and tight linkage of Prm-1 and Prm-2 on mouse chromosome 16. J. Hered. 80: 442-446, 1989.

189. Winkler, C., Yuhki, N., and O'Brien, S.J.: Comparative analysis of FLA, the major histocompatibility complex in the Felidae. In Clegg, M. T., and O'Brien, S.J. (Eds.): Molecular Evolution. New York, Wiley, Liss, 1990, pp. 29-50.

190. Yuhki, N., Winkler, C., and O'Brien, S.J.: MHC genes of the domestic cat. In Srivastava, R., Ram, B. P., and Tyle, P. (Eds.): Immunogenetics of the Major Histocompatibility Complex. New York, VCH Publishers, 1991, pp. 348-367.

191. Lalley, P. A., Davisson, M. T., Graves, J. A. M., O'Brien, S.J., Womack, J. E., Roderick, T. H., Creau-Goldberg, N., Hillyard, A. L., Doolittle, D. P., and Rogers, J. A.: Report of the committee on comparative mapping. Human Gene Mapping 10. Cytogenet. Cell Genet. 51: 503-532, 1989.

192. Modi, W. S., Seuanez, H. N., Jaye, M., Haigler, H. J., Kaplan, R., and O'Brien, S.J.: The human endonexin II (ENX2) gene is located at 4q28----q32. Cytogenet. Cell Genet. 52:167-169, 1989.

193. Modi, W. S., Dean, M., Seuanez, H. N., Mukadia, N., Matsushima, K., and O'Brien, S. J: Monocyte-derived neutrophil chemotatic factor (MDNCF/IL-8) resides in a gene cluster along with several other members of the platelet factor 4 gene superfamily. Hum. Genet. 84:185-187, 1990.

194. Baker, C. S., Palumbi, S. R., Lambertsen, R. H., Weinrich, M. T., Calambokidis, J., and O'Brien, S.J.: Influence of seasonal migration on geographic distribution of mitochondrial DNA haplotypes in humpback whales. Nature 344:238-240, 1990.

195. Janczewski, D. N., Goldman, D., and O'Brien, S.J.: Molecular genetic divergence of orang utan (Pongo pygmaeus) subspecies based on isozyme and two-dimensional gel electrophoresis. J. Hered. 81:375-387, 1990.

196. Wayne, R. K., Van Valkenburgh, B., and O'Brien, S.J.: Molecular distance and divergence time in carnivores and primates. Mol. Biol. Evol. 8: 297-319, 1991.

197. Yuhki, N. and O'Brien, S.J.: DNA recombination and pressure sustain genetic sequence diversity of the feline MHC class I genes. J. Exp. Med. 172: 621-630, 1990.

198. Halverson, D., Modi, W., Dean, M., Gelman, E. P., Dunn, K. J., Clanton, D., Oskarsson, M., O'Brien, S.J., and Blair, D. G.: An oncogenic chromosome 8-9 gene fusion isolated following transfection of human ovarian carcinoma cell line DNA. Oncogene 5: 1085-1089, 1990.

24 138

199. Bush, M., Graves, J. A. M., O'Brien, S.J., and Wildt, D. E.: Dissociative anaesthesia in free- ranging male koalas and selected marsupials in captivity. Aust. Vet. J. 67: 449-451, 1990.

200. Gilbert, D. A., Lehman, N., O'Brien, S.J., and Wayne, R. K.: Genetic fingerprinting reflects population differentiation in the California Channel Island fox. Nature 344: 764-767, 1990.

201. O'Brien, S.J., Roelke, M. E., Yuhki, N., Richards, K. W., Johnson, W. E., Franklin, W. L., Anderson, A. E., Bass, O. L. Jr., Belden, R. C., and Martenson, J. S.: Genetic introgression within the Florida panther Felis concolor coryi. Natl. Geo. Res. 6: 485-494, 1990.

202. Dionne, C. A., Kaplan, R., Seuanez, H., O'Brien, S.J., and Jaye, M.: Chromosome assignment by polymerase chain reaction techniques: Assignment of the oncogene FGF- to human chromosome 4. Biotechniques 8: 190-194, 1990.

203. Dean, M., Stewart, C., Perry, A., Gerrard, B., Beck, T., Rapp, U., Drumm, M., Iannuzzi, M., Collins, F., and O'Brien, S.J.: Genetic markers for oncogenes, growth factors, and cystic fibrosis. In Neth, R.D. et al., (Eds.): Modern Trends in Human Leukemia VIII. Heidelberg, Germany, Springer-Verlag, 1989, pp. 360-365.

204. Baker, C. S., Lambertsen, R. H., Weinrich, M. T., Calambokidis, J., Early, G., and O'Brien, S.J.: Molecular genetic identification of the sex of humpback whales (Megaptera novaeangliae). In Hoelzel, A. R. (Ed.): Genetic Ecology of Whales and Dolphins. Cambridge, International Whaling Committee, 1991, pp. 105-111.

205. Levine, M. A., Modi, W. S., and O'Brien, S.J.: Chromosomal localization of the genes encoding two forms of the G-protein beta polypeptide, beta 1 and beta 3, in man. Genomics 8: 380-386, 1990.

206. Brown, J. L., Bush, M., Packer, C., Pusey, A. E., Monfort, S. L., O'Brien, S.J., Janssen, D. L., and Wildt, D. E.: Developmental changes in pituitary-gonadal function in free-ranging lions (Panthera leo leo) of the Serengeti Plains and Ngorongoro Crater. J. Reprod. Fertil. 91: 29-40, 1991.

207. O'Brien, S.J.: Genetic map of the domestic cat, Felis catus. In O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes, Nonhuman Vertebrates, Fifth Edition. New York, Cold Spring Harbor Laboratory, 1990, pp. 4.102-4.104.

208. O'Brien, S.J., and Johnson, P. A.: An abridged human map: Proto-oncogenes, endogenous retroviral sequences, cell surface receptors, growth factors, and lymphokines. In O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes, Human Maps, Fifth Edition. New York, Cold Spring Harbor Laboratory, 1990, pp. 5.197-5.210.

209. Frolova, E. I., Dolganov, G. M., Mazo, I. A., Smirnov, D. V., Copeland, P., Stewart, C., O'Brien, S.J., and Dean, M.: Linkage mapping of the human CSF2 and IL3 genes. Proc. Natl. Acad. Sci. USA 88: 4821-4824, 1991.

210. O'Brien, S.J.: The genetic peril of the cheetah. In Seidensticker, J. (Ed.): Great Cats: Majestic Creatures of the Wild. Sydney, Australia, Weldon Owen Pty Ltd., 1991, p. 18.

211. O'Brien, S.J.: Molecular evolution of cats. In Seidensticker, J. (Ed.): Great Cats: Majestic Creatures of the Wild. Sydney, Australia, Weldon Owen Pty Ltd., 1991, p. 146.

25 139 212. Miththapala, S., Seidensticker, J., Phillips, L. G., Goodrowe, K. L., Fernando, S. B. U., Forman, L., and O'Brien, S.J.: Genetic variation in Sri Lankan leopards. Zoo Biol. 10: 139-146, 1991.

213. Goldman, D., O'Brien, S.J., Lucas-Derse, S., and Dean, M.: Linkage mapping of human polymorphic proteins identified by two-dimensional electrophoresis. Genomics 11: 875-884, 1991.

214. Johnston, L. A., Donoghue A. M., O'Brien, S.J., and Wildt, D. E.: Culture medium and protein supplementation influence in vitro fertilization and embryo development in the domestic cat. J. Exp. Zool. 257: 350-359, 1991.

215. Wildt, D. E., Bush, M., O'Brien, S.J., Murray, N. D., Taylor, A., and Graves, J. A. M.: Semen characteristics in free-living koalas (Phascolarctos cinereus). J. Reprod. Fertil. 92: 99-107, 1991.

216. Johnston, L. A., Donoghue, A. M., O'Brien, S.J., and Wildt, D. E.: Influence of temperature and gas atmosphere on in vitro fertilization and embryo development in domestic cats. J. Reprod. Fertil. 92: 377-382, 1991.

217. Packer, C., Pusey, A. E., Rowley, H., Gilbert, D. A., Martenson, J. S., and O'Brien, S.J.: Case study of a population bottleneck: Lions of the Ngorongoro Crater. Conservation Biology 5: 219-230, 1991.

218. Gilbert, D. A., Packer, C., Pusey, A. E., Stephens, J. C., and O'Brien, S.J.: Analytical DNA fingerprinting in lions: Parentage, genetic diversity, and kinship. J. Hered. 82: 378-386, 1991.

219. Packer, C., Gilbert, D. A., Pusey, A. E., and O'Brien, S.J.: Kinship, cooperation and inbreeding in African lions: A molecular genetic analysis. Nature 351: 562-565, 1991.

220. O'Brien, S.J. and Graves, J. A. M.: Report of the committee on comparative gene mapping. Human Gene Mapping 10.5: Update to the Tenth International Workshop on Comparative Gene Mapping. Cytogenet. Cell Genet. 55: 406-433, 1990.

221. Poduslo, S. E., Dean, M., Kolch, U., and O'Brien, S.J.: Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis. Am. J. Hum. Genet. 49: 106-111, 1991.

222. O'Brien, S.J. and Roelke, M. E.: What does geology have to do with panther conservation? Natl. Geo. Res. 7: 117-119, 1991.

223. O'Brien, S.J. and Mayr, E.: Bureaucratic mischief: Recognizing endangered species and subspecies. Science 251: 1187-1188, 1991.

224. O'Brien, S.J.: Mammalian genome mapping: Lessons and prospects. Curr Opin Genet Dev 1: 105-111, 1991.

225. Reid, Y. A., Gilbert, D. A., and O'Brien, S.J.: The use of DNA hypervariable probes for human cell line identification. ATCC Quarterly 10: 1-3, 1990.

226. Masuda, R., Yuhki, N., and O'Brien, S.J.: Molecular cloning, chromosomal assignment, and nucleotide sequence of the feline homeobox HOX3A. Genomics 11: 1007-1013, 1991.

227. Stephens, J. C., Gilbert, D. A., Yuhki, N., and O'Brien, S.J.: Estimation of heterozygosity for single-probe multilocus DNA fingerprints. Mol. Biol. Evol. 9: 729-743, 1992.

26 140

228. Miller, M. D., Wilson, S. D., Dorf, M. E., Seuanez, H. N., O'Brien, S.J., and Krangel, M. S.: Sequence and chromosomal location of the I-309 gene: Relationship to genes encoding a family of inflammatory cytokines. J. Immunol. 145: 2737-2744, 1990.

229. Levine, M. A., Modi, W. S., and O'Brien, S.J.: Mapping of the gene encoding the alpha subunit of the stimulatory G protein of adenylyl cyclase (GNAS1) to 20q13.2----q13.3 in human by in situ hybridization. Genomics 11: 478-479, 1991.

230. Johnston, L.A., Donoghue, A.M., O'Brien, S.J., and Wildt, D.E.: Rescue and maturation in vitro of follicular oocytes from nondomestic felid species. Biol. Reprod. 45: 898-906, 1991.

231. Dean, M., Lucas-Derse, S., Bolos, A., O'Brien, S.J., Kirkness, E. F., Fraser, C. M., and Goldman, D.: Genetic mapping of the beta 1 GABA receptor gene to human chromosome 4 using a tetranucleotide repeat polymorphism. Am J Hum Genet 49: 621-626, 1991.

232. O'Brien, S.J.: Genetic map of Felis catus (domestic cat). In O'Brien, S.J. (Ed.): Genetic Maps: Locus Maps of Complex Genomes, Nonhuman Vertebrates, Sixth Edition. New York, Cold Spring Harbor Laboratory, 1993, pp. 4.250-4.253.

233. O'Brien, S.J.: Establishing the ancestry of the red panda. In Stirling, I. (Ed.): Bears. Sydney, Australia, Weldon Owen Pty. Ltd., 1993, p. 30.

234. White, M.B., Carvalho, M., Derse, D., O'Brien, S.J., and Dean, M.: Detecting single base substitutions as heteroduplex polymorphisms. Genomics 12: 301-306, 1992.

235. Goldman, D. and O'Brien, S.J.: Two-dimensional protein electrophoresis in phylogenetic studies. Meth. Enzymol. 244:113-121, 1993.

236. Dionne, C. A., Modi, W. S., Crumley, G., O'Brien, S.J., Schlessinger, J., and Jaye, M.: BEK, a receptor for multiple members of the fibroblast growth factor (FGF) family, maps to human chromosome 10q25.3----10q26. Cytogenet. Cell Genet. 60: 34-36, 1992.

237. Baker, C.S., Gilbert, D.A., Weinrich, M.T., Lambertsen, R., Calmabokidis, J., McArdle, B., Chambers, G. K., and O'Brien, S.J.: Population characteristics of DNA fingerprints in humpback whales (Megaptera novaeangliae). J. Hered. 84: 281-290, 1993.

238. O'Brien, S.J.: Genetic erosion: A global dilemma. Natl. Geogr. 181: 136, 1992.

239. O'Brien, S.J.: Ghetto legacy. Can the high incidence of Tay-Sachs disease in Ashkenazi Jews be linked to historic epidemics of tuberculosis in industrial European cities? Current Biology 1: 209-211, 1991.

240. O'Brien, S.J.: Fuzzy thinking about the giant panda's ancestry. In Stirling, I. (Ed.): Bears. Sydney, Australia, Weldon Owen Pty. Ltd., 1993, pp. 34-35.

241. Janczewski, D. N., Yuhki, N., Gilbert, D. A., Jefferson, G. T., and O'Brien, S.J.: Molecular phylogenetic inference from saber-toothed cat fossils of Rancho La Brea. Proc. Natl. Acad. Sci. USA. 89: 9769-9773, 1992.

242. Lautenberger, J. A., Burdett, L. A., Gunnell, M., Qi, S., Watson, D. K., O'Brien, S.J., and Papas, T. S.: Genomic dispersal of the ets gene family during metazoan evolution. Oncogene 7: 1713- 1719, 1992.

27 141

243. O'Brien, S.J. and Graves, J. A. M.: Report of the committee on comparative gene mapping. Human Gene Mapping 11. Cytogenet. Cell Genet. 58: 1124-1151, 1991.

244. Hoelzel, A. R., Halley, J., O'Brien, S.J., Campagna, C., Arnbom, T., Le Boeuf, B., Ralls, K., and Dover, G. A.: Elephant seal genetic variation and the use of simulation models to investigate historical population bottlenecks. J. Hered. 84:443-449, 1993.

245. Olmsted, R. A., Langley, R., Roelke, M. E., Goeken, R. M., Adger-Johnson, D., Goff, J. P., Albert, J. P., Packer, C., Laurenson, M. K., Caro, T. M., Scheepers, L., Wildt, D. E., Bush, M., Martenson, J. S., and O'Brien, S.J.: Worldwide prevalence of lentivirus infection in wild feline species: Epidemiologic and phylogenetic aspects. J. Virol. 66: 6008-6018, 1992.

246. Jackson, C. E., Yuhki, N., Desnick, R. J., Haskins, M. E., O'Brien, S.J., and Schuchman, E. H.: Feline arylsulfatase B (ARSB): Isolation and expression of the cDNA, comparison with human ARSB, and gene localization to feline chromosome A1. Genomics 14: 403-411, 1992.

247. O'Brien S.J. and Mann, D. L.: Adaptive chaos and AIDS. Current Biology 2: 203-205, 1992.

248. O'Brien, S.J.: The molecular evolution of the bears. In Stirling, I. (Ed.): Bears. Sydney, Australia, Weldon Owen Pty. Ltd., 1993, pp. 26-33.

249. Kelley, M. J., Pech, M., Seuanez, H. N., Rubin, J. S., O'Brien, S.J., and Aaronson, S. A.: Emergence of the keratinocyte growth factor multigene family during the great ape radiation. Proc. Natl. Acad. Sci. USA 89: 9287-9291, 1992.

250. Donoghue, A. M., Johnston, L. A., Goodrowe, K. L., O'Brien, S.J. and Wildt, D. E.: Influence of day of estrous on egg viability and comparative efficiency of in vitro fertilization in domestic cats in natural or gonadotrophin-induced oestrus. J. Reprod. Fertil. 98: 85-90, 1993.

251. Menotti-Raymond, M. and O'Brien, S.J.: Dating the genetic bottleneck of the African cheetah. Proc. Natl. Acad. Sci. USA 90: 3172-3176, 1993.

252. O'Brien, S.J., Womack, J. E., Lyons, L. A., Moore, K. J., Jenkins, N. A., and Copeland, N. G.: Anchored reference loci for comparative genome mapping in mammals. Nature Genet. 3: 103- 112, 1993.

253. Roelke, M. E., Martenson, J. S. and O'Brien, S.J.: The consequences of demographic reduction and genetic depletion in the endangered Florida panther. Curr. Biol. 3: 340-350, 1993.

254. Brown, E. W., Olmsted, R. A., Martenson, J. S., and O'Brien, S.J.: Exposure to FIV and FIPV in wild and captive cheetahs. Zoo Biol. 12: 135-142, 1993.

255. Briscoe, D., Stephens, J. C., and O'Brien, S.J.: Linkage disequilibrium in admixed populations: Applications in gene mapping. J. Hered. 85: 59-63, 1994.

256. Johnston, L. A., Donoghue, A. M., O'Brien, S.J., and Wildt, D. E.: Influence of culture medium on in vitro maturation and fertilization in the domestic cat. Theriogenology 80: 829-839, 1993.

257. Brown, E. W., Miththapala, S. and O'Brien, S.J.: Prevalence of exposure to feline immunodeficiency virus in exotic felid species. J. Zoo Wildl. Med. 24: 357-364, 1993.

258. Baker, C. S., Perry, A., Bannister, J. L., Weinrich, M. T., Abernethy, R. B., Calambokidis, J.,

28 142 Lien, J., Lambertsen, R. H., Urban Ramirez, J., Vasquez, O., Clapham, P. J., Alling, A., O'Brien, S.J., and Palumbi, S. R.: Abundant mitochondrial DNA variation and world-wide population structure in humpback whales. Proc. Natl. Acad. Sci. USA 90: 8239-8243, 1993.

259. O'Brien, S.J.: Molecular genetics and phylogenetics of the Felidae: Implications for conservation. In: Cat Action Plan. K. Nowell and P. Jackson (Eds). pp xxiii-xxiv. 1996.

260. O'Brien, S.J. and Mayr, E.: Species hybridization and protection of endangered . Science 253: 251-253, 1991.

261. Janczewski, D. N., Modi, W. S., Stephens, J. C., and O'Brien S.J.: Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the Pantherine lineage of Felidae. Mol. Biol. Evol. 12: 690-707, 1995.

262. Yuhki, N. and O'Brien, S.J.: Exchanges of short polymorphic DNA segments predating speciation in feline major histocompatibility complex class I genes. J Mol Evol 39:22-33, 1994.

263. O'Brien, S.J., Peters, J., Searle, A., Womack, J., and Graves, J. A. M.: Report of the committee on comparative gene mapping. Update to the Eleventh International Workshop on Human Gene Mapping. In Cutticchia, A. J., Pearson, P. L., Klinger, H. P. (Eds.): Genome Priority Reports: Chromosome Coordinating Meeting 1992, Vol. 1. Basel, Karger, 1993, pp. 758-809.

264. O'Brien, S.J.: When endangered species hybridize: The U.S. Hybrid Policy. In Meffe, G. K. and Carroll, C. R. (Eds.): An Introduction to Conservation Biology. Sunderland, Sinauer, 1994, pp. 69-70.

265. Marshall Graves, J. A., Wakefield, M. J., Peters, J., Searle, A. G., Womack, J. E., and O'Brien, S.J.: Report of the committee on comparative gene mapping. In Cuticchia, A. J. (Ed.): Human Gene Mapping, 1994: A Compendium. Baltimore, Johns Hopkins University Press, 1995, pp. 962-1016.

266. Lopez, J. V., Yuhki, N., Masuda, R., Modi, W. S., and O'Brien, S.J.: Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39:174-190, 1994.

267. Brown, J.L., Bush, M., Packer, C., Pusey, A.E., Monfort, S.L., O'Brien, S.J., Janssen, D.L., and Wildt, D. E.: Hormonal characteristics of free-ranging female lions (Panthera leo) of the Serengeti Plains and Ngorongoro Crater. J. Reprod. Fertil. 97: 107-114, 1993.

268. Glavac, D., Ravnik-Glavac, M., O'Brien, S.J., and Dean, M.: Polymorphisms in the 3' untranslated region of the I kappa B/MAD-3 (NFKBI) gene located on chromosome 14. Hum. Genet. 93: 694-696, 1994.

269. O'Brien, S.J.: The genomics generation. Curr. Biol. 3: 395-397, 1993.

270. Okuda, M., Umeda, A., Matsumoto, Y., Momoi, Y., Watari, T., Goitsuka, R., O'Brien, S.J., Tsujimoto, H., and Hasegawa, A.: Molecular cloning and chromosomal mapping of feline p53 tumor suppressor gene. J. Vet. Med. Sci. 55: 801-805, 1993.

271. Tsujimoto, H., Fulton, R., Nishigaki, K., Matsumoto, Y., Hasegawa, A., Cevario, S., O'Brien, S.J., Terry, A., Onions, D., and Neil, J. C.: A common proviral integration region, fit-1, in T-cell tumors induced by Myc-containing feline leukemia viruses. Virology 196: 845-848, 1993.

29 143 272. Seuanez, H. N., Alves, G., and O'Brien, S.J.: Genetic characterization of parental cell lines and biochemical analysis of somatic cell hybrids between mouse (RAG) cells and fibroblasts of Ateles paniscus chamek (Primates, Platyrrhini). Am. J. Primatol. 30: 181-194, 1993.

273. Langley, R. J., Hirsch, V. M., O'Brien, S.J., Adger-Johnson, D., Goeken, R. M., and Olmsted, R. A.: Nucleotide sequence analysis of puma lentivirus (PLV-14): Genomic organization and relationship to other lentiviruses. Virology 202: 853-864, 1994.

274. Pecon-Slattery, J., Johnson, W. E., Goldman, D., and O'Brien, S.J.: Phylogenetic reconstruction of South American felids defined by protein electrophoresis. J. Mol. Evol. 39: 296-305, 1994.

275. Miththapala, S., Seidensticker, J., and O'Brien, S.J.: Phylogeographic subspecies recognition in leopards (Panthera pardus): Molecular genetic variation. Conserv. Biol. 10: 1115-1132, 1996.

276. Anagnou, N. P., Seuanez, H., Modi, W., O'Brien, S.J., Papamatheakis, J., and Moschonas, N. K.: Chromosomal mapping of two members of the human glutamate dehydrogenase (GLUD) gene family to chromosomes 10q22.3-q23 and Xq22-q23. Hum. Hered. 43: 351-356, 1993.

277. O'Brien, S.J.: Perspective on conservation genetics. In Schierwater, B., Streit, B., Wagner, G. P., and DeSalle, R. (Eds.): Molecular Ecology and Evolution: Approaches and Applications. Basel, Birkhauser Verlag, 1994, pp. 275-280.

278. Koralnik, I. J., Boeri, E., Saxinger, W. C., Lo Monico, A., Fullen, J., Gessain, A., Guo, H.-G., Gallo, R. C., Markham, P., Kalyanaraman, V., Hirsch, V., Allan, J., Murthy, K., Alfords, P., Pecon Slattery, J., O'Brien, S.J., and Franchini, G.: Phylogenetic association of human and simian T-cell leukemia/lymphotropic virus type I isolates: Evidence for interspecies transmission. J. Virol. 68: 2693-2707, 1994.

279. O'Brien, S.J., Lu, Z., Knight, J., Qui, X., Mainka, S., and Pan, W.: Conservation genetics with respect to giant pandas. Proc. Int. Giant Panda Conserv. Symp. Cheng Du, China, pp. 112-115, 1994.

280. Stephens, J. C., Briscoe, D., and O'Brien, S.J.: Mapping by admixture linkage disequilibrium (MALD) in human populations: Limits and guidelines. Am. J. Hum. Genet. 55: 809-824, 1994.

281. Brown, E. W., Yuhki, N., Packer, C., and O'Brien, S.J.: A lion lentivirus related to feline immunodeficiency virus: Epidemiologic and phylogenetic aspects. J Virol 68:5953-5968, 1994.

282. O'Brien, S.J.: The big cats tell a new story about the endangered species. Cosmos 4:14-18, 1994.

283. O'Brien, S.J., Pan, W., and Lu, Z.: Pandas, people and policy. Nature 369: 179-180, 1994.

284. Hoelzel, A. R., Lopez, J. V., Dover, G. A., and O'Brien, S.J.: Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J Mol Evol 39: 191- 199, 1994.

285. O'Brien, S.J. and Clegg, M. T.: Genomes and evolution. Curr. Opin. Genet. Dev. 3: 835-836, 1993.

286. O'Brien, S.J., Peters, J., Searle, A.G., Womack, J.E., Johnson, P.A., and Graves, J.A. M.: Comparative gene mapping committee report. In Cuticchia, A.J. and Pearson, P. L. (Eds.): Human Gene Mapping, 1993: A Compendium. Baltimore, Johns Hopkins University Press, 1994, pp. 846-892.

30 144

287. Pecon Slattery, J. and O'Brien, S.J.: Molecular phylogeny of the red panda (Ailurus fulgens). J. Hered. 86: 413-422, 1995.

288. Seuanez, H.N., Alves, G., and O'Brien, S.J.: Gene mapping in the spider monkey (Ateles paniscus chamek). J. Hered. 85: 466-473, 1994.

289. Jordan, K., O'Brien, S.J., Johnson, K.H., and O'Brien, T.D.: Assignment of islet amyloid polypeptide (IAPP) gene to feline chromosome B4 using the polymerase chain reaction technique on feline-rodent hybrid cell lines. Vet. Pathol. 32: 195-197, 1995.

290. Dean, M., Stephens, J. C., Winkler, C., Lomb, D. A., Ramsburg, M., Boaze, R., Stewart, C., Charbonneau, L., Goldman, D., Albaugh, B. J., Goedert, J. J., Beasley, R. P., Hwang, L.-Y., Buchbinder, S., Weedon, M., Johnson, P. A., Eichelberger, M., and O'Brien, S.J.: Polymorphic admixture typing in human ethnic populations. Am. J. Hum. Genet. 55: 788-808, 1994.

291. O'Brien, S.J., Martenson, J.S., Wildt, D.E., Bush, M., Winkler, C., Roelke, M.E., Marker-Kraus, L., and Grisham, J.: The cheetah legacy: Retrospective interpretations. Proc. 50th Annual IUD Conference, Zoological Society, Dublin, Ireland. October, 1995. pp. 37-55, 1995.

292. O'Brien, S.J.: A role for molecular genetics in biological conservation. Proc. Natl. Acad. Sci. USA 91:5748-5755, 1994.

293. O'Brien, S.J., Martenson, J.S., Miththapala, S., Janczewski, D.N., Pecon Slattery, J., Johnson, W.E., Gilbert, D.A., Roelke, M.E., Packer, C., Bush, M., and Wildt, D.E.: Conservation genetics of the Felidae. In Avise, J.C. and Hamrick, J.L. (Eds.): Conservation Genetics: Case Histories from Nature. New York, Chapman and Hall, pp. 50-74, 1996.

294. O'Brien, S.J.: The cheetah's conservation controversy. Conservation Biology. 8: 1153-1155, 1994.

295. Sundberg, J.P., Montali, R.J., Bush, M., Phillips, L.G., Jr., O'Brien, S.J., Jenson, A. B., Burk, R.D., and Van Ranst, M.: Papillomavirus-associated focal oral hyperplasia in wild and captive Asian lions (Panthera leo persica). J. Zoo Wildl. Med. 27: 61-70, 1996.

296. Lyons, L. A., Raymond, M. M., and O'Brien, S.J.: Comparative genomics: The next generation. Animal Biotechnology 5: 103-111, 1994.

297. Menotti-Raymond, M. A. and O'Brien, S.J.: Evolutionary conservation of ten microsatellite loci in four species of Felidae. J. Hered. 86: 319-322, 1995.

298. Waits, L. P., Sullivan, J., O'Brien, S.J., and Ward, R. H.: Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA. Mol. Phylogenet. Evol. 13: 82-92, 1999.

299. Dratch, P.A., Roslund, W., Martenson, J.S., Greenwell, R., O'Brien, S.J., and Best, T.: Molecular genetic identification of the Mexican onza as a puma (Felis concolor). Cryptozoology 12: 42-49, 1993-1996.

300. O'Brien, S.J.: Genetic and phylogenetic analyses of endangered species. Ann. Rev. Genet. 28: 467-489, 1994.

301. Carpenter, M.A., O'Brien, S.J.: Coadaptation and immunodeficiency virus: Lessons from the

31 145 Felidae. Curr. Opin. Genet. Devel. 5: 739-745, 1995.

302. Alexander, K.A., MacLachlan, N.J., Kat, P.W., House, C., O'Brien, S.J., Lerche, N. W., Sawyer, M., Frank, L.G., Holekamp, K., Smale, L., McNutt, J. W., Laurenson, M.K., Mills, M.G.L., and Osburn, B.I.: Evidence of natural bluetongue virus infection among African carnivores. Am. J. Trop. Med. Hyg. 51: 568-576, 1994.

303. Wienberg, J., Stanyon, R., Nash, W.G., O'Brien, P.C.M., Yang, F., O'Brien, S.J., and Ferguson- Smith, M.A.: Conservation of human vs. feline genome organization revealed by reciprocal chromosome painting. Cytogenet. Cell Genet. 77: 211-217, 1997.

304. Kaslow, R.A., Carrington, M., Apple, R., Park, L., Munoz, A., Saah, A.J., Goedert, J.J., Winkler, C., O'Brien, S.J., Rinaldo, C., Detels, R., Blattner, W., Phair, J., Erlich, H., and Mann, D.L.: Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nature Med. 2: 405-411, 1996.

305. Lopez, J.V., Cevario, S., and O'Brien, S.J.: Complete nucleotide sequence of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome. Genomics 33: 229-246, 1996.

306. Menotti-Raymond, M. and O'Brien, S.J.: Hypervariable genomic variation to reconstruct the natural history of populations: Lessons from the big cats. Electrophoresis 16: 1771-1774, 1995.

307. Lyons, L.A. and O’Brien, S.J.: Comparative gene mapping for the feline genome project. Strategies 9: 77-78, 1996.

308. Alexander, K.A., Kat, P.W., House, J., House, C., O'Brien, S.J., Laurenson, M.K., McNutt, J.W., and Osburn, B.I.: African horse sickness and African carnivores. Vet. Microbiol. 47: 133-140, 1995.

309. Johnson, W.E., Dratch, P.A., Martenson, J.S., and O'Brien, S.J.: Resolution of recent radiations within three evolutionary lineages of Felidae using mitochondrial restriction fragment length polymorphism variation. J. Mammal. Evol. 3: 97-120, 1996.

310. Roelke-Parker, M. E., Munson, L., Packer, C., Kock, R., Cleaveland, S., Carpenter, M., O'Brien, S.J., Pospichil, A., Hofmann-Lehmann, R., Lutz, H., Mwamengele, G. L. M., Mgasa, M. N., Machange, G. A., Summers, B. A., Appel, M. J. G.: A canine distemper virus epidemic in Serengeti lions (Panthera leo). Nature 379: 441-445, 1996.

311. Masuda, R., Lopez, J.V., Pecon Slattery, J., Yuhki, N., and O'Brien, S.J.: Molecular phylogeny of mitochondrial cytochrome b and 12S rRNA sequences in the Felidae: Ocelot and domestic cat lineages. Mol. Phylogenet. Evol. 6: 351-365, 1996.

312. Lu Zhi, Karish, W. B., Janczewski, D. N., Frazier-Taylor, H., Sajuthi, D., Gombek, F., Andau, M., Martenson, J.S., and O'Brien, S.J.: Genomic differentiation among natural populations of orang-utan (Pongo pygmaeus). Curr. Biol. 6: 1326-1336, 1996.

313. Johnson, W., Culver, M., Iriarte, J.A., Eizirik, E., Seymour, K.L., and O’Brien, S.J.: Tracking the evolution of the elusive Andean mountain cat (Oreailurus jacobita) from mitochondrial DNA. J. Hered. 89: 227-232, 1998.

314. O'Brien, S.J.: Genomic prospecting. Nature Med. 1: 742-744, 1995.

32 146 315. Lyons, L. A. and O'Brien, S.J.: Prospects for comparative genome analyses among mammals. In Gustafson, J. P. and Flavell, R. A. (Eds.): Genomes of Plants and Animals: 21st Stadler Genetics Symposium. New York, Plenum, 1996, pp. 115-125.

316. Taylor, A., Graves, J.M., Murray, N., O’Brien, S.J., Yuhki, N., and Sherwin, B.: Conservation genetics of the koala (Phascolarctos cinereus). low mitochondrial DNA variation amongst southern Australian populations. Genet. Res. 69: 25-33, 1997.

317. Johnson, W. and O'Brien, S.J.: Phylogenetic reconstruction of the Felidae using 16S rRNA and NADH-5 mitochondrial genes. J. Mol. Evol. 44(Suppl. 1): S98-S116, 1997.

318. Hofmann-Lehmann, R., Fehr, D., Grob, M., Elgizoli, M., Packer, C., Martenson, J. S., O'Brien, S.J., and Lutz, H.: Prevalence of antibodies to feline parvovirus, calicivirus, herpesvirus, coronavirus and immunodeficiency virus and of feline leukemia virus antigen and the interrelationship of these viral infections in free-ranging lions in East Africa. Clin. Diagn. Lab. Immunol. 3: 554-562, 1996.

319. Lopez, J.V., Culver, M., Stephens, J.C., Johnson, W.E., O'Brien, S.J.: Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Mol. Biol. Evol. 14: 277- 286, 1997.

320. Carpenter, M.A., Brown, E.W., Culver, M., Johnson, W.E., Pecon-Slattery, J., Brousset, D., and O'Brien, S.J.: Genetic and phylogenetic divergence of feline immunodeficiency virus in the puma (Puma concolor). J. Virol. 70: 6682-6693, 1996.

321. Yuhki, N. and O'Brien, S.J.: Nature and origin of polymorphism in feline MHC class II DRA and DRB genes. J. Immunol. 158: 2822-2833, 1997.

322. Carpenter, M.A., Appel, M.J.G., Roelke-Parker, M.E., Munson, L., Hofer, H., East, M., and O'Brien, S.J.: Genetic characterization of canine distemper virus in Serengeti carnivores. Vet. Immunol. Immunopathol. 65: 259-266, 1998.

323. Hoelzel, A.R., Stephens, J.C., and O'Brien, S.J.: Molecular genetic diversity and evolution at the MHC DQB locus in four species of pinnipeds. Mol. Biol. Evol. 16: 611-618, 1999.

324. Carpenter, M.A., Brown, E.W., MacDonald, D.W., and O'Brien, S.J. Phylogeographic patterns of feline immunodeficiency virus genetic diversity in the domestic cat. Virol. 251: 234-243, 1998.

325. Comparative Genome Organization: First International Workshop, Fraser Island, Australia. Mammalian Genome 7: 717-734, 1996.

326. Lyons, L.A., Laughlin, T.F., Copeland, N.G., Jenkins, N.A., Womack, J.E., and O'Brien, S.J. Comparative anchor tagged sequences (CATS) for integrative mapping of mammal genomes. Nature Genetics .15: 47-56, 1997.

327. Hartl, D.L., Kafatos, F.C., and O'Brien, S.J.: Genomes and evolution editorial overview: Genome evolution comes of age. Curr. Opin. Genet. Devel. 5: 705-708, 1995.

328. Menotti-Raymond, M., David, V. A., Stephens, J. C., and O’Brien, S.J.: Genetic individualization of domestic cats using feline STR loci for forensic analysis. J. Forensics Sci. 42: 1039-1051, 1997.

329. Johnson, W. E., Shinyashiki, F., Menotti-Raymond, M., Driscoll, C., Leh, C., Sunquist, M.,

33 147 Johnston, L., Bush, M., Wildt, D., Yuhki, N., and O’Brien, S.J.: Molecular genetic characterization of two insular Asian cat species, Bornean bay cat and iriomote cat. In Wasser, S. P. (Ed.): Evolutionary Theory and Processes: Modern Perspectives, Papers in Honor of Eviatar Nevo. Netherlands, Kluwer Academic Publishers, 1999, pp. 223-248.

330. O’Brien, S.J. and Goedert, J. J.: HIV causes AIDS: Koch’s postulates fulfilled. Current Opin. Immunol. 8: 613-618, 1996.

331. Giri, A., Slattery, J. P., Heneine, W., Gessain, A., Rivadeneira, E., Desrosiers, R. C., Rosen, L., Anthony, R., Pamungkas, J., Iskandriati, D., Richards, A. L., Herve, V., McClure, H., O’Brien, S.J., and Franchini, G.: The Tax gene sequences form two divergent monophyletic lineages corresponding to types I and II of simian and human T-cell leukemia/lymphotropic viruses. Virology 231: 96-104, 1997.

332. Shows, T. B., Alders, M., Bennett, S., Burbee, D., Cartwright, P., Chandrasekharappa, S., Cooper, P., Courseaux, A., Davies, C., Devignes, M.-D., Devilee, P., Elliott, R., Evanse, G., Fantes, J., Garner, H., Gaudray, P., Gerhard, D. S., Gessler, M., Higgins, M., Hummerich, H., James, M., Lagercrantz, J., Litt, M., Little, P., Mannens, M., Munroe, D., Nowak, N., O’Brien, S., Parker, N., Perlin, M., Reid, L., Richard, C., Sawicki, M., Swallow, D., Thakker, R., van Heyningen, E., Vorechovsky, I., Wadelius, C., Weber, B., and Zabel, B.: Report of the fifth international workshop on human chromosome 11 mapping (1996). Cytogenet. Cell Genet. 74: 1-56, 1996.

333. Dean, M., Carrington, M., Winkler, C., Huttley, G.A., Smith, M.W., Allikmets, R., Goedert, J.J., Buchbinder, S.P., Vittinghoff, E., Gomperts, E., Donfield, S., Vlahov, D., Kaslow, R., Saah, A., Rinaldo, C., Detels, R., HGDS, MACS, MHCS, SF City Cohort, ALIVE Study and O’Brien, S.J.: Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 273: 1856-1862, 1996.

334. Menotti-Raymond, M.A., David, V.A., and O’Brien, S.J.: Pet cat hair implicates murder suspect. Nature 386: 774, 1997.

335. Packer, C., Altizer, S., Appel, M., Brown, E., Martenson, J., O’Brien, S.J., Roelke-Parker, M., Hofmann-Lehmann, R., and Lutz, H.: Viruses of the Serengeti: Patterns of infection and mortality in African lions. J. Anim. Ecol. 68: 1161-1178, 1999.

336. O’Brien, S.J.: The family line: The human-cat connection. National Geographic Magazine 191: 77-85, 1997.

337. VandeWoude, S., O’Brien, S.J., Langelier, K., Hardy, W.D., Slattery, J.P., Zuckerman, E. E., and Hoover, E.A.: Growth of lion and puma lentiviruses in domestic cat cells and comparisons with FIV. Virology 233: 185-192, 1997.

338. VandeWoude, S., O’Brien, S.J., and Hoover, E.A.: Infectivity of lion and puma lentiviruses for domestic cats. J Gen. Virol. 78: 795-800, 1997.

339. Zagury, D., Lachgar, A., Chams, V., Fall, L. S., Bernard, J., Zagury, J. F., Bizzini, B., Gringeri, A., Santagostino, E., Rappaport, J., Feldman, M., O’Brien, S.J., Burny, A., and Gallo, R. C.: C-C chemokines, pivotal in protection against HIV type 1 infection. Proc. Natl. Acad. Sci. USA 95:3857-3861, 1998.

340. O’Brien, S.J., Cevario, S.J., Martenson, J. S., Thompson, M. E., Nash, W. G., Chang, E., Graves, J. A. M., Spencer, J. A., Cho, K.-W., Tsujimoto, H., and Lyons, L. A.: Comparative gene

34 148 mapping in the domestic cat (Felis catus). J. Hered. 88: 408-414, 1997.

341. O’Brien, S.J.: The HIV-AIDS debate is over. HIV NEWSLINE 3: 3-9, 1997.

342. O’Brien, S.J., Wienberg, J., and Lyons, L. A.: Comparative genomics: Lessons from cats. Trends Genet. 13: 393-399, 1997.

343. O’Brien, S.J. and Dean, M.: In search of AIDS-resistance genes. Sci Amer 277: 44-51, Sept. 1997.

344. O’Brien, S.J.: A genetic legacy of endangered species. In Speziale, B. J., Leonard, W. H., and Penick, J. E. (Eds.): Biology: A Community Context Student Resource. Cincinnati, South- Western Educational Publishing, pp. 144-147, 1999.

345. Okuda, M., Minehata, K., Setoguchi, A., Cho, K.-W., Nakamura, N., Nishigaki, K., Watari, T., Cevario, S., O’Brien, S.J., Tsujimoto, H., and Hasegawa, A.: Cloning and chromosomal mapping of the feline genes p21WAF1 and p27Kip1. Gene 198: 141-147, 1997.

346. Molia, S., Chomel, B.B., Kasten, R.W., Leutenegger, C.M., Steele, B.R., Marker, L., Martenson, J.S., Keet, D.F., Bengis, R.G., Peterson, R.P., Munson, L. and O’Brien, S.J.: Prevalence of Bartonella infection in wild African lions (Panthera leo) and cheetahs (Acinonyx jubatus). Vet. Microbiol 100:31-41, 2004.

347. O’Brien, T. R., Winkler, C., Dean, M., Nelson, J. A. E., Carrington, M., Michael, N. L., and White, G. C. II.: HIV-1 infection in a man homozygous for CCR5Δ32. Lancet 349: 1218, 1997.

348. An, Ping, Wei, L., Wu, X., Yuhki, N., O’Brien, S.J., and Winkler, C.: Evolutionary analysis of the 5' terminal region of hepatitis G virus isolated from different regions in China. J. Gen. Virol. 78: 2477-2482, 1997.

349. O’Brien, S.J.: Intersection of population genetics and species conservation: The cheetah’s dilemma. In Hecht, M. K., MacIntyre, R. J., and Clegg, M. T. (Eds.): Evolutionary Biology. Volume 30. New York, Plenum Press, pp. 79-91, 1998.

350. Smith, M. W., Dean, M., Carrington, M., Winkler, C., Huttley, G. A., Lomb, D. A., Goedert, J. J., O’Brien, T. R., Jacobson, L. P., Kaslow, R., Buchbinder, S., Vittinghoff, E., Vlahov, D., Hoots, K., Hilgartner, M. W., Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study, and O’Brien, S.J.: Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Science 277: 959-965, 1997.

351. Cho, K.-W., Satoh, H., Youn, H.-Y., Watari, T., Tsujimoto, H., O’Brien, S.J., and Hasegawa, A.: Assignment of the cat immunoglobulin heavy chain genes IGHM and IGHG to chromosome B3q26 and T cell receptor chain gene TCRG to A2q12-->q13 by fluorescence in situ hybridization. Cytogenet. Cell Genet. 79: 118-120, 1997.

352. Cho, K-W., Youn, H-Y, Okuda, M., Satoh, H., Cevario, S., O’Brien, S.J., Watari, T., Tsujimoto, H., and Hasegawa, A.: Cloning and mapping of cat (Felis catus) immunoglobulin and T-cell receptor genes. Immunogenetics 47: 226-233, 1998.

353. Saah, A. J., Hoover, D. R., Weng, S., Carrington, M., Mellors, J., Rinaldo, C. R., Mann, D., Apple, R., Phair, J. P., Detels, R., O’Brien, S.J., Enger, C., Johnson, P., and Kaslow, R. A. for the Multicenter AIDS Cohort Study (MACS). Association of HLA profiles with early plasma viral

35 149 load, CD4+ cell count and rate of progression to AIDS following acute HIV-1 infection. AIDS 12: 2107-2113, 1998.

354. Pecon Slattery, J. and O’Brien, S.J.: Patterns of Y and X chromosome DNA sequence divergence during the Felidae radiation. Genetics 148: 1245-1255, 1998.

355. Wentzel, J., Stephens, J. C., Johnson, W., Menotti-Raymond, M., Pecon Slattery, J., Yuhki, N., Carrington, M., Quigley, H. B., Miquelle, D. G., Tilson, R., Manansang, J., Brady, G., Lu, Z., Pan, W., Shi-Qiang, H., Johnston, L., Sunquist, M., Karanth, K. U., and O’Brien, S.J.: Subspecies of tigers: Molecular assessment using Avoucher specimens@ of geographically traceable individuals. In Seidensticker, J., Christie, S. and Jackson, P. (Eds.): Riding the Tiger: Tiger Conservation in Human-Dominated Landscapes. Cambridge University Press, Cambridge, 1999, pp 40-49.

356. Caetano, A.R., Lyons, L.A., Laughlin, T.F., O'Brien, S.J., Murray, J.D., Bowling, A.T.: Equine synteny mapping of comparative anchor tagged sequences (CATS) from human Chromosome 5. Mamm Genome. 10:1082-1084, 1999

357. O’Brien, S.J.: Molecular Genetics and Phylogenetics of the Felidae.In: Wild Cats: Status Survey and Conservation Action Plan. (Nowell, K., and Jackson, P. Eds), IUCN, Gland, Switzerland. ppXXIII-XXIV, 1996.

358. Smith, M., Dean, M., Carrington, M., Huttley, G. A., and O’Brien, S.J.: CCR5Δ32 gene deletion in HIV-1 infected patients. Lancet 350: 741, 1997.

359. Huttley, G. A., Smith, M. W., Carrington, M., and O’Brien, S.J.: A scan for linkage disequilibrium across the human genome. Genetics. 152: 1711-1722, 1999.

360. Stephens, J. C., Reich, D. E., Goldstein, D. B., Shin, H. D., Smith, M. W., Carrington, M. A., Winkler, C., Huttley, G. A., Allikmets, R., Schriml, L., Gerrard, B., Malasky, M., Ramos, M. D., Morlot, S., Tzetis, M., Oddoux, C., di Giovine, F. S., Nasioulas, G., Chandler, D., Aseev, M., Hanson, M., Kalaydjieva, L., Glavac, D., Gasparini, P., Kanavakis, E., Claustres, M., Kambouris, M., Ostrer, H., Duff, G., Baranov, V., Sibul, H., Metspalu, A., Goldman, D., Martin, N., Duffy, D., Schmidtke, J., Estivill, X., O’Brien, S.J., and Dean, M.: Dating the origin of the CCR5-Δ32 AIDS resistance gene allele by the coalescence of haplotypes. Am. J. Hum. Genet. 62: 1507- 1515, 1998.

361. Carrington, M., Kissner, T., Gerrard, B., Ivanov, S., O’Brien, S.J., and Dean, M.: Novel alleles of the chemokine-receptor gene CCR5. Am. J. Hum. Genet. 61: 1261-1267, 1997.

362. Winkler, C., Modi, W., Smith, M. W., Nelson, G. W., Wu, X., Carrington, M., Dean, M., Honjo, T., Tashiro, K., Yabe, D., Buchbinder, S., Vittinghoff, E., Goedert, J. J., O’Brien, T. R., Jacobson, L. P., Detels, R., Donfield, S., Willoughby, A., Gomperts, E., Vlahov, D., Phair, J., ALIVE Study, Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), and O’Brien, S.J.: Genetic restriction of AIDS pathogenesis by an SDF-1 chemokine gene variant. Science 279: 389-393, 1998.

363. An, P., Luo, H., Lu, T., O’Brien, S.J., and Winkler, C.: Genetic heterogeneity and molecular epidemiology of GB virus C/Hepatitis G virus in China. J. Hum. Virol. 3: 299-305, 2000.

364. O’Brien, T. R., Padian, N. S., Hodge, T., Goedert, J. J., O’Brien, S.J., and Carrington, M.: CCR-5 genotype and sexual transmission of HIV-1. AIDS 12: 444-445, 1998.

36 150

365. Nash, W. G., Wienberg, J., Ferguson-Smith, M. A., Menninger, J. C., and O’Brien, S.J.: Comparative genomics: Tracking chromosome evolution in the family Ursidae using reciprocal chromosome painting. Cytogenet. Cell Genet. 83: 182-192, 1998.

366. O’Brien, S.J.: Subspecies identification incorporating molecular genetics. In: Wild Cats: Status Survey and Conservation Action Plan. (Nowell, K., and Jackson, P. Eds), IUCN, Gland, Switzerland, pp 210-211, 1996.

367. Smith, M. W., Carrington, M., Winkler, C., Lomb, D., Dean, M., Huttley, G., and O'Brien, S.J.: CCR2 chemokine receptor and AIDS progression. Nature Med. 3: 1052-1053, 1997.

368. Nguyen, G. T., Carrington, M., Beeler, J. A., Dean, M., Aledort, L. M., Blatt, P. M., Cohen, A. R., DiMichele, D., Eyster, M. E., Kessler, C. M., Konkle, B., Leissinger, C., Luban, N., O’Brien, S.J., Goedert, J. J., and O’Brien, T. R.: Phenotypic expressions of CCR5-Δ32/Δ32 homozygosity. J. Acquir. Immune Defic. Syndr 22: 75-82, 1999.

369. Michael, N.L., Nelson, J.A. E., KewalRamani, V.N., Chang, G., O’Brien, S.J., Mascola, J. R., Volsky, B., Louder, M., White, G.C., II: Littman, D.R., Swanstrom, R., and O’Brien, T.R.: Exclusive and persistent use of the entry co-receptor CXCR4 by human immunodeficiency virus type 1 from a subject homozygous for CCR5Δ32. J. Virol. 72: 6040-6047, 1998.

370. O’Brien, S.J.: A new approach to therapy. HIV Newsline 4: 3-6, 1998.

371. Beatty, J., Terry, A., MacDonald, J., Gault, E., Cevario, S., O’Brien, S.J., Cameron, E., and Neil, J.C.: Feline immunodeficiency virus integration in B-cell lymphoma identifies a candidate tumor suppressor gene on human chromosome 15q15. Cancer Res. 62: 7175-7180, 2002.

372. Anzala, A.O., Ball, T. B., Rostron, T., O’Brien, S.J., Plummer, F. A., and Rowland-Jones, S. L.: CCR2-64I allele and genotype association with delayed AIDS progression in African women. University of Nairobi Collaboration for HIV Research. Lancet. 351: 1632-1633, 1998.

373. Hendel, H., Caillat-Zucman, Lebuanec, H., Carrington, M., O’Brien, S.J., Andrieu, J.-M., Schachter, F., Zagury, D., Rappaport, J., Winkler, C., Nelson, G. W., and Zagury, J.-F.: New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS. J. Immunol. 162: 6942-6946, 1999.

374. Eizirik, E., Bonatto, S. L., Johnson, W. E., Crawshaw, P. G., Jr., Vié, J. C., Brousset, D. M., O’Brien, S.J., and Salzano, F. M.: Phylogeographic patterns and evolution of the mitochondrial DNA control region in two neotropical cats (Mammalia, Felidae). J. Mol. Evol. 47: 613-624, 1998.

375. Lyons, L. A., Kehler, J. S., and O’Brien, S.J.: Development of comparative anchor tagged sequences (CATS) for canine genome mapping. J. Hered. 90: 15-26, 1999.

376. Pearson PL, Roderick TH, Davisson MT, Garver JJ, Warburton D, Lalley PA, O'Brien SJ. Report of the committee on comparative mapping.Birth Defects Orig Artic Ser. 1980;15(11):82-95

377. Daar, E. S., Lynn, H., Donfield, S., Gomperts, E., Hilgartner, M. W., Hoots, K., Chernoff, D., Winkler, C., and O'Brien, S.J.: Effects of plasma HIV RNA, CD4+ T lymphocytes and the chemokine receptors CCR5 and CCR2b on HIV disease progression in hemo-philiacs. Hemophilia Growth and Development Study. J.Aquir. Immune Defic. Syndr. 21: 317-325, 1999.

37 151 378. Hendel, H., Henon, N., Lebuanec, H., Lachgar, A., Poncelet, H., Caillat-Zucman, S., Winkler, C., Smith, M.W., Kenefic, L., O’Brien, S.J., Lu, W., Andrieu, J. M., Zagury, D., Schächter, F., Rappaport, J., and Zagury, J.-F.: Distinctive effects of CCR5, CCR2 and SDF1 genetic poly- morphisms in AIDS progression. J Acquir Immune Defic Syndr Hum Retrovirol 19:381-386, 1998.

379. Martin, M. P., Dean, M., Smith, M. W., Gerrard, B., Michael, N. L., Lee, B., Doms, R.W., Margolick, J., Buchbinder, S., Goedert, J. J., O’Brien, T. R., Hilgartner, M. W., Vlahov, D., O’Brien, S.J., and Carrington, M.: Genetic acceleration of AIDS progression by a promoter variant of CCR5. Science 282: 1907-1911, 1998.

380. Smith, M., Dean, M., Carrington, M., Winkler, C., and O’Brien, S.J.: Progression to AIDS. Science. 280: 1819-1820, 1998.

381. Lee, B., Doranz, B. J., Rana, S., Yi, Y., Mellado, M., Frade, J. M. R., Martinez-A, C., O’Brien, S.J., Dean, M., Collman, R. G., and Doms, R. W.: Influence of the CCR2-V64I polymorphism on human immunodeficiency virus type 1 coreceptor activity and on chemokine receptor function of CCR2b, CCR3, CCR5, and CXCR4. J. Virol. 72: 7450-7458, 1998.

382. Johnson, W. E., Pecon Slattery, J., Eizirik, E., Kim, J.-H., Menotti-Raymond, M., Bonacic, C., Cambre, R., Crawshaw, P., Nunes, A., Seuanez, H., Moreira, M. A., Seymour, K. L., Simon, F., Swanson, W., and O’Brien, S.J.: Disparate phylogeographic patterns of molecular genetic variation in four closely related South American small cat species. Mol. Ecol. 8: S79-S94, 1999.

383. Carrington, M., Nelson, G., Martin, M. P., Kissner, T., Vlahov, D., Goedert, J. J., Kaslow, R., Buchbinder, S., Hoots, K., and O’Brien, S.J.: HLA and HIV-1: Heterozygote advantage and B*35-Cw*04 disadvantage. Science 283: 1748-1752, 1999.

384. O’Brien, S.J.: AIDS: A role for host genes. Hospital Practice 33: 53-79, 1998.

385. Stephens, J. C., Smith, M. W., Shin, H. D., and O’Brien, S.J.: Tracking linkage disequilibrium in admixed populations with MALD using microsatellite loci. In Goldstein, D. B. and Schlötterer, C. (Eds.): Microsatellites: Evolution and Applications. Oxford, Oxford University Press, 1999, pp. 211-224.

386. Pecon Slattery, J., Sanner-Wachter, L., and O’Brien, S.J.: Novel gene conversion between X-Y homologues located in the nonrecombining region of the Y chromosome in Felidae (Mammalia). Proc. Natl. Acad. Sci. USA. 97: 5307-5312, 2000.

387. Martin, M. P., Carrington, M., Dean, M., O’Brien, S.J., Sheppard, H. W., Wegner, S. A., and Michael, N. L.: CXCR4 polymorphisms and HIV-1 pathogenesis. J. AIDS. 19: 430-432, 1998.

388. Thio, C. L., Carrington, M., Marti, D., O’Brien, S.J., Vlahov, D., Nelson, K. E., Astemborski, J., and Thomas, D. L.: Class II HLA alleles and hepatitis B virus persistence in African- AmericanS.J. Infec. Dis. 179: 1004-1006, 1999.

389. Su, B., Jin, L., Hu, F., Xiao, J., Luo, J., Lu, D., Zhang, W., Chu, J., Du, R., Zhencheng, Z., Qiu, X., Xue, J., Tan, J., O’Brien, S.J., and Chakraborty, R.: Distribution of two HIV-1 resistant polymorphisms (SDF1-3'A and CCR2-64I) in East Asia and world populations and its implication in AIDS epidemiology. Am. J. Hum. Genet. 65: 1047-1053, 1999.

390. Chen, Z-Q., Lautenberger, J. A., Lyons, L. A., McKenzie, L., and O’Brien, S.J.: A human genome map of comparative anchor tagged sequenceS.J. Hered. 90: 477-484, 1999.

38 152

391. Murphy, W. J., Menotti-Raymond, M., Lyons, L. A., Thompson, M. E., and O’Brien, S.J.: Development of a feline whole genome radiation hybrid panel and comparative mapping of human chromosome 12 and 22 loci. Genomics. 57: 1-8, 1999.

392. Menotti-Raymond, M., David, V. A., Lyons, L. A., Schäffer, A. A., Tomlin, J. F., Hutton, M. K., and O’Brien, S.J.: A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics. 57: 9-23, 1999.

393. O’Brien, S.J. and Yuhki, N.: Comparative genome organization of the major histocompatibility complex: Lessons from the Felidae. Immunol. Rev. 167: 133-144, 1999.

394. Dean, M., Jacobson, L. P., McFarlane, G., Margolick, J. B., Jenkins, F. J., Howard, O. M. Z., Dong, H.-F., Goedert, J. J., Buchbinder, S., Gomperts, E., Vlahov, D., Oppenheim, J. J., O’Brien, S.J., and Carrington, M.: Reduced risk of AIDS lymphoma in individuals heterozygous for the CCR5 delta32 . Cancer Res. 59: 3561-3564, 1999.

395. McKenzie, L. M., Slattery, J. P., Carrington, M., and O’Brien, S.J.: Taxonomic hierarchy of HLA class I allele sequences. Genes Immun. 1: 120-129, 1999.

396. Murphy, W. J., Stanyon, R., and O’Brien, S.J.: Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol. 2: Reviews 0005.1-0005.8, 2001.

397. Greenough, T. C., Brettler, D. B., Kirchhoff, F., Alexander, L., Desrosiers, R. C., O’Brien, S.J., Somasundaran, M., Luzuriaga, K., and Sullivan, J. L.: Long-term nonprogressive infection with human immunodeficiency virus type 1 in a hemophilia cohort. J. Infect. Dis. 180: 1790-1802, 1999.

398. Bream, J. H., Young, H. A., Rice, N., Martin, M. P., Carrington, M., and O’Brien, S.J.: CCR5 promoter alleles and specific DNA binding factors. Science. 284: 223a, 1999.

399. Lautenberger, J. A., Stephens, J. C., O’Brien, S.J., and Smith, M. W.: Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am. J. Hum. Genet. 66: 969-978, 2000.

400. Shin, H. D., Winkler, C., Bream, J., Young, H., Phair, J., Goedert, J. J., Vlahov, D., Buchbinder, S., Donfield, S., O’Brien, S.J., and Smith, M. W.: Genetic restriction of HIV-1 pathogenesis to AIDS by promoter alleles of IL10. Proc. Natl. Acad. Sci. USA. 97: 14467-14472, 2000.

401. O’Brien, S.J., Dean, M., Smith, M. W., Winkler, C., Nelson, G. W., Martin, M. P., and Carrington, M.: The human genes that limit AIDS. In Boulyjenkov, V., Berg, K., and Christen, Y. (Eds.): Genes and Resistance to Disease. Heidelberg, Springer Verlag, 2000, pp. 9-17.

402. An, P., Martin, M. P., Nelson, G., Carrington, M., Smith, M. W., Gong, Q., Vlahov, D., Phair, J., O’Brien, T., Goedert, J., Buchbinder, S., O’Brien, S.J., and Winkler, C. A.: Influence of CCR5 promoter haplotypes on AIDS progression in African Americans. AIDS 14: 2117-2122, 2000.

403. Culver, M., Johnson, W. E., Pecon Slattery, J., and O’Brien, S.J.: Genomic ancestry of the American puma (Puma concolor). J. Hered. 91: 186-197, 2000.

404. Carrington, M., Dean, M., Martin, M. P., O’Brien, S.J.: Genetics of HIV-1 infection: chemokine receptor CCR5 polymorphism and its consequences. Hum. Mol. Genet. 8: 1939-1945, 1999.

39 153 405. Murphy, W. J., Sun, S., Chen, Z.-Q., Pecon Slattery, J., and O’Brien, S.J.: Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping. Genome Res. 9: 1223-1230, 1999.

406. Caetano, A. R., Shiue, Y.-L., Lyons, L. A., O’ Brien, S.J., Laughlin, T. F., Bowling, A. T., and Murray, J. D.: A comparative gene map of the horse (Equus caballus). Genome Res. 9: 1239- 1249, 1999.

407. Driscoll, C. A., Menotti-Raymond, M., and O’Brien, S.J.: Genomic microsatellites as evolutionary chronometers: A test in wild cats. Genome Res. 12: 414-423, 2002.

408. Winkler, C. A. and O’Brien, S.J.: AIDS restriction genes in human ethnic groups: An assessment. In Essex, M., Mboup, S., Kanki, P. J., Marlink, R., and Tlou, S. D. (Eds.): AIDS in Africa, Second Edition, New York, Kluwer Academic. New York. pp. 52-73, 2002.

409. O’Brien, S.J. and Carrington, M.: Selection against susceptibility to HIV-1. Science 285: 11a, 1999.

410. O’Brien, S.J., Menotti-Raymond, M., Murphy, W. J., Nash, W. G., Wienberg, J., Stanyon, R., Copeland, N. G., Jenkins, N. A., Womack, J. E., and Marshall Graves, J. A.: The promise of comparative genomics in mammals. Science 286: 458-481, 1999.

411. Sheppard, H., Celum, C., Michael, N., O’Brien, S.J., Carrington, M., Dondero, D., Buchbinder, S.: HIV-1 infection in individuals with the CCR5-Δ32/Δ32 genotype: Acquisition of syncytium- inducing virus at seroconversion. J. AIDS 29:307-313, 2002.

412. Alexander, L., Weiskopf, E., Greenough, T. C., Gaddis, N. C., Auerbach, M. R., Malim, M. H., O’Brien, S.J., Walker, B. D., Sullivan, J. L., and Desrosiers, R. C.: Unusual polymorphisms in human immunodeficiency virus type 1 associated with nonprogressive infection. J. Virol.74: 4361-4376, 2000.

413. Culver, M., Raymond, M. A., and O’Brien, S.J.: Patterns of size homoplasy at 10 microsatellite loci in pumas (Puma concolor). Mol. Biol. Evol. 18: 1151-1156, 2001.

414. Munson, L., Marker, L., Dubovi, E., Spencer, J.A., Evermann, J.F., and O’Brien, S.J.: Serosurvey of viral infections in free-ranging Namibian cheetahs (Acinonyx jubatus). J. Wildlife Dis. 40:23-31, 2004.

415. Martínez-Cruz, B. David, V.A., Godoy, J.A. Negro, J. J., O’Brien, S.J., Johnson, W.E. Eighteen polymorphic microsatellite markers for the highly endangered Spanish Imperial Eagle (Aquila adalberti) and related species. Molecular Ecology 2:323-326. 2002.

416. Murphy, W. J., Sun, S., Chen, Z.-Q., Yuhki, N., Hirschmann, D., Menotti-Raymond, M., and O’Brien, S.J.: A radiation hybrid map of the cat genome: Implications for comparative mapping. Genome Res. 10: 691-702, 2000.

417. O’Brien, S.J., Lander, E.S., Haskins, M., Giger, U., Pederson, N.C., Wildt, D., Murphy, W.J., Yuhki, N., and Menotti-Raymond, M. NHGRI White Paper, Sequencing the genome of the domestic cat, Felis catus. http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/CatSEQ.pdf

418. Sarno, R. J., Franklin, W. L., O’Brien, S.J., and Johnson, W. E.: Patterns of mtDNA and

40 154 microsatellite variation in an island and mainland population of guanacos in southern Chile. Animal Conservation. 4:93-101, 2001.

419. O’Brien, S.J.: Adaptive cycles: Parasites selectively reduce inbreeding in Soay sheep. Trends Ecol. Evol. 15: 7-9, 2000.

420. O’Brien, S.J. and Stanyon, R.: Phylogenomics: Ancestral primate viewed. Nature. 402: 365-366, 1999.

421. Pecon Slattery, J., Murphy, W. J., and O’Brien, S.J.: Patterns of diversity among SINE elements isolated from three Y-chromosome genes in carnivores. Mol. Biol. Evol. 17: 825-829, 2000.

422. O’Brien, S.J., Gallo, R., and Essex, M.: Remembering Takis Papas. Cancer Res. 60: Cover Legend, October 15, 2000.

423. Daar, E. S., Lynn, H., Donfield, S., Gomperts, E., O’Brien, S.J., Hilgartner, M. W., Hoots, W. K., Chernoff, D., Arkin, S., Wong, W.-Y., Winkler, C. A., and the Hemophilia Growth and Development Study: Hepatitis C virus load is associated with human immunodeficiency virus type 1 disease progression in hemophiliacs. J. Infect. Dis. 183: 589-595, 2001.

424. Kim, J.-H., Eizirik, E., O’Brien, S.J., and Johnson, W. E.: Structure and evolution of the mitochondrial DNA control region in the great cats (Panthera). .1:279-292, 2001.

425. Eizirik, E., Kim, J.-H., Menotti-Raymond, M., Crawshaw, P. G. Jr., O’Brien, S.J., and Johnson, W. E.: Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae). Mol. Ecol.10:65-79, 2001.

426. Sun, S., Murphy, W. J., Menotti-Raymond, M., and O’Brien, S.J.: Integration of the feline radiation hybrid and linkage maps. Mammalian Genome 12: 436-441, 2001.

427. Lu, Z., Johnson, W. E., Menotti-Raymond, M., Yuhki, N., Martenson, J., Mainka, S., Shi-qiang, H., Zhihe, Z., Li, G., Pan, W., and O’Brien, S.J.: Patterns of genetic diversity in remaining giant panda populations. Conservation Biol. 15: 1596-1607, 2001.

428. Menotti-Raymond, M., David, V., Wachter, L., Yuhki, N. and O’Brien, S.J.: Quantitative polymerase chain reaction-based assay for estimating DNA yield extracted from domestic cat specimens. Croat. Med. J. 44: 327-331, 2003.

429. Chomel, B.B., Kikuchi, Y., Martenson, J.S., Roelke-Parker, M.E., Chang, C.C., Kasten, R.W., Foley, J.E. Laudre, J., Murphy, K., Swift, P.K., Kramer, V.L., and O’Brien, S.J.: Seroprevalence of Bartonella infection in American free-ranging and captive pumas (Felis concolor) and bobcats (Lynx rufus). Vet Res. 35:233-241, 2004.

430. O’Brien, S.J.: Human genetic factors that impact HIV infection and progression. Clinical Care Options for HIV Symposium. In Phair, J. P. and King, E. (Eds.): Medscape HIV/AIDS Annual Update 2000. New York, Medscape, pp. 19-28, 2000.

431. O’Brien, S.J. and Moore, J.: The effect of genetic variation in chemokines and their receptors on HIV transmission and progression to AIDS. Immunol. Rev. 177: 99-111, 2000.

432. O’Brien, S.J.: The Cat Family. In D. Macdonald, (ed.), Encyclopedia of Mammals. Oxford, Oxford University Press, 2001, pp. 8-9.

41 155 433. Yamashita, T. E., Phair, J. P., Munoz, A., Margolick, J. B., Detels, R., O’Brien, S.J., Mellors, J. W., Wolinsky, S., and Jacobson, L. P.: Immunologic and virologic response to highly active antiretroviral therapy in the Multicenter AIDS Cohort Study. AIDS 15:735-746, 2001.

434. Sarno, R.J., L. Villalba, C. Bonacic, B. Gonzalez, B. Zapata, D.W. MacDonald, S.J. O'Brien, and W. E. Johnson. Phylogeography and subspecies assessment of vicuñas in Chile and Bolivia utilizing mtDNA and microsatellite markers: implications for vicuña conservation and management. Conservation Genet. 5:89-102, 2004.

435. Modi, W.S., Goedert, J.J., Strathdee, S., Buchbinder, S., Detels, R., Donfield, S., O’Brien, S.J. and Winkler, C.: MCP-1-MCP-3-Eotaxin gene cluster influences HIV-1 transmission AIDS 17:2357-2365, 2003.

436. Uphyrkina, O., Johnson, W., Quigley, H., Miquelle, D., Marker, L., Bush, M., and O’Brien, S.J.: Phylogenetics, genome diversity and the origin of modern leopard, Panthera pardus. Mol. Ecol. 10:2617-2633, 2001.

437. Smith MW, Lautenberger JA, Shin HD, Chretien JP, Shrestha S, Gilbert DA, O'Brien SJ. Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet. 2001 Nov;69(5):1080-94.

438. Gao, X., Nelson, G. W., Karacki, P., Martin, M. P., Phair, J., Kaslow, R., Goedert, J. J., Buchbinder, S., Koots, K., Vlahov, D., O’Brien, S.J., and Carrington, M.: Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. New Engl J Med 344:1668-1675, 2001.

439. Roelke-Parker, M. E, Slattery, J.P., VandeWoude, S., and O’Brien, S.J. T-lymphocyte profiles in FIV infected wild lions and pumas reveal CD4 depletion. J Wildlife Dis.42: 234-248, 2006.

440. O’Brien, S.J., Nelson, G. W., Winkler, C. A., and Smith, M. W.: Polygenic and multifactorial disease gene association in man: Lessons from AIDS. Ann Rev Genet 34: 563-591, 2000.

441. Beck, T. W., Menninger, J., Voight, G., Newmann, K., Nishigaki, Y., Nash, W. G., Stephens, R. M., Wang, Y., de Jong, P. J., O’Brien, S.J., and Yuhki, N.: Comparative feline genomics: BAC/PAC contig map of the major histocompatibility complex class II region. Genomics 71:282- 295, 2001.

442. Comstock, K. E., Georgiadis, N., Pecon-Slattery, J., Roca, A. L., Ostrander, E. A., O’Brien, S.J., and Wasser, S. K.: Patterns of molecular genetic variation among African elephant populations. Mol. Ecol. 11: 2489-2498, 2002.

443. Roca, A. L., Georgiadis, N., Pecon-Slattery, J., and O’Brien, S.J.: Genetic evidence for two species of elephant in Africa. Science 293: 1473-1477, 2001.

444. Sarno, R. J., David, V. A., Franklin, W. L., O’Brien, S.J., and Johnson, W. E.: Development of microsatellite markers in the guanaco, Lama guanicoe: Utility for South American camelids. Mol. Ecol. 9: 1922-1924, 2000.

445. Vande Woude, S., Hageman, C. A., O’Brien, S.J., and Hoover, E. A.: Nonpathogenic lion and puma lentiviruses impart resistance to superinfection by virulent feline immunodeficiency virus. J. Acquir Immune Defic Syndr 29:1-10, 2002.

42 156 446. Roca, A., Slattery, J.P., and O’Brien, S.J.: Genomically intact endogenous feline leukemia viruses of recent origin. J Virol. 78: 4370-4375, 2004.

447. O’Brien, S.J.: Cell culture forensics. Proc. Natl. Acad. Sci. USA 98: 7656-7658, 2001.

448. Parker, J. S. L., Murphy, W. J., Wang, D., O’Brien, S.J., and Parrish, C. R.: Canine and feline parvoviruses can use the human or feline transferrin receptors to bind, enter and infect cells. J. Virol. 75: 3896-3902, 2001.

449. Johnson, W.E., Eizirik, E., Roelke-Parker, M., O’Brien, S.J.: Applications of genetic concepts and molecular methods to carnivore conservation. In: Carnivore Conservation (J. Gittleman, S. Funk, P. Macdonald, and R. Wayne, eds), Cambridge University Press Pp. 335-358, 2001.

450. Murphy, W. J., Eizirik, E., Johnson, W. E., Zhang, Y. P., Ryder, O. A., and O’Brien, S.J.: Molecular phylogenetics and the origins of placental mammals. Nature. 409: 614-618, 2001.

451. Eizirik, E., Murphy, W. J., and O’Brien, S.J.: Molecular dating and biogeography of the early placental mammal radiation. J. Hered. 92: 212-219, 2001.

452. An, P., Nelson, G. W., Wang, L., Donfield, S., Goedert, J. J., Phair, J., Vlahov, D., Buchbinder, S., Farrar, W. L., Modi, W., O’Brien, S.J. and Winkler, C. A.: Modulating influence on HIV/AIDS by interacting RANTES gene variants. Proc Natl Acad Sci USA 99:10002-10007, 2002

453. Carrington, M., Nelson, G., and O’Brien, S.J.: Review and Commentary: Considering genetic profiles in functional studies of immune responsiveness to HIV-1. Immunol Lett 79:131-140, 2001.

454. Thio, C. L., Thomas, D. L., Goedert, J. J., Vlahov, D., Nelson, K. E., Hilgartner, M. W., O’Brien, S.J., Karacki, P., Marti, D., Astemborski, J., and Carrington, M.: Racial differences in HLA-Class II associations with hepatitis C virus outcomes. J. Infect. Dis. 184: 16-21, 2001.

455. Nash, W. G., Menninger, J. C., Wienberg, J., Padilla-Nash, H. M., O’Brien, S.J.: The pattern of phylogenomic evolution of the Canidae. Cytogenet. Cell Genet. 95: 210-224, 2001.

456. O’Brien, S.J., Eizirik, E., and Murphy, W. J.: Genomics. On choosing mammalian genomes for sequencing. Science. 292: 2264-2266, 2001.

457. Yang, O.O., Boscardin, W.J, Matud, J., Hausner, M.A., Hultin, L.E., Hultin, P.M., Shih, R., Ferbas, J., Siegal, F.P., Shodell, M., Shearer, G.M., Grene, E., Carrington, M., O'Brien, S., Price, C.B., Detels, R., Jamieson, B.D., Giorgi, J.V.: Immunologic profile of highly exposed yet HIV type 1-seronegative men. AIDS Res Hum Retroviruses. 18:1051-1065, 2002.

458. Uphyrkina, O., Miquelle, D., Quigley, H., Driscoll, C., and O’Brien, S.J.: Conservation genetics of the far eastern leopard (P. p. orientalis). J. Hered. 93:303-311, 2002.

459. Johnson, W., O’Brien, S.J., and Culver, M.: Small Cats. In D. Macdonald, ed., Encyclopedia of Mammals. Oxford, Oxford University Press, 2001, pp. 32-34.

460. Dean, M., Carrington, M., O’Brien, S.J.: Balanced polymorphism selected by genetic versus infectious human disease. Ann. Rev. Genomics Hum Genet 3:263-292, 2002.

461. Menotti-Raymond, M., David, V. A., Chen, Z.-Q., Menotti, K., Sun, S., Schaffer, A. A.,

43 157 Agarwala, R., Tomlin, J. F., O’Brien, S.J. and Murphy, W. J.: Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J. Hered. 94: 95-106, 2003.

462. Yamaguchi, N., Sarno, R. J., Johnson, W. E., O’Brien, S.J., and Macdonald, D. W.: Multiple paternity and reproductive tactics of free-ranging American mink, Mustela vison. J. Mammal. 85: 432-439, 2004.

463. Palomares, F., Godoy, J. A., Piriz, A., O’Brien, S.J., and Johnson, W. E.: Faecal genetic analysis to determine presence and distribution of elusive carnivores: Design and feasibility for the Iberian lynx. Mol. Ecol. 11: 2171-2182, 2002.

464. Breen, E.C., Boscardin, W.J., Detels, R., Jacobson, L.P., Smith, M.W., O’Brien, S.J., Chmiel, J. S., Rinaldo, C.R., Lai, S., and Martínez-Maza, O. Non-Hodgkin’s B cell - lymphoma in persons with acquired immunodeficiency syndrome is associated with increased serum levels of IL10, or the IL10 promoter –592 C/C genotype. Clin. Immunol. 109: 119-129, 2003.

465. Murphy, W. J., Eizirik, E., O’Brien, S.J., Madsen, O., Scally, M., Douady, C., Teeling, E., Ryder, O.A., Stanhope, M., de Jong, W. W., and Springer, M. S.: Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351, 2001.

466. Duggal, P., An, P., Beaty, T., Strathdee, S. A., Farzadegan, H., Markham, R. B., Johnson, L., O’Brien, S.J., Vlahov, D., and Winkler, C. A.: Genetic influence of CXCR6 chemokine receptor alleles on PCP-mediated AIDS progression among African-Americans. Genes Immun. 4: 245- 250, 2003.

467. O’Brien, S.J., Gao, X., and Carrington, M.: HLA and AIDS: A cautionary tale. Trends Mol. Med. 7: 379-381, 2001.

468. Yuhki, N., Beck, T., Stephens, R. M., Nishigaki, Y., Newmann, K., and O’Brien, S.J.: Comparative genome organization of human, murine and feline MHC class II region. Genome Res. 13: 1169-1179, 2003.

469. Eizirik, E., Yuhki, N., Johnson, W., Menotti-Raymond, M., Hannah, S. S. and O’Brien, S.J. Molecular genetics and evolution of melanism in the cat family (Mamalia Felidae.). Cur Biol. 13: 448-453, 2003

470. Carrington, M., Gao, X., O’Brien, S.J.: HLA and AIDS progression. Letter to Editor, New England Journal of Medicine 345:924-925, 2001.

471. Martin, M.P., Gao, X., Lee, H. -L, Nelson, G., Detels, R., Goedert, J.J., Buchbinder, S., Hoots, K., Vlahov, D., Trowsdale, J., Wilson, M., O’Brien, S.J. and Carrington, M.: Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nature Genet. 31: 429-434, 2002.

472. An, P., Vlahov, D., Margolick, J.B., Phair, J., O’Brien, T.R., Lautenberger, J., O’Brien, S.J. and Winkler, C.A.: A tumor necrosis factor-alpha-inducible promoter variant of interferon-gamma accelerates CD4+ T cell depletion in human immunodeficiency virus-1-infected individuals. J Infect Dis.188:228-231, 2003.

473. Johnson, W.E., Godoy, J.A., Palomares, F., Delibes, M., Fernandes, M., Revilla, E., O’Brien, S.J.: Phylogenetic and phylogeographic analysis of Iberian lynx population. J. Hered. 95:19-28, 2004.

44 158

474. O’Brien, S.J.: Feline Genetics. Encyclopedia of Genetics. Academic Press.pp 684-685, 2001

475. Liu, C., Carrington, M., Kaslow, R., Rinaldo, C., Jacobson, L., Margolick, J., Phair, J., O’Brien, S.J., Detels, R.: Association of polymorphisms in HLA Class I and TAP genes with resistance to HIV-1 infection. J Infect Dis 187: 1404-1410, 2003.

476. O’Brien, S.J., Menotti-Raymond, M., Murphy, W.J., Yuhki, N. The Feline Genome Project. Ann Rev Genetics 36:657-686, 2002.

477. Copeland, N., Jenkins, N., O’Brien, S.J. Mmu 16- Comparative Genomic Highlights. Science 296: 1617-1618, 2002.

478. Beck, T., Menninger, J., Murphy, W.J., Nash, W.G., Yuhki, N., and O’Brien, S.J.: The feline major histocompatibility complex is rearranged by an inversion with a breakpoint in the distal class I region. Immunogenetics 56:702-709, 2005.

479. Murphy, W.J., Page, J.E., Smith, C. Jr., Desrosiers, R.C., and O’Brien, S.J.: A radiation hybrid mapping panel for the Rhesus macacque. J. Hered. 92: 516-519, 2001.

480. Springer, M.S., Murphy, W. J. Eizirik, E., O’Brien, S.J.: Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Nat. Acad. Sci. USA 100:1056-1061, 2003.

481. David, V.A., Sun, S., Fujun, S, Zhihe, Z, Zhang, Y-P, Guiquan, Z, Hemin, Z, Zhong, X, Ellis, S. Wildt, D. S.J. O'Brien: Paternity analysis in captive bred giant pandas. In: Giant Pandas: Biology, Veterinary and Management and Medicine, (Wildt, D.E., Zhang, A., Zhang, H., and Janssen, D.L. and Ellis, S. Eds.), Cambridge University Press, England pp 245-273, 2003.

482. Eizirik, E., Murphy, W.J., Springer, M.S., O’Brien, S.J. Molecular phylogeny and dating of early primate divergences. In: Anthropoid Origins, New Visions. Ross, C.F. and Kay, R.F. Eds., Kluwer/Plenum. pp 45-64, 2004.

483. Lento, G.M., Baker, C.S., David, V., Yuhki, N., Gales, N.J., O’Brien, S.J.: Automated single- strand conformation polymorphism reveals low diversity of a Major Histocompatibility Complex Class II gene in the threatened New Zealand sea lion. Molec. Ecol. 3: 346-349, 2003.

484. Carrington, M., O’Brien, S.J. The Influence of HLA Genotype on AIDS. Ann. Rev. Med. 54: 535-551, 2003.

485. Uphyrkina, O. and O’Brien, S.J.: Applying molecular genetic tools to the conservation and action plan for the critically endangered Far Eastern leopard (Panthera pardus orientalis). C.R. Biologies 326:S93-S97, 2003.

486. Jin, X., Gao, X., Ramanathan, M., Deschenes, G.R., Nelson, G., O’Brien, S.J., Goedert, J. J., Ho, D. D., O’Brien, T. R., Carrington, M.: Human immunodeficiency virus Type 1 (HIV-1)-specific CD8+-T-cell responses for groups of HIV-1-infected individuals with different HLA-B*35 genotypeS.J. Virol. 76: 12603-12610, 2002.

487. Butler, J. M., David, V. A., O'Brien, S.J., and Menotti-Raymond, M.: The "MeowPlex": A new DNA test using tetranucleotide STR markers for the domestic cat. Profiles in DNA 5:7-10, 2002.

488. Modi, W.S., O’Brien, T.R., Vlahov, D., Buchbinder, S., Gomperts, E., Phair, J., and O’Brien, S.J. and Winkler, C.: Haplotype diversity in the Interleukin-4 gene is not associated with HIV-1

45 159 transmission and AIDS progression. Immunogenet 55:157-164, 2003.

489. Kikuchi, Y., Chomel, B.B., Kasten, R.W., Martenson, J.S., Swift, P.K., and O’Brien, S.J.: Seroprevalence of Toxoplasma gondii in American free-ranging or captive pumas (Felis concolor) and bobcats (Lynx rufus). Vet Parasitol 120:1-9, 2004.

490. Pecon-Slattery, J., Pearks-Wilkerson, A.J., Murphy, W.J., and O’Brien, S.J.: Phylogenetic assessment of introns and SINEs within the Y-chromosome using the cat family Felidae as a species tree. Mol Biol Evol 21:2299-2309, 2004.

491. Murphy, W.J., Frönicke, L., O'Brien, S.J. and Stanyon, R.: The origin of human chromosome 1 and its homologs in placental mammals. Genome Res. 13: 1880-1888, 2003.

492. House, C., Alexander, K.A., Kat, P.W., O'Brien, S.J., Mangiafico, J.: Serum antibody to Rift Valley fever virus in African carnivores. Ann N Y Acad Sci. 1996 Jul 23;791:345-9.

493. Luo, S.-J., Kim, J.-H., Johnson, W.E., van der Walt, J., Martenson, J., Yuhki, N., Miquelle, D.G., Uphyrkina, O., Goodrich, J.M., Quigley, H.B., Tilson, R., Brady, G., Martelli, P., Subramaniam, V., McDougal, C., Hean, S., Huang, S.-Q., Pan, W., Karanth, U.K., Sunquist, M., Smith, J.L.D., and O'Brien, S.J.:Phylogeography and genetic ancestory of tigers (Panthera tigris). PLoS Biology 2:2277-2293, 2004.

494. Troyer, J.L., Pecon-Slattery, J., Roelke Parker, M.E., Black, L., Packer, C., and O’Brien, S.J.: Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free- ranging population of African lions. J Virol.78: 3777-3791, 2004.

495. Nelson, G.W. and O’Brien, S.J.: Using mutual information to measure the impact of multiple genetic factors on AIDS. J Acquir Immune Defic Syndr 42: 347-354, 2006.

496. Thio, C.L., Mosbruger, T.L., Kaslow, R.A., Karp, C.L., Strathdee, S.A., Vlahov, D., O’Brien, S.J., Astemborski, J., and Thomas, D.L.: Cytotoxic T-lymphocyte antigen 4 gene and recovery from hepatitis B virus infection. J Virol 78:11258-11262, 2004

497. Kuznetsov, S., Matveeva, N.M., Murphy, W.J., O’Brien, S.J. and Serov, O.L.: Mapping of 53 loci in American mink (Mustela vison). J. Hered. 94:386-391, 2003.

498. Teeling, E.C., Madsen, O., Murphy, W.J., Springer, M.S., and O’Brien, S.J.: Nuclear gene sequences confirm an ancient link between New Zealand’s short-tailed bat and South American noctilionoid bats. Molec. Phylogenet. Evol. 28: 308-319, 2003.

499. Swanson, W.F., Johnson, W.E., Cambre, R.C., Citino, S.B., Quigley, K.B., Brousset, D.M., Morais, R.N., Moreira, N., O’Brien, S.J. and Wildt, D.E.: Reproductive status of endemic felid species in Latin American zoos and implications for ex situ conservation. Zoo Biol. 0:1-21, 2003.

500. O’Brien, S.J. and Nelson, G.W.: Human genes that limit AIDS. Nature Genetics.36:565-574, 2004.

501. Daar, E. S., Lynn, H., Donfield, S., Lail, A., O’Brien, S.J., Huang, W., and Winkler, C.: Stromal cell-derived factor-1 genotype, coreptor tropism, and HIV type 1 disease progression. Journal of Infectious Diseases 192:1597-1605, 2005.

502. Silverberg M.J., Smith, M.W. Chmiel, J.S., Detels, R., Margolick, J.B., Rinaldo, C.R., O’Brien,

46 160 S.J., and Muñoz, A.: Fraction of cases of acquired immunodeficiency syndrome prevented by the interactions of identified restriction gene variants. Am J Epidemiol. 159: 232-241, 2004.

503. Murphy, W.J., Bourque, G., Tesler, G., Pevzner, P. and O’Brien, S.J.: Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum. Genomics. 1: 30-40, 2003.

504. Roca, A.L., Georgiadis, N. and O’Brien, S.J.: African elephant genetics: request for samples. Pachyderm. 33:93-95, 2002.

505. He Q., Lowrie, C., Shelton, G.D., Castellani, R.J., Menotti-Raymond, M., Murphy, W., O'Brien, S.J., Swanson, W.F., Fyfe, J.C.: Inherited motor disease in domestic cats: a model of spinal muscular atrophy. Pediatr Res. 57:324-30, 2005.

506. Thio, C.L, Thomas, D.L., Karacki, P., Gao, X., Marti, D., Kaslow, R.A., Goedert, J.J., Hilgartner, M, Strathdee, S., Duggal, P., O'Brien, S.J., Astemborski, J., and Carrington, M.: Comprehensive Analysis of Class I and Class II HLA Antigens and Chronic Hepatitis B Virus Infection. J Virol. 77:12083-12087, 2003.

507. Baker, C.S., Vant, M.D., Dalebout, M.L., Lento, G.M., O'Brien, S.J., Yuhki, N.: Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti) Immunogenetics 58:283-296. 2006.

508. Roca, A.L., Georgiadis, N. and O’Brien, S.J.: Cytonuclear genomic dissociation in African elephant species. Nature Genetics.37:96-100, 2005.

509. Marker, L.L., Wilkerson, A.J., Sarno, R.J., Martenson, J., Breitenmoser-Wursten, C., O’Brien, S.J., and Johnson, W.E.: Molecular genetic insights on cheetah (Acinonyx jubatus) ecology and conservation in Namibia. J Hered 99: 2-13, 2008.

510. Thio, C.L., Gao, X., Goedert, J.J., Vlahov, D., Nelson, K.E., Hilgartner, M.W., O’Brien, S.J., Karacki, P., Astemborski, J., Carrington, M., and Thomas, D.L.: HLA-Cw*04 and Hepatitis C virus persistence. J. Virol. 76:4792-4797, 2002.

511. O’Brien, S.J. and Fraser, C.M.: Genomes and evolution. The power of comparative genomics. Curr Opin Genet Dev 15:569-571, 2005.

512. O'Brien SJ. Owl monkey cell line. Science. 1981 Jun 12; 212:1214.

513. Oleksyk, T.K., Goldfarb, L.G., Sivtseva, T., Danilova, A.P., Osakovsky, V.L., Shrestha, S., O'Brien, S.J., and Smith, M.W.: Evaluating association and transmission of eight inflammatory genes with Viliuisk encephalomyelitis susceptibility. Eur J Immunogenet, 31:121-128, 2004

514. Menotti-Raymond, M.A., David, V.A., Wachter, L.A., Butler, J.M., and O'Brien, S.J.: An STR forensic typing system for genetic individualization of domestic cat (Felis catus) Samples. J Forensic Sciences 50:1061-1070, 2005.

515. Thio, C. L., S. J. O'Brien, et al. (2002). "The importance of assessing effect modification when asserting racial differences in associations between human leukocyte antigen class II alleles and hepatitis C virus outcomes - Reply." Journal of Infectious Diseases 185(2): 267-268

47 161

516. Roca, A.L., Nash, W.G., Menninger, J.C., Murphy, W.J., and O’Brien, S.J.: Insertional Polymorphisms of Endogenous Feline Leukemia ViruseS.J. Virol. 79: 3979-3986. 2005.

517. Dean M, Carrington M, Goedert J, O'Brien SJ. Participants in HIV Study: .Science. 1996 Nov 15;274(5290):1069

518. Duggal, P., Winkler, C.A., An, P., Farzadegan, H., O’Brien, S.J., Beaty, T.H. and Vlahov, D.: The effect of RANTES chemokine genetic variations on initial HIV-1 plasma RNA among seroincident injection drug users (IUDs). JAIDS 38:584-589. 2005.

519. O’Brien, S.J. and Nelson, G.: AIDS restriction genes - a review. Russian Journal of AIDS, Cancer and Public Health 10: 42-57, YEAR

520. Dawson, L., Bateman-House, A.S. Mueller-Agnew, D., Bok, H., Brock, D.W., Chakravarti, A., Greene, M., King, P.A., O’Brien, S.J., Sachs, D.H., Schill, K.E., Siegel, A., Solter, D., Suter, S.M., Verfaillie, C.M., Walters, L.B., Gearhart, J.D., Faden, R.R.: Safety issues in cell-based intervention trials. Fertil. Steril. 80: 1077-1085. 2003. Erratum in: Fertil Steril. 81:226, 2004.

521. Pearks-Wilkerson, A.J., Teeling, E.C., Troyer, J.L., Bar-Gal, G.K., Roelke, M., Marker, L., Pecon-Slattery, J., O’Brien, S.J.: Coronavirus outbreak in cheetahs: Lessons for SARS. Curr Biol. 14: R227-R228. 2004.

522. O’Brien S.J and W J Murphy: A dog’s breakfast? Science 301:1854-1855. 2003

523. Karacki, P.S., Gao Xiaojiang, Thio, C.L., Thomas, D.L., Goedert, J.J., Vlahov, D., Kaslow, R.A., Strathdee, S., Hilgartner, M.W., O’Brien, S.J., and Carrington, M: MICA and recovery from hepatitis C virus and hepatitis B virus infections. Genes Immun. 5:261-266, 2004.

524. Eizirik, E. and O’Brien, S.J.: Evolution of melanism in the felidae. Cat News 38:37-39. 2003.

525. Faden R.R., Dawson, L., Bateman-House, A.S., Agnew, M.D., Bok, H., Brock, D.W., Chakravarti, A., Gao, X-J., Greene, M., Hansen. J.A., King, P.A., O’Brien, S.J., Sachs, D.H., Schill, K.E., Siegel, A., Solter, D. Suter, S.M. Verfaillie, C.M., Walters, L.B. and Gearhart, J.D.: Public stem cell banks: considerations of justice in stem cell research and therapy. Hastings Cent Rep 33:13-27, 2003.

526. Ballou, J.D., Miller, P.S., Zhong, X., Rongping, W., Hemin, Z., Anju, Z., Shiqiang, H., Shan, S., David, V., O’Brien, S.J., Seal, U.S., and Wildt. D.: Analyses of demographic and genetic trends for developing a captive breeding master plan for giant pandas. In: Giant Pandas: Biology, Veterinary and Management and Medicine, (Wildt, D.E., Zhang, A., Zhang, H., and Janssen, D.L. and Ellis, S. Eds.), Cambridge University Press, England, 2003.

527. Johnson, W.E., Eizirik, E., O’Brien, S.J.: Evolución y Genética de poblaciones de jaguar: implicaciones para los esfuerzos futuros de conservación. The Jaguar Book. Pp. 519-534. 2003.

528. Liu, C., Carrington, M, Kaslow, R.A. Gao, X., Rinaldo, C.R., Jacobson, L.P., Margolick, J.B., Phair, J., O’Brien, S.J., and Detels, R.: Lack of association between HLA Class II alleles and resistance to HIV-1 infection among white, non-Hispanic homosexual men. J Acquir Immune Defic Syndr. 37:1313-1317, 2004.

529. Menotti-Raymond, M., David, V.A., Agarwala, R., Schäffer, Stephens, R., O’Brien, S.J., Murphy, W.J.: Radiation hybrid mapping of 304 novel microsatellites in the domestic cat

48 162 genome. Cytogenet Genome Res.:102: 272-276, 2003.

530. Winkler, C.A., Hendel, H., Carrington, M., Smith, M.W., Nelson, G.W., O’Brien, S.J., Phair, J., Vlahov, D., Rappaport, J., Haumont, P., Bertin-Maghit, S., Lu, W., Andrieu, J.-M., Schächter, F., Therwath, A. and Zagury, J.-F.: Early dominant effects of CCR2-CCR5 haplotypes in HIV-1 disease progression. J AIDS 37:1534-1538, 2004.

531. Springer, M. S., Murphy, W. J., Eizirik, E., and S.J. O’Brien. A molecular view on relationships among the extant orders of placental mammals. In: Molecular evidence for the rise of Placental Mammals, major placental clades (K.D. Rose & J.D. Archibald, eds.) The Johns Hopkins University Press, Baltimore, MD. 2004.

532. Roca, A.L., Kahila Bar-Gal, G., Eizirik, E., Helgen, K.M., Maria, R., Springer, M.S., O’Brien, S.J. and Murphy, W.J.: Mesozoic origin for West Indian insectivores. Nature 429:649-651. 2004.

533. Zhang, Zhi-He, Shen, Fu-Gun, Sun Shan, David, V.A., Zhang, An-Ju, O’Brien, S.J.: Paternity assignment of giant panda by microsatellite genotyping. Hereditas (Beijing) 25: 404-510. 2003.

534. Martin, M.P., Lederman, M., Hutcheson, H., Nelson, G.W. Goedert, J.J., Detels, R., Buchbinder, S., Hoots, K., Vlahov, D., O’Brien, S.J. and Carrington, M.: Association of DC SIGN promoter polymorphisms with increased risk for parenteral but not mucosal acquisition of HIV-1 infection. J Virol 78:14053-14056. 2004.

535. Winkler, C., An, P., and O’Brien, S.J.: Patterns of ethnic diversity among the genes that influence AIDS. Hum Mol Genet. 13: R9-R19. 2004.

536. Guo, X.C., O’Brien, S.J., Zeng, Y.: Impact of host genetic polymorphism on HIV/AIDS infection and progression. Chin Sci Bulletin 51:2705-2713, 2006.

537. Troyer, J., Pecon-Slattery, J. Roelke-Parker, M., Johnson, W., VandeWoude, S., Vazquez-Salat, Nuria, Brown, M., Frank, L., Woodroffe, R., Winterbach, C., Winterbach, H., Hemson, G., Bush, M., Alexander, K.A., Revilla, E., and O’Brien, S.J.: Seroprevalence and genomic diversity of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species. J Virol. 79:8282-8294. 2005.

538. Smith, M.W., Patterson, N.J., Lautenberger, J.A., Truelove, A.L., McDonald, G.J., Waliszewska, A., Kessing, B.D., Kessing, B.D., Malasky, M.J., Scafe, C., Le, E., De Jager, P.L., Mignault, A.A., Yi, Z., de The, G., Essex, M., Sankale, J.-L., Moore, J.H., Poku, K., Phair, J.P., Goedert, J.J., Vlahov, Williams, S.M., Tishkoff, S.A., Winkler, C.A., De La Vega, F.M., Woodage, T., Sninsky, J.J., Hafler, D.A., Altshuler, D., Gilbert, D.A., O’Brien, S.J. and Reich, D.E.: A high density admixture map for disease gene discovery in African Americans. Am. J. Hum. Genet. 74: 1001-1013, 2004.

539. Patterson, N., Hattangadi, N., Lane, B., Lohmueller, K.E., Hafler, D.A., Oksenberg, J.R., Hauser, S.L., Smith, M., O’Brien, S.J., Altshuler, D., Daly, M., and Reich, D.: Methods for high density admixture mapping of disease genes. Am. J. Hum. Gen. 74: 979-1000, 2004.

540. An, P. Bleiber, G., Duggal, P., Nelson, G., May, M., Mangeat, B., Alobwede, I., Trono, D., Vlahov, D., Donfield, S., Goedert, J.J., Phair, J., Buchbinder, S., O'Brien, S.J., Telenti, A., and Winkler, C.A.: APOBEC3G genetic variants and their influence on the progression to AIDS. J Virol 78:11070-11076, 2004.

541. De La Vega, F.M., Isaac, H., Collins, A., Scafe, C.R., Halldórsson, B.V., Su, X., Lippert, R.A.,

49 163 Wang, Y., Laig-Webster, M., Koehler, R.T., Ziegle, J.S., Wogan, L.T., Stevens, J.F., Leinen, K.M., Olson, S.J., Guegler, K.J., You, X., Xu, L.H., Hemken, H.G., Kalush, F., Itakura, M., O’Brien, S.J., Clark, A.G., Istrail, S., Hunkapiller, M.W., Spier, E.G., and Gilbert, D.A.: The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res 15:454-462, 2005.

542. Khakoo, S.I., Thio, C.L., Martin, M.P., Brooks, C.R., Gao, X., Astemborski, J., Goedert, J.J., Vlahov, D., Hilgarten, M., Cox, S., Little, A.-M., Alexander, G.J. Cramp, M.E., O’Brien, S.J., Rosenberg, W.M.C., Thomas, D.L., and Carrington, M.: HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection. Science 305:872-874, 2004.

543. Gao, X., Bashirova, A., Iversen, A.K.N., Phair, J., Goedert, J.J., Buchbinder, S., Hoots, K., Vlahov, D., Altfeld, M., O’Brien, S.J., and Carrington, M.: AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis. Nat Med. 11: 1290-1292, 2006.

544. O'Brien SJ. Comparative genomics in vertebrates: a role for the platypus. Reprod Fertil Dev. 2009;21(8):vii-ix.

545. Johnson, W.E., Eizirik, E., Murphy, W.J., Pecon-Slattery, J., Antunes, A., Teeling, E. and O’Brien, S.J.: The late Miocene radiation of modern felidae: A genetic assessment. Science.311:73-77. 2006.

546. King, V., Goodfellow, P., Pearks-Wilkerson, A.J., O’Brien, S.J., Pecon-Slattery, J.: Evolution of the male determining gene SRY and adjacent genomic flanks within the cat family Fedidae. Genetics 175: 1855-1867, 2007.

547. Kim, J.-H., Antunes, A., Luo, S., Menninger, J., Nash, W.G., O’Brien, S.J., Johnson, W.E.: Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus fields. Gene 366: 292-302, 2006.

548. O’Brien, S.J., Eisenberg, J.F., Miyamoto, M., Hedges, S.B., Kumar, S., Wilson, D.E. Minotti- Raymond, M., Murphy, W.J., Nash, W.G., Lyons, L.A., Menninger, J.C., Stanyon, R., Wienberg, J., Copeland, N.G., Jenkins, N.A., Gellin, J., Yerle, J., Andersson, L., Womack, J., Broad, T., Postlethwait, J., Serov, O., Bailey E., James, M.R., Marshal Graves, J.A., et al. Genone Maps 10. Comparative genomics. Mammalian radiations. Wall chart. Science 286:463-478,1999.

549. Murphy, W.J. Pevzner, P., O’Brien, S.J.: Mammalian phylogenetics comes of age. Trends Genet 20:631-639, 2004.

550. Thio, C.L., Goedert, J.J., Mosbruger, T., Vlahov, D., Strathdee, S.A., O'Brien, S.J., Astemborski, J., Thomas, D.L.: An analysis of tumor necrosis factor alpha gene polymorphisms and haplotypes with natural clearance of hepatitis C virus infection. Genes Immun.5:294-300, 2004.

551. Vila, C., Leonard, J.A., Iriarte, A., O’Brien, S.J., Johnson, W.E., and Wayne, R.K.: Detecting the vanishing populations of the highly endangered Darwin’s fox, Pseudalopex fulvipes. Animal Conservation 7:147-153, 2004.

552. Jones, J.W., Culver, M., David, V., Struthers, J., Johnson, N., Neves, R.J., O' Brien, S.J., and Hallerman, E.M.: Development and Characterization of Microsatellite Loci in the Endangered Oyster Mussel Epioblasma capsaeformis (Bivalvia:Unionidae) Molecular Ecology Notes, 10.1111/j.1471-8286, 2004.

50 164

553. Guo, X.-C., Scott, K.,Yan, L., Dean, M., David, V., Nelson, G., Johnson, r., Dilks-Hutcheson, H., Lautenberger, J., Kessing, B., Martenson, J., Li, G., Shan, S., Hong, D., Yuming, Z., de The, G., Jian L., Zeng, Y., O’Brien, S.J, Winklker, C. A..: Genetic factors leading to chronic Epstein-Barr virus infection and nasopharyngeal carcinoma in South East China: Study design, methods and feasibility. Human Genomics 2: 365-375, 2006.

554. Thio, C.L., Mosbruger, T., Astemborski, J., Greer, S., Vlahov, D., O’Brien, S.J., and Thomas, D.L.: Mannose binding lectin genotypes influence recovery from hepatitis B virus infection. J Virol 79:9192-9196, 2005.

555. O’Brien, S.J.: Male Musings Book Review of “Adam’s Curse: A future without men” by Bryan Sykes. W. W. Norton & Company, New York, 2004. http://www.genomenewsnetwork.org/articles/2004/09/03/adams_curse.php

556. Oleksyk, T.K., Thio, C.L. Truelove, A.L., Goedert, J.J., Donfield, S.M., Kirk, G.D., Thomas, D.L., O'Brien, S.J. and Smith, M.W.: Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance. Genes and Immunity 6:347-357, 2005.

557. Teeling, E., Springer, M.S., Madsen, O., Bates, P., O’Brien, S.J., and Murphy, W.J.: A molecular phylogeny for bats illuminates biogeography and the fossils record. Science 307:580-584, 2005.

558. Buckley-Beason, V.A., Johnson, W.E., Nash, W.G., Stanyon, R., Menninger, J.C. Driscoll, c.A., Howard, J., Bush, M. Page, J.E., Roelke, M.E., Stone, G., Martelli, P.P., Wen, C., Ling, L., Duraisingam, R.K., Lam, P.V. and O’Brien, S.J.: Molecular Evidence for Species-Level Distinctions in Clouded Leopards. Curr Biol 16:2371-2376, 2006.

559. O’Brien, S.J.: Cats. Curr Biol. 14:R988-R990, 2004.

560. O’Brien, S.J., and Johnson, W.: Big cat genomics. Ann. Rev. Genomic and Human Genetics 6:407-429, 2005.

561. Hendel, H., Winkler, C., An, P., Binns-Roemer, E., Nelson, G., Haumont, P., O'Brien, S.J., Khalilli, K. Zagury, D., Rappaport, J., and Zagury, J.-F.: Validation of Genetic Case-Control Studies in AIDS and Application to the CX3CR1 Polymorphism 26, 507-511, 2001.

562. Bashirova, A.A., Bleiber, G., Qi, Y., Hutcheson, H., Yamashita, T., Johnson, R.C., Cheng, J., Alter, G., Goedert, J., Buchbinder, S., Hoots, K., Vlahov, D., May, M., Maldarelli, F., Jacobson, L., O’Brien, S.J., Telenti, A., and Carrington, M.: Consistent effects of TSG101 genetic variability on multiple outcomes of exposure to human immunodeficiency virus type 1 J. Virol. 80:6757-6763. 2006

563. Vazquez-Salat, N., Yuhki, N., Beck, T., O’Brien, S.J., and Murphy, W.J.: Gene conservation between mammalian CCR2 and CCR5 chemokine receptor genes: A potential mechanism for receptor dimerization. Genomics 90:213-224, 2007.

564. Guo, X-C, O’Brien, S.J., Winkler, C., Scott, K., Hutcheson, H., David, V., Kessing, B., Zheng, Y-M., Liao, J., Lui, Y., de The, G., Zeng, Y.: Association study of chromosome 4 STRs polymorphisms with nasopharyngeal carcinoma. Hereditas (Beijing) 28: 783-790, 2006.

565. Smith, M.W., and O’Brien, S.J.: Mapping by Admixture Disequilibrium: Advances, Limits and Guidelines. Nature Genetics Reviews. 6: 623-632, 2005.

51 165 566. Murphy, W.J., Agarwala, R., Schaffer, A.A., Stephens, R., Smith, Jr., C., Crumpler, N.J., David, V.A., and O’Brien, S.J.: A rhesus macaque radiation hybrid map and comparative analysis with human genome. Genomics 86: 383-395, 2005.

567. Schmidt-Küntzel, A., Eizirik, E., O'Brien, S.J., Menotti-Raymond, M.: Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of the albino and brown loci. J Hered. 2005 Jul-Aug;96(4):289-301. Epub 2005 Apr 27.

568. Shrestha, S., Stradthdee, S.A., Galai, N., Oleksyk, T., Fallin, D., Mehta. S., Schaid, D., Vlahov, D., O’Brien, S.J., and Smith, M.W.: Behavioral risk exposure and host genetics of susceptibility to HIV-1 infection. J Infect Dis 193: 16-26, 2006.

569. Murphy, W.J., Larkin, D.M., Everts-van de Wind, A., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., Hitte, G., Meyers, S.N., Ostrander, A.E., Pape, G., Parker, H.G., Raudsepp, T., Rogatcheva, M.B., Schook. L.B., Skow, L.C., Welge, M., Womack, J.E., O’Brien, S.J., Pevzner, P.A., Lewin, H.A.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-617, 2005.

570. O’Brien, S.J., Luo, S.-J., Kim, J.-H., and Johnson, W.E.: Molecular genetic analysis reveals six living subspecies of tiger, Panthera tigris. Cat News 42: 6-8.

571. Walsh, E.C., Sabeti, P., Hutcheson, H., Fry, B., Schaffner, S.F., de Bakker, P., Varilly, P., Roy, J., Cooper, R., Zeng, Y., Guo, Xiuchan, Lander, E.S., O’Brien, S.J., Altshuler, D.: Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet. 199: 92- 102, 2006.

572. Pereira, M.J.R., Rebelo, H., Teeling, E.C., O’Brien, S.J., New, T., Bu, S.S.H., Swe, KM., Mie, M.K., Bates, P.J.: Status of the world's smallest mammal, the bumble-bee bat Craseonycteris thonglongyai, in Myanmar. ORYX 40: 456-463, 2006.

573. Lind, J.M., Hutcheson, H.B., Williams, S.M., Moore, J.H., Essex, M., Ruiz-Pesini, E., Wallace, D.C., Tishkoff, S.A., O’Brien, S.J., and Smith, M.W.: Elevated male European and female African contributions to the genomes of African American individuals. Hum Genet. 120: 713- 722, 2007.

574. Luo, S.J., Kim, J-H., Johnson, W. E., Miquelle, D. G., Huang, S-G., Pan W-S., Smith. J. L. D., O’Brien, S.J.: Proceedings in phyogeography and genetic ancestry of Tigers (Panthera tigris) in China and across the range. Zoological Research 27:441-448, 2006.

575. Sarno, R.J., Bonaciuc, C., Gonzalez, G., Zazpata, B., O’Brien, S.J., Johnson, W.E.: Capture and shearing of vicuñas vicugna vicugna for economic gain and its apparent social group disruption. Molecular Ecology In preparation.

576. Oleksyk, T.K., Zhao, K., Gilbert, D.A., de La Vega, F.M., O’Brien, S.J., Smith, M.W.: Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations. PLoS ONE 3:e1712, 2008.

577. Helgadottir, A., Manolescu, A., Helgason, A., Thorleifsson, G., Thorsteinsdottir, U., Gudbjartsson, D., Gretarsdottir, S., Magnusson, K.P., Gudmundsson, G., Hicks, A., Jonsson, T., Grant, S.F.A., Sainz, F., O’Brien, S.J., Sigurlaug Sveinbjornsdottir, S., Valdimarsson, E.M., Matthiasson, S.E., Levey, A.I., Thorgeirsson, G., Abrahamson, J., Reilly, M., Zafari, M., Wolfe, M., Gudnason, V., Quyyumi, A.A., Topol, E.J., Rader, D., Gulcher, J., Hakonarson, H., Kong, A., Stefansson, K.: A variant of the gene encoding Leukotriene A4 Hydrolase confers ethnic

52 166 specific risk of myocardial infarction. Nature Genetics 38: 68-74, 2006.

578. Gao, X., Single, R.M., Karacki, P., Marti, D., O’Brien, S.J.: Diversity of MICA and linkage disequilibrium with HLA-B in two North American populations. Human Immunol 67: 152-158, 2006.

579. Perez-Gelabert, D.e., Roca, A.L., O’Brien, S.J., Menninger, J., Nash, W., Pontius, J., and Yuhki, N.: Chromosomal assignment and genomic analysis of endogenous retrovirus RD-114 indomestic and wild cats.

580. Roca, A.L., and. O’Brien, S.J.: Genetic inferences from Afrotheria and the evolution of elephants. Curr Opin Genet Dev 15:652-659. 2005.

581. Modi, W.S., Scott, K., Goedert, J.J., Vlahov, D., Buchbinder, S., Detels, R., Donfield, S., O’Brien, S.J., and Winkler, C.: Haplotype analysis of the SDF-1 (CXCL12) gene in a longitudinal HIV-1/AIDS cohort study. Genes and Immunity.6:691-698, 2006.

582. DRISCOLL, CARLOS A., DAVID W. MACDONALD,and STEPHEN J. OBRIEN From Wild Animals to Domestic Pets, an Evolutionary View of Domestication in “In the Light of Evolution III: Two Centuries of Darwin”, by National Research Council, John C. Avise, and Francisco J. Ayala ED 2009.

583. Sabeti, P.C., Walsh, E., Schaffner, S., Varilly, P., Fry, B., Cullen, M., Mikkelsen, T., Roy, J., Patterson, N., Cooper, R., Altshuler, D., and Lander, E.S.: The case for selection at CCR5Δ32. PLoSBiol.3:1963-1969, 2005.

584. Capelli, C., MacPhee, R.D.E., Roca, A.L., Brisighelli, F., Georgiadis, N., O’Brien, S.J., and Greenwood, A.D.: A nuclear DNA phylogeny of the woolly mammoth (Mammuthus primigenius). Mol Phylogenet Evol 40: 620-627, 2006.

585. Springer, M.S., Burk-Herrick, A., Meredith, R., Eizirik, E., Teeling, E., O'Brien, S.J., Murphy, W.J.: The adequacy of morphology for reconstructing the early history of placental mammals. Syst Biol. 2007 Aug;56(4):673-84.

586. Fyfe, J.C., Menotti-Raymond, M., David, V.A., Brichta, L., Schäffer, A.A., Agarwala, R., Murphy, W.J., Wedemeyer, W.J., Gregory, B.L., Buzzell, B.G., Drummond, M.C., Wirth, B., O'Brien, S.J.: An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res. 2006 Sep;16(9):1084-90. Epub 2006 Aug 9.

587. O’Brien, S.J.: The dog and its genome. Nature 438:740, 2005.

588. Welzel, T.M., Gao, X., Pfeiffer, R., Martin, M.P., O’Brien, S.J., Goedert, J.J., Carrington, M. and O’Brien, T.R.: HLA Bw4 alleles and HIV-1 transmission in heterosexual couples. AIDS 21: 225- 229, 2007.

589. Napolitano, C, Bennett, M., Johnson, W.E., O’Brien, S.J., Marquet, P.A., Barria, I., Poulin, E., and Iriarte, A.: Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identeification of faecal samples. Mol Ecol 17: 678-690, 2008.

590. Hutcheson, H., Lautenberger, J., Nelson, G., Pontuis, J.J., Kessing, B.D., Smith, M.W., Johonson, R., Stephens, R., Phair, J., Goedert, J., Donfield., S., and O’Brien, S.J.: Detecting AIDS

53 167 Restriction Genes: From Candidate Genes to Genome-Wide Association Discovery. Vaccine 26: 2951-2965, 2008.

591. Thio, C.L., Astemborski, J., Bashirova, A., Mosbruger, T., Greer, S., Witt, M.D., Goedert, J.J., Hilgartner, M., Majeske, A., O’Brien, S.J., Thomas, D.L., and Carrington, M.: Genetic protection against HBV conferred by CCR5Δ32: evidence that CCR5 contributes to viral persistence. J Virol 81:441-445, 2007.

592. O’Brien, S.J., Troyer, J., Roelke, M., Pecon-Slattery, J. and Marker, L.: Plagues and adaptations: Lessons from the Felidae modes for AIDS and SARS. Biol Conserv 131:255-267, 2006.

593. Nash, W.G., Menninger, J.C., Padilla-Nash, H. M. and O’Brien, S.J.: Ancestral carnivore karyotype (2n=38) lives today in ringtails. J Hered 99: 241-253, 2008.

594. Javanbakht, H., An, P., Gold, B., Petersen, D.C., O;hUigin,C., Nelson, G.W., O’Brien, S.J., Kirk, G.D., Detels, R., Buchbinder, S., Donfield, S., Shulenin, S., Song, B., Perron, J.J., Stremlau, M., Sodroski, J., Dean, M., and Winkler, C Effects of human TRIM5alpha polymorphisms on antiretroviral function and susceptibility to human immunodeficiency virus infection.Virology 354: 15-27, 2006

595. Qi, Y., Martin, M.P., Gao, X., Jacobson, L., Goedert, J.J., Buchbinder, S., Kirk, G.D., O’Brien, S.J., Trowsdale, J., and Carrington, fM.: KIR/HLA Pleiotropism: Protection against Both HIV and Opportunistic Infections. PLoS Pathog. 2:741-745-2006.

596. Antunes, A., Troyer, J.L., Roelke, M.E., Pecon-Slattery, J., Packer, C., Winterbach, C., Winterbach, H., Hemson, G., Frank, L., Stander, P., Siefert, L., Driciru, M., Funston, P.J., Alexander, K.A., Prager, K.C., Mills, G., Wildt, D., Bush, M., O'Brien, S.J., Johnson, W.E.: The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics. PLoS Genet. 2008 Nov;4(11):e1000251. Epub 2008 Nov 7.

597. Ishida, Y., David, V.A., Eizirik, E., Schäffer, A.A., Neelam, B.A., Roelke, M.E., Hannah, S.S., O'brien, S.J., Menotti-Raymond, M.: A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat. Genomics. 2006 Dec;88(6):698-705.

598. Modi, W.S., Lautenberger, J., Scott, K., Ping, A., Goedert, J.J., Kurt, G.D., Buchbinder, J., Donfield, S., O’Brien, S.J., and Winkler, C.: Genetic variation in the CCL18 – CCL3 – CCL4 chemokine gene cluster influences HIV-1 transmission and AIDS disease progression. Am J Hum Genet 79:120-128. 2006.

599. Perelman, P.L., Graphodatsky, A.S., Dragoo, J.W., Serdyukova, N.A., Stone, G., Cavagna, P., Menotti, A., Nie, W., O'Brien, P.C., Wang, J., Burkett, S., Yuki, K., Roelke, M.E., O'Brien, S.J., Yang, F., Stanyon, R.: Chromosome painting shows that skunks (Mephitidae, Carnivora) have highly rearranged karyotypes. Chromosome Res. 2008;16(8):1215-31. Epub 2008 Nov 25.

600. O’Brien, S.J. and Johnson, W.E.: The evolution of cats. Genomic paw prints in the DNA of the world’s wild cats have clarified the cat family tree and uncovered several remarkable migrations in their past. Sci Am 297:68-75, 2007.

601. Pontius, J. U., Mullikin, J. C., Smith, D., Lindblad-Toh, K., Gnerre, S., Clamp, M., Stephens, R., Neelam, B., Volfovsky, N., Schäffer, A. A., Agarwala, R., Narfström K., Murphy, W. J., Giger, U., Roca, A. L., O’hUigin, C., Antunes, A., Menotti-Raymond, M., Yuhki, N., Pecon-Slattery, J., Johnson, W. E., Driscoll, C. and O’Brien, S.J.: Initial sequence and comparative analysis of the cat genome. Genome Research 11: 1675-1689, 2007.

54 168

602. Driscoll, C.A., Menotti-Raymond, M., Roca, A.L., Hupe, K., Johnson, W.E., Geffen, E., Harley, E.H., Delibes, M., Pontier, D., Kitchener, A.C., Yamaguchi, N., O'brien, S.J., Macdonald, D.W.: The Near Eastern origin of cat domestication. Science. 2007 Jul 27;317(5837):519-23.

603. Menotti-Raymond, M., David, V.A., Schäffer, A.A., Stephens, R., Wells, D., Kumar-Singh, R., O'Brien, S.J., Narfström, K.: Mutation in CEP290 discovered for cat model of human retinal degeneration. J Hered. 2007 May-Jun;98(3):211-20. Epub 2007 May 16.

604. Murphy, W.J., Davis, B., David, V.A., Agarwala, R., Schäffer, A.A., Pearks Wilkerson, A.J., Neelam, B., O'Brien, S.J., Menotti-Raymond, M.: A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes. Genomics. 2007 Feb;89(2):189-96. Epub 2006 Sep 25.

605. Martin, M. P., Qi, Y., Gao, X-J., Brown, E. E., Phair, J., Goedert, J. J., Buchbinder, S., Kirk, G. D., O’Brien, S.J., Parham, P., McVica. E. W., Carrington, M.: Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1. Nat Genet 39:733-740, 2007.

606. Truelove, A. L., Oleksyk, T. K., Shrestha, S., Thio, C. L., Goedert, J. J., Donfield, S. M., Kirk, G.D., Thomas, D. L., O’Brien, S.J., and Smith, M. W.: Evaluation of IL10, IL19 and IL20 gene polymorphisms and chronic hepatits B infection outcome. Int J Immunogenet 35:255-264, 2008.

607. Luo, S-J., Cai, Q-X., David, V. A., Zhang, Li., Martelli, P., Lim, N. T-L., Ferrand, N., Chin, S-C., Guabert, P., Ramos, M., J., O’Brien, S.J., Antunes, A., Johnson, W. E.: Isolation and characterization of microsatellite markers in pangolias (mammalia, Pholidota, Manis spp). Mol Ecol Notes 7:269-272, 2007.

608. Menotti-Raymond, M., O’Brien, S.J.: The domestic cat, Felis catus, as a model of hereditary and infectious disease. In: Source Book for Models for Biomedical Research. Michael Conn ed. Humana Press Inc., Totawa, NJ. pp 221-232. 2008.

609. Bar-Gal, G.K., Kessing, B., Pecon-Slattery, J., Tetu, S., VandeWoude, S., Hoover, E. and O’Brien, S.J.: Phylo-diversity of feline immunodeficiency virus (FIV) in domestic cats. In preparation.

610. An., P., Duggal, P., Wang, L.H., O’Brien, S.J., Donfield, S., Goedert, J.J., Phair, J., Buchbinder, S., Kirk, G.D., and Winker, C.A.: Polymorphisms of CUL5 area ssociated with CD4+ T cell loss in HIV-1 infected individuals. PLoS Genetics 3: e19, 2007.

611. O’Brien, S.J, An interview with. Q&A. Curr Biol. 17: R152-R154, 2007.

612. Menotti-Raymond, M., David, V.A., Pflueger, S.M., Lindblad-Toh, K., Wade, C.M., O'Brien, S.J., Johnson, W.E.: Patterns of molecular genetic variation among cat breeds. Genomics. 2008 Jan;91(1):1-11. Epub 2007 Oct 25.

613. Kehler, J.S., David, V.A., Schäffer, A.A., Eizirik, E., Ryugo, D.K., Hannah, S.S., O’Brien, S.J., Menotti-Raymond, M. Four independent mutations in the feline fibroblast growth factor 5 gene determine the long-haired phenotype in domestic cats. J Hered. 98:555-66, 2007.

614. Miller-Butterworth, C.M., Murphy, W.J., O’Brien, S.J., Jacobs, D.S., Springer, M.S., and Teeling, E.C.: A family matter: conclusive resolution of the taxonomic position of the long- fingered bats, miniopterus. Mol Biol Evol 24:1553-1561, 2007.

55 169 615. Luo, S.J., Johnson, W.E., David, V.A., Menotti-Raymond, M., Stanyon, R., Cai, Q.X., Beck, T., Yuhki, N., Pecon-Slattery, J., Smith, J.L., O'Brien, S.J.: Development of Y chromosome intraspecific polymorphic markers in the Felidae. J Hered. 2007;98(5):400-13. Epub 2007 Jul 23.

616. An, P. Wang, L.H., Hutcheson, H., Nelson, G., O’Brien, S.J., Donfield, S., Goedert, J.J., Phair, J., Buchbinder, S., Kirk, G.D., and Winkler, C.A.: Regulatory polymorphisms in the Cyclophilin A gene, PPIA accelerate progression to AIDS. PLoS Pathogens 3:849-857, 2007.

617. Yuhki, N., Beck, T., Stephens, R., Neelam, B., and O’Brien, S.J.: Comparative genomic structure of human, dog, cat MHC: -HLA, DLA, and FLA-. J Hered 98:390-399, 2007.

618. Antunes, A., Pontius, Ramos, M.J., O’Brien, S.J. and Johnson, W.E.: Mitochondrial introgressions into the nuclear genome of the domestic cat. J Hered 98:414-420, 2007.

619. Springer, M.S., Murphy, W.J., Eizirik, E., Madsen. O., Scally, M., Douady, C.J., Teeling. E.C., Stanhope, M.J., de Jong, W.W., and O’Brien, S.J.: A molecular classification for the living orders of placental mammals of the phylogenetic placement of primates. In: Primate Origins: Adaptations and Evolution. (Ravosa, M.J. and Dagosto, M. Eds.), Springer, 2006.

620. Wilting, A., Buckley-Beason, V.A., Feldhaar, H., Gadau, J., O’Brien, S.J., and Linsenimair, K.D.: Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra. Front Zool 4:15, 2007.

621. Troyer, J.L., VandeWoude, S., Slattery, J., McIntosh, C., Franklin, S., Antunes, A., Johnson, W., and O’Brien, S.J. FIV-cross-species transmission: an evolutionary prospective. Vet Immunol Immunopathol 123: 159-166, 2008.

622. Baena, A., Mootnick, A.R., Falvo, J.V. Tystskova, A.V., Ligeiro, F., Diop, O.M., Brieva, C., Gagneux, O’Brien, S.J., Ryder, A.O., and Goldfeld, A.E. Primate TNF promoters reveal makers of phylogeny and evolution of innate immunity. PLoS ONE 2:e621, 2007.

623. Martin, M.P., Pascal, V., Yeager, M., Phair, J., Kirk, G.D., Hoots, K., O’Brien, S.J., Anderson, S., and Carrington, M. A mustation in KIR3DS1 that results in truncation and lack of cell surface expression. Immunogenetics 59: 823-829, 2007.

624. Menotti-Raymond, M.A., David, V.A., and O’Brien, S.J. STR based forensic analysis of felid samples from domestic and exotic cats. In: Non-Human DNA Typing: Theory and Casework Applications, Coyle, H. (Ed.), Marcel Dekker, Inc., New York, 2008.

625. Wilting, A., Feldhaar, H., Buckley-Beason, V.A., Linsenmair, K.E., and O’Brien, S.J.: Two modern species of clouded leopards: a molecular perspective. Cat News 47: 10-11, 2007.

626. Cunningham, M.W., Brown, M.A., Shindle, D.B., Terrell, S.P., Hayes, K.A., Ferree, B.C., McBride, R.T., Blankenship, E.L., Jansen, D., Citino, S.B., Roelke, M.E., Kiltie, R.A., Troyer, J.L., O'Brien, S.J.: Epizootiology and management of feline leukemia virus in the Florida puma. J Wildl Dis. 2008 Jul;44(3):537-52.

627. Brown, M., Cunningham, M.W., Roca, A.L., Troyer, J.L., Johnson, W.E. and O’Brien, S.J.: Genetic characterization of emerging feline leukemia virus in the free-ranging Florida panter population. Emerg Infect Dis 14: 252-259, 2008.

628. Roelke, M.E., Brown, M.A., Troyer, J.L., Winterbach, H., Winterbach, C., Hemson, G., Smith, D., Johnson, R.C., Pecon-Slattery, J., Roca, A.L., Alexander, K.A., Klein, L., Martelli, P.,

56 170 Krishnasamy, K., O'Brien, S.J.: Pathological manifestations of feline immunodeficiency virus (FIV) infection in wild African lions. Virology. 2009 Jul 20;390(1):1-12.

629. Pecon-Slattery, J., McCracken, C., Troyer, J., VandeWoude, S., Roelke, M., Sondgareth, K., Winterbach, C., Winterbach, H., and O’Brien, S.J.: Genome organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild. BMC Genomics 9:66, 2008.

630. Zeng, Z., Guan, L., An., P., Sun, S., O’Brien, S.J., and Winkler, C.A.: A population based study to investigate the host genetic facdtors associated with Hepatitus B infection and pathogenesis in the Chinese population. BMC Infect Dis 8:1, 2008.

631. Driscoll, C.A., Yamaguchi, N., Bar-Gal, G.K., Roca, A.L., Luo, S., Macdonald, D.W., O'Brien, S.J.: Mitochondrial phylogeography illuminates the origin of the extinct caspian tiger and its relationship to the amur tiger. PLoS One. 2009;4(1):e4125. Epub 2009 Jan 14.

632. Luo, S.J., Johnson, W.E., Martenson, J., Antunes, A., Uphyrkina. O., Martelli, P., Tarasov, V., Smith, J.L.D., O’Brien, S.J.: Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations. Curr Biol 18:592-596, 2008.

633. Fisher, R.W., Ambrose, Z., Fritz, E.A., Hartmann, C.J., Hensley, L.E., Huggins, J.W., Jahrling, P.B., KewalRamani, V.N., Mucker, E.M., Paragas, J., Young, H.A., and O’Brien, S.J.: The CCR5 chemokine receptor is not required for monkeypox or variola entry into human monocytes. In prep

634. Hendrickson, S.L., Jacobson, L.P., Nelson, G., Phair, J.P., Johnson, R., Margolick, J.B., Detels, R., Rinaldo, C., and O’Brien, S.J.: Host Genetic Influences on Highly Active Antiretroviral Therapy Efficacy and AIDS-Free Survival J Acquir Immune Defic Syndr 48:263-271, 2008.

635. Hendrickson, S.L., Hutcheson, H.B., Ruiz-Pesini, E., Poole, J.C., Lautenberger, J., Sezgin, E., Kingsley, L., Goedert, J.J., Vlahov, D., Donfield, S., Wallace, D.C., O'Brien, S.J.: Mitochondrial DNA haplogroups influence AIDS progression. AIDS. 2008 Nov 30;22(18):2429-39.

636. Eizirik, E., Johnson, W.E. and O’Brien, S.J.: Molecular systematics and revised classification of the family Felidae (Mammalia, Carnivora). J Mammol In Press.

637. Trigo, T.C., Freitas, T.R.O., Kunzler, G., Cardoso, L., Silva, J.C.R., Johnson, W.E., O’Brien, S.J., Bonatto, S.L., Eizirik, E.: Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil.Mol Ecol. 2008 Sep 10. [Epub ahead of print]

638. Yuhki, N., Mullikin, J., Beck, T., Stephens, R., and O’Brien, S.J.: Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat.PLoS One 3:e2674, 2008.

639. da Fonseca, R., Johnson, W.E., O’Brien, S.J., Ramos, M.J., and Antunes, A.: The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics 9:119, 2008.

640. Pontius, J.U., O'Brien, S.J.: Genome Annotation Resource Fields--GARFIELD: a genome browser for Felis catus. J Hered. 2007;98(5):386-9. Epub 2007 Jul 23.

641. O’Brien, S.J., Johnson, W., Driscoll, C., Pontius, J., Pecon-Slattery, J., Menotti-Raymond, M.: State of Cat Genomics. Trends in Genetics 24: 268-279, 2008.

57 171

642. Coomber, N., David, V.A., O'Brien, S.J., Menotti-Raymond, M.: Validation of a short tandem repeat multiplex typing system for genetic individualization of domestic cat samples. Croat Med J. 2007 Aug;48(4):547-55.

643. Pecon-Slattery, J., Troyer, J.L., Johnson, W.E. O’Brien, S.J.: Evolution of feline immunodeficiency virus in Felidae: implications for human health and wildlife ecology. Vet Immunol Immunopathol 123:32-44, 2008.

644. Pontius, J.U., and O’Brien, S.J.: Use of online resources for the annotation of the Felis catus genome. IFRRS J Submitted.

645. Benson, JF, Hostetler, JA, Onorato, DP, Johnson, WE, Roelke, M, O’Brien, SJ, Jansen, D, Oli, MK,. Introgression and adult panther survival. The influence of genetic introgression on the survival and cause-specific mortality of sub-adult and adult- Florida panthers. Submitted.

646. Murphy, W.J. and O’Brien, S.J.: Designing and optimizing comparative anchor primers for comparative gene mapping and phylogenetic inference. Nature Protocols 2: 3022-3030, 2007.

647. Krause, J., Unger, T., Noçon, Malaspinas, A-S., Stiller, M., Kolokotronis, S-O., Soibelizon, L., Spriggs, H., Dear, P.H., Briggs, A.W., Bray, S.C.E., O’Brien, S.J., Rabeder, G., Matheus, P., Cooper, A., Slatkin, M., Pääbo, S., Hofreiter, M.: Mitrochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol 8:220, 2008.

648. Roelke, M.E., Johnson, W.E., Millán, Palomares, F., Revilla, E., Rodríguez, Calzada, Ferreras, P., León-Vizcaíno, L., Delibes, M., O’Brien, S.J.: Exposure to disease agents in the endangered Iberian lynx (Lynx pardinus). Euro J Wildl Res 54:171-178, 2008.

649. Eizirik, E., Johnson, W.E., and O’Brien, S.J.: In: Manejo e Conservação de Carnívoros Neotropicais. Definindo uniadades evolutivamente significativas e unidades de manejo para a conservação de carnívoros neotropicais. Morato, R.G., Rodrigues, F.H.G., Eizirik, E., Mangini, P.R., Cascelli de Azevedo, F.C., Marinho-Filho, J. (Eds.) pp. 47, 2007.

650. Johnson, W.E., Eizirik, E., Waits, L., and O’Brien, S.J. In: Manejo e Conservação de Carnívoros Neotropicais. Molecular ecology and carnivore conservation: The applications of molecular techniques for inferring identify kinship, and social structure in the neotropics. Morato, R.G., Rodrigues, F.H.G., Eizirik, E., Mangini, P.R., Cascelli de Azevedo, F.C., Marinho-Filho, J. (Eds.) pp. 67, 2007.

651. Werdelin, L., O’Brien, S.J., Johnson, W.E., Yamaguchi, N.: Phylogeny and evolution of cats (Felidae). Macdonald, D., and Loverage A. (eds.). In: Biology and Conservation of Wild Felids. Oxford University Press. 2009 In Press

652. Graphodatsky, A.S., Perelman, P., Sokolovskaya, N.V. Beklemisheva, V.R., Serdukova, N.A., O’Brien, S.J., Ferguson-Smith, M.A., Yang, F.: Phylo-genomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting. Chromosome Res 16: 129-143, 2008.

653. Luo, S-J., Johnson, W.E., Smith, J.L.D., O’Brien, S.J.: What is a tiger? Genetics and Phyogeography. In: Tigers of the World. Ed. Tilson, R. In press

654. Münk, C., Beck, T., Zielonka, J., Hotz-Wagenblatt, A., Chareza, S., Battenberg, M., Thielebein, J., Cichutek, K., Bravo, I.G., O’Brien, S.J., Löchelt, M., Yuhki, N.: Functions, structure and read-

58 172 through alternative splicing of feline APOBEC3 genes. Genome Biol 9:R48, 2008.

655. Culver, M., P. W. Hedrick, et al. (2008). "Estimation of the bottleneck size in Florida panthers." Animal Conservation 11(2): 104-110.

656. Shearer, W.T., Nelson, G.W., McIntosh, K., Thompson, B., Lu, M., Rich, K.C., LaRussa, P.S., Blattner, A., Brouwers, P., and O’Brien, S.J.: Association between genotypes and infant HIV disease progression: The women and infants transmission study. In prep

657. O’Brien, S.J.: The platypus genome unraveled. Cell 133:953-955, 2008.

658. Schmidt-Kuntzel, A., Nelson, G., David, V.A., Schaffer, A.A., Eizirik, E., Roelke, M.E., Kehler, J.S., Hannah, S.S., O'Brien, S.J., Menotti-Raymond, M.: A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti. Genetics. 2009 Apr;181(4):1415-25.

659. Li, X., Glaser, D., Li, W., Johnson, W.E., O'Brien, S.J., Beauchamp, G.K., Brand, J.G.: Analyses of sweet receptor gene (Tas1r2) and preference for sweet stimuli in species of Carnivora. J Hered. 2009 Jul-Aug;100 Suppl 1:S90-100..

660. Driscoll, C.A., Clutton-Brock, J., Kitchener, A.C., O'Brien, S.J.: The Taming of the cat. Genetic and archaeological findings hint that wildcats became housecats earlier--and in a different place-- than previously thought. Sci Am. 2009 Jun;300(6):68-75.

661. Menotti-Raymond, M., David, V.A., Schäffer, A.A., Tomlin, J.F., Eizirik, E., Phillip, C., Wells, D., Pontius, J.U., Hannah, S.S., O'Brien, S.J.: An autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics. 2009 Apr;93(4):305-13.

662. Guo, X, O'Brien, S.J., Zeng, Y., Nelson, G.W., and Winkler, C.A.: GSTM1 and GSTT1 gene deletions and the risk for nasopharyngeal carcinoma in Han Chinese. Epidemiol. Biomarkers Prev. 17: 1760-1763, 2008.

663. Urban, T.J., Weintrob, A.C., Fellay, J., Colombo, S., Shianna, K.V., Gumbs, C., Rotger, M., Pelak, K., Dang, K.K., Detels, R., Martinson, J.J., O'Brien, S.J., Letvin, N.L., McMichael, A.J., Haynes, B.F., Carrington, M., Telenti, A., Michael, N.L., Goldstein, D.B.: CCL3L1 and HIV/AIDS susceptibility. Nat Med. 2009 Oct;15(10):1110-2.

664. Guo, X., Johnson, R.C., Deng, H., Liao, J., Guan, L., Nelson, G.W., Tang, M., Zheng, Y., de The, G., O'Brien, S.J., Winkler, C.A., Zeng, Y.: Evaluation of nonviral risk factors for nasopharyngeal carcinoma in a high-risk population of Southern China. Int J Cancer. 2009 Jun 15;124(12):2942- 7.

665. Roca, A.L., Georgiadis, N., and O'Brien, S.J. Cyto-nuclear genomic dissociation and the African elephant species question. Quat Int 169-170: 4-16, 2007.

666. Hendrickson, S., Nelson, G.W. and O'Brien, S.J. The Explained Fraction as a Statistical "Yardstick" for Genetic Association Studies. In preparation.

667. Brown, M.A., Troyer, J.L., Pecon-Slattery, J., Roelke, M.E., O'Brien, S.J.: Genetics and pathogenesis of feline infectious peritonitis virus. Emerg Infect Dis. 2009 Sep;15(9):1445-52.

668. Sezgin, E., Lind, J.M., Shrestha, S., Hendrickson, S., Goedert, J.J., Donfield, S., Kirk, G.D., Phair, J.P., Troyer, J.L., O'Brien, S.J., Smith, M.W. 2009: Association of Y chromosome

59 173 haplogroup I with HIV progression, and HAART outcome. Hum Genet. 125(3):281-94

669. Oleksyk, T.K., Smith, M.W., and O’Brien, S.J. Genome-wide scans for selection. 2010 Philos Trans R Soc Lond B 365(1537):185-205

670. Oleksyk, T.K., Shrestha, S., Truelove, A.L., Goedert, J.J., Donfield, S.M., Phair, J., Mehta, S., O'Brien, S.J., Smith, M.W.: Extended IL10 haplotypes and their association with HIV progression to AIDS. Genes Immun. 2009 Jun;10(4):309-22.

671. Lewin, H.A., Larkin, D.M., Pontius, J., O'Brien, S.J.: Every genome sequence needs a good map. Genome Res. 2009 Nov;19(11):1925-8

672. Hendrickson, S.L., Kingsley, L.A., Ruiz-Pesini, E., Poole, J.C., Jacobson, L.P., Palella, F.J., Bream, J.H., Wallace, D.C., O'brien, S.J.: Mitochondrial DNA haplogroups influence lipoatrophy after highly active antiretroviral therapy. J Acquir Immune Defic Syndr. 2009 Jun 1;51(2):111-6.

673. Herbeck, J.T., Gottlieb, G.S., Winkler, C.A., Nelson, G.W., An, P., Maust, B.S., Wong, K.G., Troyer, J.L., Goedert, J.J., Kessing, B.D., Detels, R., Wolinsky, S.M., Martinson, J., Buchbinder, S., Kirk, G.D., Jacobson, L.P., Margolick, J.B., Kaslow, R.A., O'Brien, S.J., Mullins, J.I.: Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS. J Infect Dis. 2010 Feb 15;201(4):618-26.

674. LaRue, R.S., Andresdottir, V., Blanchard, Y., Conticello, S.G., Derse, D., Emerman, M., Greene, W.C., Jonsson, S.R., Landau, N.R., Lochelt, M., Malik, H.S., Malim, M.H., Munk, C., O'Brien, S.J., Pathak, V.K., Strebel, K., Wain-Hobson, S., Yu, X.F., Yuhki, N., Harris, R.S.: Guidelines for naming nonprimate APOBEC3 genes and proteins. J Virol. 2009 Jan;83(2):494-7. Epub 2008 Nov 5.

675. O'Brien, S.J. Stewardship of Human Biospecimens, DNA, Genotype, and Clinical Data in the GWAS Era. Annu. Rev. Genomics Hum. Genet. 2009. 10:193–209. http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev-genom-082908- 150133?cookieSet=1

676. Pontius, J.U., O'Brien, S.J. Artifacts of the 1.9x feline genome assembly derived from the feline- specific satellite sequence. J Hered. 2009 Jul-Aug;100 Suppl 1:S14-8. Epub 2009 Jun 16.

677. Menotti-Raymond, M., David, V.A., Eizirik, E., Roelke, M.E., Ghaffari, H., O'Brien, S.J. Mapping of the domestic cat "SILVER" coat color locus identifies a unique genomic location for silver in mammals. J Hered. 2009 Jul-Aug;100 Suppl 1:S8-13. Epub 2009 Apr 27.

678. Tang, M., Zeng, Y., Poisson, A., Marti, D., Guan, L., Zheng, Y., Deng, H., Liao, J., Guo, X., Sun, S., Nelson, G., de The, G., Winkler, C.A., O'Brien, S.J., Carrington, M., Gao, X.: Haplotype- dependent HLA susceptibility to nasopharyngeal carcinoma in a Southern Chinese population. Genes Immun. 2010 Jun;11(4):334-42. Epub 2010 Jan 14.

679. Tang,1,2 Minzhong Tao Peng,3 Xiaojiang Gao,4 Li Guan,5 Lisa Maslan,5 Zhiming Liu,3 Lequn Li,3 Minhao Peng,3 Tangwei Liu,3 Yi Zeng,1 Cheryl A. Winkler,5 Mary Carrington,4 and Stephen J. O’Brien2* Genetic Association between HLA Class I Alleles and Hepatitis B Virus-Related Hepatocellular Carcinoma in a Southern Chinese Population.

680. Driscoll, C.A., Macdonald, D.W., O'Brien, S.J.: From wild animals to domestic pets, an evolutionary view of domestication. Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9971- 8..

60 174

681. Klein, G., Klein, E., Klotman, M., Klotman, P., kotler, M., Kurth, R., Lafeuillade, A., La Placa, M., Lewis, J., Lillo, F., Lisziewicz, J., Lomonico, A., Lopalco, L., Lori, F., Lusso, P., Macchi, B., Malim, M., Margolis, L., Markham, P.D., McClure, M., Miller, M., Mingari, M.C., Moretta, L., Noonan, D., O’Brien, S.J., Okamoto, T., Pal, R., Palese, P., Panet, A., Pantaleo, G., Pavalakis, G., Pistello, M., Plotkin, S., Poli, G., Pomerantz, R., Radaelli, A., Guroff, M.R. Roederer, M., Sarngadharan, M.G., Schols, D., Secchiero, P., Shearer, G., Siccardi, A., Stevenson, M., Svoboda, J., Tartaglia, J., Torelli, G., Tornesello, M.L., Tschachler, E., Vaccarezza, M., Vallbracht, A., Van Lunzen, J., Varnier, O., Vicenzi, E., Von Melchner, H., Witz, I., Zagury, D., Zagury, J.F., Zauli, G., and Zipeto, D., Unsung Hero Robert C. Gallo. Science 3234:206, 2009

682. Luo, S.J., Johnson. W.E., Martelli, P., Zhang, Y.P., Smith, J.L.D., and O’Brien, S.J. Phylogeography and evolutionary history of the Asian leopard cat (Prionailurus bengalensis) inferred from multiple DNA genealogies. In preparation.

683. Luo, S.J., Johnson. W.E., Martelli, P., Smith, J.L.D., and O’Brien, S.J. Multiple genealogies reveal significant Indochinese-Sundaic faunal transition at the Isthumus of Kra: Evidence from six Asian felid species. PLoS Genetics , Submitted

684. Brown MA, Munkhtsog B, Troyer JL, Ross S, Sellers R, Fine AE, Swanson WF, Roelke ME, O'Brien SJ. Feline immunodeficiency virus (FIV) in wild Pallas' cats.Vet Immunol Immunopathol. 2010 Mar 15;134(1-2):90-5.

685. Sezgin E, Drosdak A, McIntosh C, Kessing B, Lautenberger JA, Goedert JJ, Phair JP, Troyer JL, Smith MW, O'Brien SJ. Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I. J Hum Genet. 2010 Jun 24. [Epub ahead of print]

686. Narfstrom, K., David, V., Jarret, O., Beatty, J., Barrs, V., Wilkie, D., O'Brien, S., Menotti- Raymond, M.: Retinal degeneration in the Abyssinian and Somali cat (rdAc): correlation between genotype and phenotype and rdAc allele frequency in two continents. Vet Ophthalmol. 2009 Sep- Oct;12(5):285-91.

687. Menotti-Raymond, M., David, V.A., Pflueger, S., Roelke, M.E., Kehler, J., O'Brien, S.J., Narfstrom, K.: Widespread retinal degenerative disease mutation (rdAc) discovered among a large number of popular cat breeds. Vet J. 2009 Sep 9;]

688. Mullikin JC, Hansen NF, Shen L, Ebling H, Donahue WF, Tao W, Saranga DJ, Brand A, Rubenfield MJ, Young AC, Cruz P, Sequencing NC Program, Driscoll C, David V, Al-Murrani SW, Locniskar MF, Abrahamsen MS, O'Brien SJ, Smith DR, Brockman JA. Light whole genome sequence for SNP discovery across domestic cat breeds. BMC Genomics. 2010 Jun 24;11(1):406. [Epub ahead of print]

689. O’Brien, S. J. Impressions from NAS Darwin Celebration. 2009. Science. http://blogs.sciencemag.org/cgi-bin/mt/mt- search.cgi?search=Impressions+from+NAS+Darwin+Celebration&IncludeBlogs=7

690. Eizirik, E., Murphy, W.J., Koepfli, K.P., Johnson, W.E., Dragoo, J.W., Wayne, R.K., O'Brien, S.J.: Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Mol Phylogenet Evol. 2010 Jul;56(1):49-63. Epub 2010 Feb 4.

61 175 691. Fellay, J, Dongliang Ge, Kevin V Shianna, Sara Colombo, Bruno Ledergerber,Elizabeth T Cirulli, Thomas J Urban1, Kunlin Zhang, Curtis E Gumbs, Jason P Smith, Antonella Castagna, Alessandro Cozzi-Lepri, Andrea De Luca, Philippa Easterbrook, jhh Huldrych F Günthard, Simon Mallal, Cristina Mussini, Judith Dalmau, Javier Martinez-Picado, José M Miro, Niels Obel, Steven M Wolinsky, Jeremy J Martinson, RogerDetels, Joseph B Margolick, Lisa P Jacobson, Patrick Descombes, Stylianos EAntonarakis, Jacques S Beckmann, Stephen J O’Brien, Norman L Letvin, Andrew J. McMichael, Barton F Haynes, Mary Carrington, Sheng Feng, Amalio Telenti & David B. Goldstein for the NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI). Common genetic variation and the control of HIV-1 in humans. PLOSGenetics. 2009 Dec;5(12):e1000791. Epub 2009 Dec 24.

692. Johnson,Warren E. , David P. Onorato, Melody E. Roelke, E. Darrell Land, Mark Cunningham, Chris Belden, Roy McBride, Deborah Jansen, Mark Lotz, David Shindle, JoGayle Howard, David E. Wildt, Linda M. Penfold, Jeffrey A. Hostetler, Madan K. Oli, and Stephen J. O’Brien . 2010 .Genetic Restoration of the Florida Panther Science In Press

693. Eizirik, E., David, V.A., Buckley-Beason, V., Roelke, M.E., Schaeffer, A.A., Hannah, S.S., Narfstrom, K., O'Brien, S.J., Menotti-Raymond, M.: Defining and mapping mammalian coat pattern genes: multiple genomic regions implicated in domestic cat stripes and spots. Genetics. 2010 Jan;184(1):267-75..

694. Hendrickson, S.L., Jabs, D.A., Van Natta, M., Lewis, R.A., Wallace, D.C., O'Brien, S.J.: Mitochondrial haplogroups are associated with risk of neuroretinal disorder in HIV-positive patients. J Acquir Immune Defic Syndr. 2010 Apr 1;53(4):451-5.

695. Menotti-Raymond, M., Deckman, K.H., David, V., Myrkalo, J., O'Brien, S.J., Narfstrom, K.: Mutation discovered in a feline model of human congenital retinal blinding disease. Invest Ophthalmol Vis Sci. 2010 Jun;51(6):2852-9.

696. Hendrickson, SL, Lautenberger, J, Chinn, L, Phair, J, Goedert, JJ, Vlahov, D, Donfield, S. Buchbinder, SP, Troyer, J, O’Brien, SJ. Nuclear-encoded mitochondrial genes and AIDS progression. Submitted PLOSONE.

697. O’Brien, SJ. Comparative Genomics in Vertebrates: A role for Platypus. Australian Journal of Zoology, 2009, 57, vii–ix.

698. Sezgin E, Hendrickson SL, Jabs DA, Van Natta ML, Lewis RA, Troyer JL, O'Brien SJ. Effect of host genetics on incidence of HIV neuroretinal disorder in patients with AIDS. J Acquir Immune Defic Syndr. 2010 Aug 1;54(4):343-51.

699. Troyer, JL, Lautenberger, J, Nelson, GW, Pontius, J, Kessing, B, McIntosh, C, An, P, Johnson, RC, Chinn, L, Sezgin, E, Li, G, Hendrickson, SL, Donfield, S, Goedert, JJ, Phair, J, Buchbinder, S, Vlahov, D, Limou, S, Delaneau, O, Zagury, JF, Smith, M, Winkler, CA, O’Brien, SJ. PARD3B AIDS restriction discovered by genome-wide association study. Jour. Infectious Disease In press

700. Genome 10K Community of Scientists: A Proposal to Obtain Whole-genomeSsequence for 10,000 Vertebrate Species. J Hered. 2009 Nov-Dec;100(6):659-74.

701. Johnson, R, Nelson, GW, Troyer, JL, Lautenberger, JA, Kessing, BD, Winkler, CA, O’Brien, SJ. Accounting for multiple comparisons in a genome wide association study (GWAS). BMC

62 176 Genomics. In Press

702. Chinn, L, Tang, T. HDFs High-density SNP association study of host genes required for HIV-1 infection. Jour. Inf Disease. In Press.

703. Hendrickson, SL, O’Brien SJ, Nelson GW. Decorrelating association statistics for diseases with rich clinical data. submitted for publication.

704. Sezgin, E., Hendrickson, S.L., Jabs, D.A., Van Natta, M.L., Lewis, R.A., Troyer, J.L., O’Brien, S.J.: Effect of Host Genetics on Incidence of HIV Neuroretinal Disorder in Patients With AIDS. J Acquir Immune Defic Syndr. 2010 Jun 4; [Epub ahead of print]

705. Guo X, Zhang Y, Li J, Ma J, Wei Z, Tang W, O’Brien SJ. Strong Influence of HLA-DP Gene Variants on Development Persistent Chronic HBV Carriers in Chinese Han Population.

706.) An P, Winkler C, Guan L, O’Brien SJ, Zeng Z. The HBV study consortium HLA-DP variation is a major genetic determinant of hepatitis B virus infection and clearance in Chinese. . Jour. Infectious Disease In press

707.) Perelman P, Johnson WE, Roos C, Seuánez HN, Moreira MA, Horvath JE, Kessing B, Pontius J, Roelke M, Rumpler Y, Paula M, Schneider C, Silva A, O’Brien SJ, Pecon-Slattery J. Molecular Phylogeny of Primates. PLOS Genetics In Press

708.) Johnson WE, Perelman P, O’Brien SJ. Camelid genomics: Anticipating the future. Jour Camelid Science IN press

709.) da Fonseca RR, Johnson WE, O’Brien SJ, Vasconcelos V, Antunes A. Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases. BMC Evolutionary Biology 2010, 10:281 http://www.biomedcentral.com/1471-2148/10/281

710.) Guo X, Zeng Y, Deng H, Liao J, Zheng Y, Li J, Kessing B, O'Brien SJ. Genetic Polymorphisms of CYP2E1, GSTP1, NQO1 and MPO and the Risk of Nasopharyngeal Carcinoma in a Han Chinese Population of Southern China BMC Res Notes. 2010 Jul 27;3(1):212.

711.) Driscoll CA, Sanderson E, Christie S, Luo SJ, Seidensticker J, Miquelle D, Goodrich J, Dinerstein E, Shrethsta M, Zhuralev Y, Jhala YV, Yadav SP, Pikunov DG, Darman Y, Breitenmoser U, Chestin I, Jungius H, Yamaguchi N, Pereladova O, Wildt DE, Macdonald DW, O’Brien SJ. A Postulate for Tiger Recovery. Submitted to Conservation Biology

712 ) Shrestha,B Reed M, Starks PT,Kaufman, GE, Goldstone JV, Roelke ME, O’Brien SJ, Koepfli KP, Court MH. Evolution of a major drug metabolizing enzyme defect in the domestic cat and other Felidae: Phylogenetic timing and the role of hypercarnivory. Submitted

713) Sezgin E, Jabs DA, Hendrickson SL, Van Natta M, Zdanov A, Lewis RA, Smith MW, Troyer JL, O'Brien SJ. Effect of Host Genetics on the Development of Cytomegalovirus Retinitis in Patients with AIDS.J Infect Dis. 2010 Jun 25. [Epub ahead of print]

63 177

714. LUO, Shu-Jin Warren E. JOHNSON, and Stephen J. O’BRIEN. Applying molecular genetic tools to tiger conservation Integrative Zoology 2010; 5: 351-362

715. Moore, Andy, Christiaan and Hanli Winterbach3, Fenton (Woody) Cotterill4 And Stephen O’Brien EVIDENCE FOR ANCESTRAL WETLAND LIONS AND EVOLUTION OF SPECIALIZATION DRIVEN BY CLIMATIC AND GEOMORPHIC IMPERATIVES

716. Zheng Yingying, Li Guan, Stephen J. O’Brien, Zheng Zeng, the HBV study consortium APOBEC3B deletion/insertion polymorphism and hepatocellular carcinoma with hepatitis B virus infection in Chinese Han population

717 .Alkan, Can, M. Francesca Cardone, Francesca Antonacci1, Stephen J. O’Brien, Oliver A. Ryder, Stefania Purgato, Giuliano Della Valle, Evan E. Eichler, and Mario Ventura . Genome-wide Characterization of Centromeric Satellites from Multiple Mammalian Genomes

718. Guo Xiuchan , Cheryl A. Winkler, Ji Li, Li Guan, Minzhong Tang, Yi Zeng and Stephen J. O’Brien Validation of Nasopharyngeal Carcinoma (NPC) Risk Loci from Two Genome- Wide Association Studies in a Large NPC cohort 719. Menotti-Raymond, Marilyn , Victor A. David, ., Bruce S. Weir, , Stephen J. O’Brien, A Population Genetic Database of Cat Breeds Developed in Coordination with a Domestic Cat STR Multiplex Jour Forensic Sciences Submitted

720 Tang Comprehensive profiling of HLA polymorphism in Nasopharyngeal Carcinoma by a large scale study

721 Tang et al HLA Class I analysis in a high NPC incident rate region of southern Chinese population

722 Daniëlle van Manen1, Olivier Delaneau2, Neeltje A. Kootstra1, Brigitte Boeser- Nunnink1, Sophie Limou2, Sebastiaan M. Bol1, Judith Burger1, Aeilko H. Zwinderman3, Perry D. Moerland3,4, Ruben van ’t Slot5, Joshua T. Herbeck6, Jeremy Martinson7, Jennifer L. Troyer8, Stephen J. O’Brien8, James I. Mullins6, Jean-François Zagury2, Angélique B. van ‘t Wout1, and Hanneke Schuitemaker1 Genome-Wide Association Scan in HIV-1-Infected Individuals Identifying Multiple Variants Influencing Disease Course

64 178

723 Hostetler, Jeffrey A. ,David P. Onoratob, James D. Nicholsc, Warren E. Johnsond, Melody E. Roelked,e, Stephen J. O’Briend, Deborah Jansenf, Madan K. Olia Genetic Introgression and the Survival of Florida Panther Kittens Biolog Conservation In Press

724 Troyer1, Jennifer L. Melody E. Roelke1, Jillian J. Jesperson2, Natalie Baggett2, Valerie Buckley-Beason2,3, Meggan Craft4,5, Craig Packer4, Jill Pecon-Slattery2, and Stephen J. O’Brien2 FIV strain diversity and dynamics; examples from the wild

65 179

Curriculum Vitae David Haussler Investigator, Howard Hughes Medical Institute Distinguished Professor, Biomolecular Engineering, University of California, Santa Cruz Director, Center for Biomolecular Science and Engineering Affiliate, Crown College

1156 High Street, Tel: (831) 459-2105 501 Engineering 2, MS: CBSE/ITI Fax: (831) 459-1809 University of California [email protected] Santa Cruz, CA 95064 www.cbse.ucsc.edu/people/haussler

Employment 2004- Professor, Biomolecular Engineering, University of California, Santa Cruz

2000- Investigator, Howard Hughes Medical Institute

1993-2004 Professor, Computer Science, University of California, Santa Cruz

1989-1993 Associate Professor, Computer Science, University of California, Santa Cruz

1986-1989 Assistant Professor, Computer Science, University of California, Santa Cruz

1982-1986 Assistant Professor, Mathematics and Computer Science, University of Denver, CO

Education Ph.D. 1982 University of Colorado at Boulder, Computer Science Received Graduate Student Research Award

M.S. 1979 California Polytechnic State University at San Luis Obispo, Applied Mathematics Received Mathematics Award

B.A. 1975 Connecticut College, New London, CT, Mathematics Magna Cum Laude, Phi Beta Kappa, received Julia Bower Mathematics Award

Honors & Awards 2009 Curt Stern Award, American Society of Human Genetics

2009 Fellow, International Society for Computational Biology

2008 Senior Scientist Accomplishment Award, International Society for Computational Biology

2006- Member, National Academy of Sciences

2006- Fellow, American Academy of Arts and Sciences

2006 Dickson Prize in Science, Carnegie Mellon University

2005 World Technology Network Award, IT Software Category

2005 Classic Paper Award, American Association of Artificial Intelligence, for “Quantifying the inductive bias in concept learning,” 1986

Short CV 1 Last Updated 12/22/2010 180

2005 Distinguished Engineering Alumni Award, University of Colorado, Boulder

2004 Allen Newell Award, Association for Computing Machinery and the American Association for Artificial Intelligence

2003 Tech Award Laureate, San Jose Tech Museum of Innovation

2003- Fellow, American Association for the Advancement of Science

2003 Distinguished Scientist of the Year Award, Boston Biomedical/Clinical Ligand Assay Society

2001-02 UCSC Faculty Research Lecturer

2001 Featured Scientist, Incyte Genomics

2001- Fellow, California Academy of Sciences

2001 Scientist of the Year, Research and Development Magazine

2000-03 Awarded UC Presidential Chair of Computer Science

1992- Fellow, American Association of Artificial Intelligence

Publications Peer-Reviewed Journal Publications Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC cancer genomics browser: update 2011.Nucleic Acids Res. 2010 Nov 8. PMID: 21059681

Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Nov 7. PMID: 21057495

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2010 Oct 30. PMID: 21037257

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6. PMID: 21030649

1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. PMID: 20981092

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2010 Oct 18. PMID: 20959295

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to

Short CV 2 Last Updated 12/22/2010 181

profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Sep 19. PMID: 20852635

Lowe CB, Bejerano G, Salama SR, Haussler D. J Hered. Endangered species hold clues to human evolution. 2010 Jul- Aug;101(4):437-47. PMID: 20332163

Kern AD, Haussler D. A population genetic hidden Markov model for detecting genomic regions under selection. Mol Biol Evol. 2010 Jul;27(7):1673-85. PMID: 20185453

Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. PMID: 20613842.

Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010 Jun 15;26(12):i237-i245. PMID: 20529912.

Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-Biased Evolution Near Human Accelerated Regions. PLoS Genet. 2010 May 20;6(5):e1000960. PMID: 20502635.

International Cancer Genome Consortium, International network of cancer genome projects. Nature. 2010 Apr 15;464(7291):993-8.

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney, BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. PMID: 19920125.

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hilman-Jackson J, Hart RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. PMID: 19906737.

Genome 10K Community of Scientists. Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered. 2009 Nov-Dec;100(6):659-74. PMID: 19892720.

The MGC Project Team. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19(12):2324-33. PMID: 19767417.

Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23. PMID: 19498102.

Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, Kent WJ, Haussler D, Wang T. The UCSC cancer genomics browser. Nature Methods. 2009 Apr;6(4):239-40. PMID: 19333237.

Han J, Pedersen JS, Kwon SC, Belair CD, Kim YK, Yeom KH, Yang WY, Haussler D, Blelloch R, Kim VN. Posttranscriptional crossregulation between Drosha and DGCR8.Cell. 2009 Jan 9;136(1):75-84. PMID: 19135890.

Kuhn, RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC genome browser database: update 2009. Nucleic Acids Res. 2009 Jan;37:D755-61. PMID: 18996895.

Short CV 3 Last Updated 12/22/2010 182

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. BMC Genomics. 2008 October 8;9:466. PMID: 18842134.

Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14254-61. PMID: 18787111.

Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol. 2008 Oct;15(8):1007-27. PMID: 18774902.

Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods Mol Biol. 2008;422:171-84. PMID: 18629667.

Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC genome browser. Methods Mol Biol. 2008;422:133-44. PMID: 18629665.

Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. UCSC genome browser tutorial. Genomics. 2008 Aug;92(2):75- 84. PMID: 18514479.

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar1;24(5):637-44. PMID: 18218656.

Zeng J, Yan J, Wang T, Mosbrook-Davis D, Dolan KT, Christensen R, Stormo GD, Haussler D, Lathrop RH, Brachmann RK, Burgess SM. Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. Nucleic Acids Res. 2008 Jan;36(1):e8. PMID: 18086703.

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC genome browser database: 2008 update. Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9. PMID: 18086701.

Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. Comparative genomics search for losses of long- established genes on the human lineage. PLoS Comput Biol. 2007 Dec;3(12):e247. PMID: 18085818.

Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci USA. 2007 Nov 20;104(47):18613-8. PMID: 18003932.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 8;450(7167):219-32. PMID: 17994088.

Karolchik D, Bejerano G, Hinrichs AS, Kuhn RM, Miller W, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Comparative genomic analysis using the UCSC genome browser. Methods Mol Biol. 2007;395:17-34. PMID: 17993665.

Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D, Brent MR. Targeted discovery of novel human exons by comparative genomics. Genome Res. 2007 Dec;17(12):1763-73. PMID: 17989246

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-Way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. 2007 Dec;17(12):1797-808. PMID: 17984227.

Short CV 4 Last Updated 12/22/2010 183

Yeang CH, Haussler D. Detecting co-evolution in and among protein domains. PLoS Comput Biol. 2007 Nov;3(11):e211. PMID: 17983264.

Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct;17(10):1420-30. PMID: 17785536.

Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. Human genome ultraconserved elements are ultraselected. Science. 2007 Aug 17;317(5840):915. PMID: 17702936.

Yeang CH, Darot JF, Noller HF, Haussler D. Detecting the coevolution of biosequences-an example of RNA interaction prediction. Mol Biol Evol. 2007 Sep;24(9):2119-31. PMID: 17636042.

ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. PMID: 17571346.

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun;17(6):760-74. PMID: 17567995.

Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci USA. 2007 May 8;104(19):8005-10. PMID: 17463089.

Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13;316(5822):222-34. PMID: 17431167.

Ohlson J, Pedersen JS, Haussler D, Ohman M. Editing modifies the GABA(A) receptor subunit alpha 3.RNA. 2007 May;13(5):698-703. PMID: 17369310

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ. The UCSC genome browser database: update 2007. Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73. PMID: 17142222.

Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS; ENCODE Project Consortium; Haussler D, Kent WJ. The ENCODE Project at UCSC. Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7. PMID: 17166863.

Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM, Haussler D, Kent WJ. Variation resources at UCSC. Nucleic Acids Res. 2007 Jan;35(Database issue)716-20. PMID: 17151077.

Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom K, Kent W J, Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13;2(10):e168. PMID: 17040131.

Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Reconstructing contiguous regions of an ancestral genome. Genome Res. 2006 Dec;16(12):1557-65. PMID: 16983148.

Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14;443(7108):167-72. PMID: 16915236.

Short CV 5 Last Updated 12/22/2010 184

Wu J, Haussler D. Coding exon detection using comparative sequences, J Comput Biol. 2006 Jul-Aug;13(6):1148-64. PMID: 16901234.

Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC known genes. Bioinformatics. 2006 May 1;22(9):1036-46. PMID: 16500937.

Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent WJ, Miller W, Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr 2;(4):e33. PMID: 16628248.

Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4;441(7089):87-90. PMID: 16625209.

Sugnet CW, Srinivasan K, Clark TA, O’Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, Ares M. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol. 2006 Jan;2(1):e4. PMID: 16424921.

Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M., Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan- Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC genome browser database: update 2006. Nucleic Acids Res. 2006 Jan;34(Database issue):D590-8. PMID: 16381938.

Lucena B, Haussler D. Counterexample to a claim about the reconstruction of ancestral character states. Syst Biol. 2005 Aug;54(4):693-5. PMID: 16126665.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, , worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819.

Bejerano G, Siepel AC, Kent WJ, Haussler D. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods. 2005 Jul;2(7):535-45. PMID: 16170870.

Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15;21(12):2814-20. PMID: 15827081.

Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005 May;15(5):737-41. PMID: 15867434.

Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol. 2005 Jan;3(1):e5. PMID: 15630477.

Hsu F, Pringle TH, Kuhn RM, Karolchik D, Diekhans M, Haussler D, Kent WJ. The UCSC proteome browser. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D454-8. PMID: 15608236.

Blanchette M, Green ED, Miller W, Haussler D. Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res. 2004 Dec;14(12):2412-23. PMID: 15574820.

International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716. PMID: 15592404.

MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. PMID: 15489334.

ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA Elements Project.Science. 2004 Oct 21;306(5696):636-40. PMID: 15499007.

Short CV 6 Last Updated 12/22/2010 185

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931-45. PMID: 15496913.

Furey TS, Diekhans M, Lu Y, Graves TA, Oddy L, Randall-Maher J, Hillier LW, Wilson RK, Haussler D. Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Res. 2004 Oct;14(10B):2034-40. PMID: 15489323.

She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. The structure and evolution of centromeric transition regions within the human genome. Nature. 2004 Aug 19;430(7002):857-64. PMID: 15318213.

Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics. 2004 Aug 4;20 Suppl 1:I161-8. PMID: 15262795.

Bejerano G, Haussler D, Blanchette M. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics. 2004 Aug 4;20 Suppl 1:I40-8. PMID: 15262779.

Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science. 2004 May 28;304(5675):1321-5. PMID: 15131266.

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521. PMID: 15057822.

Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC. Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res. 2004 Apr;14(4):517-27. PMID: 15059992.

Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 2004 Apr;14(4):528-38. PMID: 15059993.

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014.

Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biol. 2004;5(4):R23. PMID: 15059256.

Roskin KM, Diekhans M, Haussler D. Score functions for determining regional conservation in two-species local alignments. J Comput Biol. 2004 Mar;11(2-3):395-411. PMID: 15285898.

Siepel A, Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol. 2004 Mar;11(2-3):413-28. PMID: 15285899.

Siepel A, Haussler D. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol. 2004 Mar;21(3):468-88. PMID: 14660683.

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. UCSC table browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. PMID: 14681465.

Margulies EH, Blanchette M, Haussler D, Green ED; NISC Comparative Sequencing Program. Identification and characterization of multi-species conserved sequences. Genome Res. 2003 Dec;13(12):2507-18. PMID: 14656959.

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA. 2003 Sep 30;100(20):11484-9. PMID: 14500911.

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan

Short CV 7 Last Updated 12/22/2010 186

R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003 Aug 14;424(6950):788-93. PMID: 12917688.

Furey TS, Haussler D. Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet. 2003 May 1;12(9):1037-44. PMID: 12700172.

Winters-Hilt S, Vercoutere W, DeGuzman VS, Deamer D, Akeson M, Haussler D. Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophys J. 2003 Feb;84(2Pt1):967-76. PMID: 12547778.

Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 2003 Jan;13(1):13-26. PMID: 12529302.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312.

Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC genome browser database. Nucleic Acids Res. 2003 Jan:31(1):51-4. PMID: 12519945.

The Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 5;420(6915):520-62. PMID: 12466850.

Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers RG Jr, Haussler D. Information-theoretic dissection of pair-wise contact potentials. Proteins. 2002 Oct 1;49(1):7-14. PMID: 12211011.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. PMID: 12045153.

Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics. 2002 Jan;18(1):147-59. PMID: 11836223.

Kent WJ, Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Res. 2001 Sep;11(9):1541-8. PMID: 11544197.

Vercoutere W, Winters-Hilt S, Olsen H, Deamer D, Haussler D, Akeson M. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol. 2001 Mar;19(3):248-52. PMID: 11231558.

The BAC Resource Consortium. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001 Feb 15;409(6822):953-8. PMID: 11237021.

The International Human Genome Mapping Consortium. A physical map of the human genome. Nature. 2001 Feb 15;409(6822):934-41. PMID: 11237014.

The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921. PMID: 11237011.

Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000 Oct;16(10):906-14. PMID: 11120680.

Short CV 8 Last Updated 12/22/2010 187

Reese MG, Kulp D, Tammana H, Haussler D. Genie--gene finding in Drosophila melanogaster. Genome Res. 2000 Apr;10(4):529-38. PMID: 10779493.

Jaakkola T, Diekhans M, Haussler D. A discriminative framework for detecting remote protein homologies. J Comput Biol. 2000 Feb-Apr;7(1-2):95-114. PMID: 10890390.

Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA. 2000 Jan 4;97(1):262-7. PMID: 10618406.

Spingola M, Grate L, Haussler D, Ares M Jr. Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA. 1999 Feb;5(2):221-34. PMID: 10024174.

Haussler D. Computational genefinding. Trends in Biochemical Sciences, Supplementary Guide to Bioinformatics. 1998;23(1):12-15.

Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol. 1998 Dec 11;284(4):1201-10. PMID: 9837738.

Haussler D, Kivinen J, Warmuth M. Sequential prediction of individual sequences under general loss functions. IEEE Transactions on Information Theory, 1998 Sep;44(5):1906-25.

Cesa- N, Haussler D. A graph-theoretic generalization of the Sauer-Shelah lemma. Discrete Applied Mathematics. 1998 Aug;86(1):27-35.

Haussler D, Opper M. Mutual information, metric entropy, and cumulative relative entropy risk. Annals of Statistics. 1997 Dec;25(6):2451-92.

Karplus K, Sjölander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. Predicting protein structure using hidden Markov models. Proteins. 1997;29(Suppl 1):134-9. PMID: 9485505.

Reese MG, Eeckman FH, Kulp D, Haussler D. Improved splice site detection in Genie. J Comput Biol.1997 Fall;4(3):311- 23. PMID: 9278062.

Cesa-Bianchi N, Freund Y, Haussler D, Helmbold D, Schapire R, Warmuth M. How to use expert advice. J. ACM. 1997 Jul;44(3):427-85.

Alon N, Ben-David S, Cesa-Bianchi N, Haussler D. Scale-sensitive dimensions, uniform convergence, and learnability. Journal of the ACM 1997 Jul;44(4):615-31.

Haussler D. A general minimax result for relative entropy. IEEE Transactions on Information Theory. 1997 Jul;43(4):1276- 80.

Haussler D, Kearns M, Seung HS, Tishby N. Rigorous learning curve bounds from statistical mechanics. Machine Learning. 1996 Nov;25(2/3):195-236.

Fayyad U, Haussler D, Stolorz P. Mining scientific data. Communications of the ACM, 1996 Nov;39(11):51-7.

Sjölander K, Karplus K , Brown M, Hughey R, Krogh A, Mian IS, Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci. 1996 Aug;12(4):327-45. PMID: 8902360.

Opper M, Haussler D. Bounds for predictive errors in the statistical mechanics of supervised learning. Phys Rev Lett. 1995 Nov 13;75(20):3772-5. PMID 10059723.

Haussler D, Long PM. A generalization of Sauer's lemma. Journal of Combinatorial Theory Series A. 1995 Aug;71(2):219- 40.

Short CV 9 Last Updated 12/22/2010 188

Knill E, Ehrenfeucht A, Haussler D. The Size of K-pseudotrees. Discrete Mathematics 1995 May;141(1-3):185-94.

Haussler D. Sphere packing numbers for subsets of the Boolean n-cube with bounded Vapnik-Chervonenkis dimension. Journal of Combinatorial Theory Series A. 1995 Feb;69(2):217-32.

Ben-David S, Cesa-Bianchi N, Haussler D, Long P. Characterizations of learnability for classes of {0,...,n}-valued functions. Journal of Computer Systems Science. 1995;50(1):74-86.

Haussler D, Littlestone N, Warmuth M. Predicting 0,1-functions on Randomly Drawn Points. Information and Computation. 1994 Dec;115(2):248-92.

Sakakibara Y, Brown M, Hughey R, Mian IS, Sjölander K, Underwood RC, Haussler D. Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res. 1994 Nov 25;22(23):5112-20. PMID: 7800507.

Krogh A, Mian IS, Haussler D. A hidden Markov model that finds genes in E-coli DNA. Nucleic Acids Res. 1994 Nov 11;22(22):4768-78. PMID: 7984429.

Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. Hidden Markov models in computational biology. applications to protein modeling. J Mol Biol. 1994 Feb;235(5):1501-31.

Haussler D, Kearns M, Schapire R. Bounds on the sample complexity of Bayesian learning using information theory and the VC dimension. Machine Learning. 1994 Jan;4(1):83-114.

Haussler D. Decision Theoretic Generalizations of the PAC model for neural net and other learning applications. Information and Computation. 1992 Sept;100(1):78-150.

Opper M, Haussler D. Generalization performance of Bayes optimal prediction algorithm for learning a perceptron. Physical Review Letters. 1991 May;66(20):2677-81.

Haussler D, Kearns M, Littlestone N, Warmuth M. Equivalence of models of polynomial learnability. Information and Computation. 1991 Dec;95(2):129-61.

Pagallo G, Haussler D. Boolean feature discovery in empirical learning. Machine Learning, 1990 Mar;5(1):71-99.

Ehrenfeucht A, Haussler D. Learning decision trees from random examples. Information and Computation. 1989 Sep;82(3):231-46.

Blumer A, Ehrenfeucht A, Haussler D. Average sizes of suffix trees and DAWGs. Discrete Applied Mathematics. 1989;24(1):37-45.

Baum E, Haussler D. What size net gives valid generalization. Neural Computation. 1989;1(1):151-60.

Haussler D. Learning conjunctive concepts in structural domains. Machine Learning. 1989 Oct;4(1):7-40.

Blumer A, Ehrenfeucht A, Haussler D, Warmuth M. Learnability and the Vapnik-Chervonenkis dimension. Journal of the ACM. 1989 Oct;36(4):929-65.

Ehrenfeucht A, Haussler D, Kearns M, Valiant L. A general lower bound on the number of examples needed for learning. Information and Computation. 1989 Sep;82(3):247-61.

Ehrenfeucht A, Haussler D. A new distance metric on strings computable in linear time. Discrete Applied Mathematics. 1988;20(3):191-203.

Haussler D. Quantifying inductive bias: AI learning algorithms and valiant’s learning framework. Artificial Intelligence. 1988;36(2):177-221.

Ehrenfeucht A, Haemer J, Haussler D. Quasi-monotonic sequences: theory, algorithms and applications. SIAM J Alg and Disc Meth. 1987;8(3):410-29.

Short CV 10 Last Updated 12/22/2010 189

Blumer A, Ehrenfeucht A, Haussler D, Warmuth M. Occam’s razor. Inf Proc Let. 1987 Apr;24(6):377-80.

Haussler D, Welzl E. Epsilon-nets and simplex range queries. Discrete and Computational Geometry. 1987;2(2):127-51.

Blumer A, Blumer J, Ehrenfeucht A, Haussler D, McConnell R. Complete inverted files for efficient text retrieval and analysis. J. ACM. 1987;34(3):578-89.

Main MG, Bucher W, Haussler D. Applications of an infinite square-free co-CFL. Theoretical Computer Science. 1987;49(2,3):113-20.

Clift B, Haussler D, McConnell R, Schneider TD, Stormo GD. Sequence landscapes. Nucleic Acids Res. 1986 Jan10;14(1):141-58. PMID: 3753762.

Edelsbrunner H, Haussler D. The complexity of cells in three dimensions. Discrete Mathematics. 1986;60(1):139-46.

Bucher W, Ehrenfeucht A, Haussler D. On total regulators generated by derivation relations. Theoretical Computer Science. 1985;40(0):131-48.

Haussler D. Another generalization of Higman’s well-quasi-order result on a finitely generated free monoid. Discrete Mathematics. 1985;57(3):237-43.

Blumer A, Blumer J, Haussler D, Ehrenfeucht A, Chen MT, Seiferas J. The smallest automaton recognizing the subwords of a text. Theoretical Computer Science. 1985;40(1):31-56.

Warmuth M, Haussler D. On the complexity of iterated shuffle. Journal Computer Systems Science. 1984 Jun;28(3):345- 58.

Ehrenfeucht A, Haussler D, Rozenberg G, Zeiger P. On DOS mappings and DOS languages. Semigroup Forum. 1984;29(1):123-48.

Ehrenfeucht A, Haussler D, Rozenberg G. On ambiguity in DOS systems. RAIRO Informatique Theorique. 1984;18(1):279-95.

Ehrenfeucht A, Haussler D, Rozenberg G. On regularity of context-free languages. Theoretical Computer Science. 1983;27(3):311-32.

Haussler D. Insertion languages. Information Sciences. 1983;31:77-89.

Haussler D. Model Completeness of an algebra of languages. Proc. Amer. Math. Soc. 1981;83(2):371-3.

Haussler D, Zeiger P. Very special languages and representations of recursively enumerable languages. Information and Control. 1980;47(3):201-11.

Brumbaugh P, Haussler D, Bressler R, Haussler M. Radio receptor assay for 1 alpha, 25-dihydroxyvitamin D3. Science. 1974;183(3):1089-91. PMID: 48120383

Book Chapters Siepel A, Haussler D. Phylogenetic hidden Markov models. In Nielsen R (ed): Statistical Methods in Molecular Evolution, Springer, 2004.

Haussler D, Opper M. Metric entropy and minimax risk in classification. In Mycielski J, Rozenberg G, Salomaa A (eds): Lecture Notes in Computer Science: Studies in Logic and Computer Science, 1997:1261:212-35.

Haussler D, Barron A. How well do Bayes methods work for on-line prediction of +1,-1 values? In Proceedings of the Third NEC Symposium on Computation and Cognition, SIAM, Princeton, NJ, 1992:74-100.

Short CV 11 Last Updated 12/22/2010 190

Haussler D. Decision theoretic generalizations of the PAC model for neural net and other learning applications. In Workshop on Supervised Learning, Santa Fe Institute Press, 1995.

Haussler D, Warmuth M. The probably approximately correct (PAC) and other learning models. In Workshop on Supervised Learning, Santa Fe Institute Press, 1995.

Haussler D, Warmuth M. The probably approximately correct (PAC) and other learning models. In Meyrowitz A, Chipman S (eds): Machine Learning: Induction, Analogy and Discovery.

Haussler D. Generalizing the PAC model. In Mehra P, Wah BW (eds): Artificial Neural Networks: Concepts and Theory, IEEE Society Press, 1992.

Haussler D. PAC learning and generalization. In Smolensky P, Mozer M, Rumelhart D (eds): Mathematical Perspectives on Neural Networks.

Haussler, D. Occam’s razor; Quantifying inductive bias: AI learning algorithms and Valiant’s learning framework; and what size net gives valid generalization. Reprinted in Shavlik J, Dietterich T (eds): Readings in Machine Learning, Morgan Kaufmann, Los Altos, CA, 1990.

Haussler D. Applying Valiant’s learning framework to AI concept learning problems. In Michalski R, Kodratoff Y. (eds): Machine Learning: An Artificial Intelligence Approach, Vol. III, Morgan Kaufmann, Los Altos, 1990:641-69.

Conference Papers Darot J, Yeang CH, Haussler D. Detecting the dependent evolution of biosequences. Proceedings of the 10th International Conference on Research in Computational Molecular Biology, RECOMB, 2006.

Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection. Proceedings of the 10th International Conference on Research in Computational Molecular Biology, RECOMB, 2006.

Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W. Global predictions and tests of erythroid regulatory regions. Cold Spring Harbor Symposium, Quant. Biology, 2003:68:335-44.

Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D. The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harbor Symposium, Quant. Biology, 2004:68:245-54.

Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. Proceedings of the 8th International Conference on Research in Computational Molecular Biology, RECOMB, 2004:177-86.

Jojic V, Jojic N, Meek C, Geiger D, Siepel A, Haussler D, Heckerman D. Efficient approximations for learning phylogenetic HMM models from data. Proceedings of ISMB 2004 and Bioinformatics, 2004.

Siepel A, Haussler D. Computational identification of evolutionarily conserved exons. Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology, RECOMB, 2004.

Sugnet CW, Kent WJ, Ares M Jr, Haussler D. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pacific Symposium on Biocomputing (PSB), 2004. [Online Proceedings]

Wang H, Hubbell E, Hu JS, Mei G, Cline M, Lu G, Clark T, Saini-Rose MA, Ares M, Kulp DC, Haussler D. Gene-structure- based splice variant deconvolution using a microarray platform. Proceedings of ISMB and Bioinformatics, 2003:19(Suppl. 1):i315-22.

Roskin KM, Diekhans M, Haussler D. Scoring two-species local alignments to statistically separate neutrally evolving from selected DNA segments. Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology, RECOMB, 2003:257-66.

Short CV 12 Last Updated 12/22/2010 191

Siepel A, Haussler D. Combining phylogenetic and hidden Markov models in biosequence analysis. Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology, RECOMB, 2003:277-86.

Rogic S, Furey TS, Kent WJ, Haussler D. Human genetic discovery using STS markers and the draft assembly browser. Proceedings of Genome Sequencing and Biology, Cold Spring Harbor, NY, May 2001:221.

Furey TS, Rogic S, Kent WJ, and Haussler D. From STS and cytogenetic maps to the human genome assembly and back. Proceedings of Genome Sequencing and Biology, Cold Spring Harbor, NY, May 2001:76.

Pavlidis P, Furey T, Liberto M, Haussler D, Grundy WN. Promoter region-based classification of genes. Proceedings of the Pacific Symposium on Biocomputing, HI, 2000.

Haghighi F, Diekhans M, Haussler D, Grundy WN. Discriminative gene finding methods. Genome Sequencing and Biology, Cold Spring Harbor, NY, May 2000.

Kent WJ, Kulp D, Wheeler R, Reese M, Zahler A, Haussler D. Alternate splicing of human genes. Genome Sequencing and Biology, Cold Spring Harbor, NY, May 2000.

Jaakkola T, Diekhans M, Haussler D. Using the Fisher kernel method to detect remote protein homologies. Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology, AAAI Press, 1999:149-158. [Winner of best paper award]

Lazareva-Ulitsky B, Haussler D. A probabilistic approach to consensus multiple alignment. Proceedings of the Pacific Symposium on Biocomputing, World Scientific Press, 1999:150-61.

Jaakkola T, Haussler D. Probabilistic kernel regression models. Proceedings of 7th Workshop on Artificial Intelligence and Statistics, 1998.

Jaakkola T, Haussler D. Exploiting generative models in discriminative classifiers. Advances in Neural Information Processing Systems, 1998.

Opper M, Haussler D. Worst case prediction over sequences under log loss. The Mathematics of Information Coding, Extraction and Distribution, Cybenko G, O’Leary D, Rissanen J, eds., Springer Verlag, 1997.

Reese M, Eeckman F, Kulp D, Haussler D. Improved splice site detection in genie. 1st International Conference on Computational Molecular Biology, Santa Fe, NM, 1997.

Kulp D, Haussler D, Reese M, Eeckman F. Integrating database homology in a probabilistic gene structure model. Pacific Symposium on Biocomputing, World Scientific Press, HI, 1997.

Haussler D. A brief look at some machine learning problems in genomics. Proceedings of the 10th Annual Computational Learning Theory Conference, ACM Press, Santa Cruz, CA, 1997:109-13.

Fayyad U, Haussler D, Stolorz P. KDD for science data analysis: issues and examples. Proc.3rd International Conference on Knowledge Discovery and Data Mining, Portland, OR, 1996.

Kulp D, Haussler D, Reese M, Eeckman F. A generalized hidden Markov model for the recognition of human genes in DNA. 4th International Conference on Intelligent Systems in Molecular Biology, St. Louis, MO, AAAI/MIT Press, June 1996.

Mirelli V, Haussler D. A hybrid parametric/case-based approach to object recognition using Bayes decision theory. Proceedings of SPIE Symposium on Electronic Imaging: Science and Technology, San Jose, CA, February 1996.

Gulko B, Haussler D. Using multiple alignments and phylogenetic trees to detect RNA secondary structure. Proceedings of the Pacific Symposium on Biocomputing, pp. 350-367, L. Hunter and T. Klein, eds., World Scientific Press, January 1996: 350-67.

Short CV 13 Last Updated 12/22/2010 192

Haussler D. A generalized hidden Markov model for DNA parsing. extended abstract of talk for the Workshop on Gene- Finding and Gene Structure Prediction, University of Pennsylvania, October 1995.

Opper M, Haussler D. General bounds for predictive errors in supervised learning. Proceedings of the Workshop on the Theory of Neural Networks: The Statistical Mechanics Perspective, World Scientific Press, 1995:51-8.

Haussler D, Opper M. Mutual information and Bayes methods for learning a distribution. Proceedings of the workshop on the Theory of Neural Networks: The Statistical Mechanics Perspective, World Scientific Press, 1995:42-50.

Haussler D, and Opper M. General bounds on the mutual information between a parameter and n conditionally independent observations. Proceedings of the Eighth Annual Computational Learning Theory Conference (COLT), Santa Cruz, CA, ACM Press, 1995:402-11.

Haussler D, Kivinen J, Warmuth M. Tight worst-case loss bounds for predicting with expert advice. Proceedings of the European Conference on Computational Learning Theory (EUROCOLT), 1994.

Haussler D, Kearns M, Seung HS, Tishby N. Rigorous learning curve bounds from statistical mechanics. Proceedings of the 7th ACM Conference on Computational Learning Theory, ACM Press, 1994.

Stormo G, Haussler D. Optimally parsing a sequence into different classes based on multiple types of evidence. 2nd International Conference on Intelligent Systems in Molecular Biology, Menlo Park, CA, AAAI/MIT Press, 1994:369-75.

Grate L, Herbster M, Hughey R, Haussler D, Mian IS, Noller H. RNA Modeling using Gibbs sampling and stochastic context-free grammars. 2nd International Conference on Intelligent Systems in Molecular Biology, Menlo Park, CA, AAAI/MIT Press, August 1994:138-46.

Sakakibara Y, Brown M, Hughey R, Mian IS, Sjölander K, Underwood R, Haussler D. Stochastic context-free grammars for modeling RNA. Proceedings of the Hawaii International Conference on System Sciences, Los Alamitos, CA, IEEE Computer Society Press, 1994.

Sakakibara Y, Brown M, Hughey R, Mian IS, Sjölander K, Underwood R, Haussler D. Recent methods for RNA modeling using stochastic context-free grammars. Proceedings of the Asilomar Conference on Combinatorial Pattern Matching, Springer-Verlag publisher, New York, NY, 1994.

Alon N, Ben-David S, Cesa-Bianchi N, Haussler D. Scale-sensitive dimensions, uniform convergence, and learnability. 34th IEEE Symposium on Foundations of Computer Science, Palo Alto, CA, October 1993.

Haussler D. Dirichlet mixture priors for hidden Markov models. Joint Meeting of the American Statistical Association, San Francisco, CA, August 1993.

Brown M, Hughey R, Mian IS, Sjölander K, Underwood R, Haussler D. Using Dirichlet mixture priors to derive hidden Markov models for protein families. First International Conference on Intelligent Systems for Molecular Biology, Washington, DC, July 1993.

Barron A, Clarke B, Haussler D. Information bounds for the risk of Bayesian predictions and the redundancy of universal codes. International Symposium on Information Theory, San Antonio, TX, January 1993.

Krogh A, Mian IS, Haussler D. Parsing DNA with hidden Markov models. Alternative Readings of the Genetic Code, Parknasilla, County Kerry, Ireland, May 1993.

Haussler D, Krogh A, Brown M, Mian IS, Sjölander K. Protein modeling with hidden Markov models: an analysis of globins. 26th Hawaii Systems Conference, January 1993. [Awarded best paper in AI methods in biotechnology track]

Cesa-Bianchi N, Freund Y, Helmbold D, Haussler D, Schapire R, Warmuth M. How to use expert advice, (extended abstract), 25th ACM Symposium on Theoretical Computer Science (STOC), 1993:382-91.

Haussler D, Krogh A. DNA Alignment and clustering. Neural Networks for Computing, Snowbird, UT, Sandi von Pier (ed), AT&T Bell Laboratories, Crawfords Corner Road, Rm. 4E-422, Holmdel, NJ 07733. April 7, 1992.

Short CV 14 Last Updated 12/22/2010 193

Haussler D, Barron A. How well do Bayes methods work for on-line prediction of +1,-1 values? 3rd NEC Symposium on Computation and Cognition, Princeton, NJ, 1992.

Haussler D, Kearns M, Opper M, Schapire R. Estimating average-case learning curves using Bayesian, statistical physics and VC dimension methods. 5th Conference on Neural Information Processing Systems, Denver, CO, 1991.

Freund Y, Haussler D. Unsupervised learning of distributions on binary vectors using two-layer networks. 5th Conference on Neural Information Processing Systems, Denver, CO, 1991.

Haussler D, Kearns M, Schapire R. Bounds on the sample complexity of Bayesian learning using information theory and the VC dimension. 4th Workshop on Computational Learning Theory (COLT), Santa Cruz, CA, August 1991:61-74.

Opper M, Haussler D. Calculation of the learning curve of Bayes optimal classification algorithm for learning a perceptron with noise. 4th Workshop on Computational Learning Theory (COLT), Santa Cruz, CA, August 1991:75-87.

Haussler D. Uniting the VC and TLS theories of generalization. Neural Networks for Computing, Snowbird, UT, April 1991.

Haussler D, Long P. A generalization of Sauer’s lemma. Southeastern Conference on Combinatorics, Graph Theory and Computing, Baton Rouge, LA, February 1991.

Haussler D. Probably approximately correct learning. AAAI, 1990:1101-8.

Haussler D. Sample size bounds for training multi-layer nets of quasi-linear, product and radial basis functions. Neural Networks for Computing, Snowbird, UT, April 1990.

Haussler D, Warmuth M. Analyzing the performance of learning algorithms. ONR Workshop on Knowledge Acquisition, Crystal City, VA, November 1989.

Milosavljevic A, Haussler D, and Jurka J. Parsimonious classification of aligned molecular sequences. Bio-Matrix, White Mountain Conference Center, Waterville Valley, NH, August 1989.

Haussler D. Generalizing the PAC Model: Sample size bounds from metric dimension-based uniform convergence results. 1989 IEEE Symp. on Foundations of Computer Science (FOCS), Research Triangle, NC, October 1989;40-5.

Milosavljevic A, Haussler D, Jurka J. Informed parsimonious inference of prototypical genetic sequences. 2nd Workshop on Computational Learning Theory, Santa Cruz, CA, August 1989.

Pagallo G, Haussler D. Two algorithms that learn DNF by discovering relevant features. 6th International Workshop on Machine Learning, Cornell University, Ithaca, NY, July 1989.

Baum E, Haussler D. What size net gives valid generalization. IEEE Conference on Neural Information Processing Systems, Denver, CO, November 1988.

Haussler D, Littlestone N, Warmuth M. Predicting 0,1-functions on randomly drawn points. 29th IEEE Symposium on Foundations of Computer Science, White Plains, NY, October 1988:100-9.

Haussler D, Kearns M, Littlestone N, Warmuth M. Equivalence for models of polynomial learnability. 1st Workshop on Computational Learning Theory, MIT, Cambridge, MA, August 1988.

Ehrenfeucht A, Haussler D. Learning decision trees from random examples. 1st Workshop on Computational Learning Theory, MIT, Cambridge, MA, August 1988.

Ehrenfeucht A, Haussler D, Kearns M, Valiant L. A general lower bound on the number of examples needed for learning. First Workshop on Computational Learning Theory, MIT, Cambridge, MA, August 1988.

Haussler D. Learning conjunctive concepts in structural domains. AAA, Seattle, WA, July 1987:466-70.

Short CV 15 Last Updated 12/22/2010 194

Haussler D. Bias, Version spaces and Valiant’s learning framework. 4th International Workshop on Machine Learning, Irvine, CA, June 1987.

Alon N, Haussler D, Welzl E. Partitioning and geometric embedding of range spaces of finite Vapnik-Chervonenkis dimension. 3rd International Conference on Computational Geometry, Waterloo, Canada, June 1987:331-40.

Blumer A, Ehrenfeucht A, Haussler D. Average sizes of suffix trees and DAWGs. 1st Montreal Conference on Combinatorics and Computer Science, University of Montreal, Canada. May 1987.

Haussler D. Learning internal disjunctive concepts. 20th Asilomar Conference on Signals, Systems and Computers, Pacific Grove, CA. November 1986.

Haussler D. Quantifying the inductive bias in concept learning. AAAI, Philadelphia, PA, August, 1986.

Haussler D, Welzl E. Range spaces and Epsilon-nets. SIAM Workshop on Computational and Discrete Geometry, Santa Cruz, CA, July 1986.

Haussler D. A methodology for assessing the learnability of knowledge structures. 1st Annual Rocky Mountain Conference on Artificial Intelligence, Boulder, CO, June 1986.

Haussler D, Welzl E. Epsilon-nets and simplex range queries. 2nd International Conference on Computational Geometry, Yorktown Heights, NY, June 1986.

Blumer A, Ehrenfeucht A, Haussler D, Warmuth M. Classifying learnable geometric concepts with the Vapnik- Chervonenkis dimension. 18th ACM Symposium on Theoretical Computational Science, Berkeley, CA, May 1986:273-82.

Bucher W, Ehrenfeucht A, Haussler D. On total regulators generated by derivation relations. Proc. 12th International Coll. Aut. Lang. Prog, Nafplion, Greece, July 1985:71-9.

Main MG, Bucher W, Haussler D. Applications of an infinite squarefree co-CFL. Proc. 12th International Coll. Aut. Lang. Prog., Nafplion, Greece, July 1985:404-12.

Blumer A, Blumer J, Ehrenfeucht A, Haussler D, McConnell R. Building the minimal DFA for the set of all subwords of a word on-line in linear time. Proc. 11th International Coll. Aut. Lang. Prog., Antwerp, Belgium, July 1984:109-18.

Blumer A, Blumer J, Ehrenfeucht A, Haussler D, McConnell R. Building a complete inverted file for a set of text files in linear time. Proceedings of the 16th ACM Symposium on Theoretical Computational Science, Washington, D.C., May 1984:349-58.

Ehrenfeucht A, Rozenberg G, Haussler D. Conditions enforcing regularity of context-free languages. Proc. 9th Int. Coll. Aut. Lang. Prog., Aarhus, Denmark, July 1982:187-91.

Non-refereed Papers Roskin KM, Diekhans M, Kent, WJ, Haussler D. Score functions for assessing conservation in locally aligned regions of DNA from two species. University of California, Santa Cruz, Santa Cruz, CA Tech Report UCSC-CRL-02-30. Sep, 2002.

Haussler D. The challenge of bioinformatics. R&D Magazine. 2001 Nov;43(11):8S-SC3 (in conjunction with Scientist of the Year Award).

Haussler D, Jaakkola T, Winters-Hilt S. Tradeoffs between generative and discriminative hidden Markov models. Computer Science Department, University of California, Santa Cruz, Santa Cruz, CA. 1998.

Professional Activity Invited Conference Lectures 2010

Short CV 16 Last Updated 12/22/2010 195

“Genomics and the Genome 10K Project, invited speaker, Chance and Necessity in Evolution, International Union of Biological Sciences & Istituto per gli Studi Filosofici of Naples, Ravello, Italy, October

“Cancer Genomics and the TCGA project,” invited speaker, Molecular Diagnostics in Cancer Therapeutic Development, American Association for Cancer Research, Denver, CO. September.

“Cancer Genomics Data Analysis,” invited speaker, Pfizer, Cancer Genomics Data Analysis, San Diego, CA. August.

“Cancer Genomics Data Analysis,” invited speaker, Moore’s UCSD Cancer Center, Translational Onocology Symposium, San Diego, CA. August.

“Comparative Genomics and the Genome 10K Project” invited speaker, American Genetic Association, Conservation Genomics, Hilo, Hi. July

“$1000 Genomes,” invited speaker, HiTSeq, Intelligent Systems for Molecular Biology, Boston, MA. July.

“$100 Genomes,” invited speaker, Jason Study, The MITRE Corporation, San Diego, CA. June

“Cactus graphs for genome comparisons,” invited speaker, CASB-16, University of California San Diego, San Diego, CA. May.

”Rearranging genomes,” invited speaker, RECOMB be 2010, University of California San Diego, San Diego, CA. May.

“TCGA data analysis pipeline,” invited speaker, The Cancer Genome Atlas Steering Committee. Bethesda, MD. April.

“Comparative genomics for vertebrates,” invited speaker, National Human Genome Research Institute Informatics and Analysis Planning Meeting, Bethesda, MD. April.

“Data analysis and dissemination,” invited speaker, American Association for Cancer Research Annual Meeting 2010, The Cancer Genome Atlas. Washington, DC. April.

“The Genome 10K Project: a genetic map of 10,000 species,” invited speaker, University of California, Santa Cruz Women's Club, Santa Cruz , CA. March.

“Mapping cancer genomics data to pathways,” invited speaker, Cancer Profiling and Pathways Conference, San Francisco, CA. February.

2009 “The supercomputing challenge to decode the evolution and diversity of our genomes,” invited speaker, Supercomputing 2009 Conference, Portland, OR. November.

“Genomes in the Clouds: UCSC genomics browsers and distributed bio computation,” invited speaker, Supercomputing 2009 Conference, Portland, OR. November.

“Cancer Genomics: the informatics of discovery from billions of measurements,” featured speaker, UCSF Biomedical Sciences Seminar Series, San Francisco, CA. October.

“Reconstructing the 500 million year record of evolution in the vertebrate genome,” featured lecturer, Annual Meeting of the Fellows of the California Academy of Sciences, San Francisco, CA. October.

“Molecular evolution and cancer genetics,” keynote speaker, 8th Annual International Conference on Computational Systems Bioinformatics, Stanford University, Palo Alto, CA. August.

“The evolution of non-coding functional elements in our genome,” invited speaker, Evolution of the Molecular Landscape, 74th Cold Spring Harbor Symposium, Cold Spring Harbor, NY. May.

Short CV 17 Last Updated 12/22/2010 196

“The evolution of non-coding functional elements in our genome,” invited speaker, Harvey Mudd College, Pasadena, CA. April.

“Transposon-induced rewriting of vertebrate gene regulation,” invited speaker, AAAS Annual Meeting: Our Life and its Life: Origins and Futures, Chicago, IL. February.

“Statistical and algorithmic methods to explore evolution,” invited speaker, NIH Darwin Day, Bethesda, MD. February.

“Molecular evolution and disease,” invited speaker, HHMI Scientific Meeting: Human Disease, Genetics, Models and Progress Toward Treatments, Chevy Chase, MD. February.

“Evidence that transposons shaped vertebrate gene regulatory networks,” invited speaker, 2nd International Conference and Workshop Genomic Impact of Eukaryotic Transposable Elements, Asilomar, Monterey, CA. February.

“100 million years of evolutionary history of the human genome,” invited speaker, Jon Postel Distinguished Lecture, UCLA, Los Angeles, CA. January.

2008 “UCSC cancer genomics browser for TCGA data,” invited speaker, TCGA Steering Committee, Washington, D.C. December.

“Non-coding RNA: Red-headed stepchild of the human genome,” invited speaker, 58th Annual Meeting of ASHG, Philadelphia, PA. November.

“Human gene predictions,” MGC-ESC Meeting, invited speaker, Rockville, MD. September.

“100 million years of evolutionary history of the human genome,” invited speaker, ISCB Conference, Toronto, CAN. July.

“100 million years of evolutionary history of the human genome,” invited speaker, 23rd Conference on AAAI-08, Chicago, IL. July.

“Computing how we became human,” invited speaker, 40th ACM Symposium on Theory of Computing, Victoria, BC. May.

“A rapidly evolved RNA gene may have played a role in the evolution of the cerebral cortex,” invited speaker, European Human Genetics Conference, Barcelona, Spain. May.

“100 million years of evolutionary history of the human genome,” plenary speaker, HapMap, Human Evolution and the Future of Life, Copenhagen, Denmark. May.

“Evolutionary genomics of the human genome,” Distinguished Lecturer, Computer Science at Columbia University, New York, NY. May.

“Computing how we became human,” invited speaker, Renaissance Technologies Corporation Symposium, New York, NY. May.

“A rapidly evolved RNA gene may have played a role in the evolution of cerebral cortex,” invited speaker, Anatomy, Development, and Evolution of the Brain, UCSB, Santa Barbara, CA. April.

“The personal genome: consequences for society,” 7th Annual Genome Sciences Symposium, Seattle, WA. April.

“The infinite sites model of genome evolution,” invited speaker, Gordon Conference in Molecular Evolution, Ventura, CA. February.

2007 “Reconstructing 100 million years of human evolutionary history,” honored speaker, NIH Intramural Sequencing Center’s 10th Anniversary Symposium, Bethesda, MD. October.

Short CV 18 Last Updated 12/22/2010 197

“Rapidly evolving non-coding regions and brain evolution,” honored speaker, 57th Annual American Society of Human Genetics Meeting, San Diego, CA. August.

“Reconstructing 100 million years of human evolutionary history,” Pacific Biosciences, Menlo Park, CA. July.

“Reconstructing 100 million years of human evolutionary history,” honored speaker, Vertebrate Comparative Genomics, US National Academy of Sciences and the Australian Academy of Science, Beckman Center of the National Academy of Sciences, Irvine, CA. May.

“Reconstructing the evolutionary history of the human genome,” Frontiers in Biology seminar series, Stanford University, Palo Alto, CA. May.

“The infinite sites model of genome evolution,” Biology of Genomes meeting, Cold Springs Harbor Conference, Cold Springs Harbor, NY. May.

“A rapidly evolved RNA gene may have played a role in the evolution of the cerebral cortex,” honored speaker, UCSD Project for Explaining the Origin of Humans Symposium, La Jolla, CA. March.

2006 “Reconstructing the evolutionary history of the human genome,” 3rd University of California, Santa Cruz/QB3 Symposium of Bioinformatics, Santa Cruz, CA. December.

“Reconstructing 100 million years of human evolutionary history,” Center for Algorithmic and System Biology Algorithmic Biology Meeting, UCSD, La Jolla, CA. November.

“Reconstructing 100 million years of human evolutionary history,” Johns Hopkins University, Baltimore, MD. November.

“Ultraconserved elements, living fossil transposons, and rapid bursts of change: reconstructing the uneven evolutionary history of the human genome,” International Symposium on Genomics, Hangzhou, China. October.

“Reconstructing 100 million years of human evolutionary history,” Beckman Center for Molecular and Genetic Medicine at Stanford, Stanford, CA. October.

“Reconstructing 100 million years of human evolutionary history,” honored speaker, Scientific Forum for Cabrillo Festival of Contemporary Music, world premiere of the Frans Lanting orchestral-photographic performance “Life: A Journey Through Time,” Santa Cruz, CA. July.

“Exploring the evolutionary history of the human genome over the last 100 million years,” keynote address, ACM SIGMOND International conference on Management of Data, Chicago, IL. June.

“Ultraconserved elements, living fossil transposons, and rapid bursts of change: reconstructing the uneven evolutionary history of the human genome,” 23rd International Conference on Machine Learning (ICML), Carnegie Mellon University, Pittsburgh, PA. June.

“Ultraconserved elements, living fossil transposons, distal enhancers, and mysterious RNA genes: reconstructing the detailed evolutionary history of the human genome,” Annual Society for Molecular Biology and Evolution Meeting, Genomes, Evolution, and Bioinformatics, Arizona State University, Tempe, AZ. May.

“Ultraconserved elements, living fossil transposons, distal enhancers, and mysterious RNA genes: reconstructing the detailed evolutionary history of the human genome,” inaugural speech, Broad Distinguished Lecture Series in Computational Biology, Eli & Edythe L. Broad Institute, Cambridge, MA. May.

“Feasibility of reconstructing the 100 million year history of the human genome,” Genomes and Biology, Cold Spring Harbor, NY. May.

“Exploring the evolutionary history of the human genome over the last 100 million years,” Human Evolution Symposium, UCSF, San Francisco, CA. May.

Short CV 19 Last Updated 12/22/2010 198

“Applying comparative genomics to assist in the completion of the Mammalian Gene Collection,” Mammalian Gene Collection Annual Meeting, Washington, DC. April.

“The infinite sites model of genome evolution,” Workshop on Reconstruction of Ancestral Genomes, Barbados. April.

“Ultraconserved elements, living fossil transposons, and rapid bursts of change: reconstructing the uneven evolutionary history of the human genome,” keynote address, 10th Annual Conference on Research in Computational Molecular Biology, Venice, Italy. March.

“Ultraconserved elements, living fossil transposons, and rapid bursts of change: reconstructing the uneven evolutionary history of the human genome,” Dickson Prize award talk, Carnegie-Mellon University, Pittsburg, PA. March.

“Ultraconserved elements, living fossil transposons, and rapid bursts of change: reconstructing the uneven evolutionary history of the human genome,” keynote address, Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor, NY. March.

“Ultraconserved elements, living fossil transposons, distal enhancers, and mysterious RNA genes: reconstructing the detailed evolutionary history of the human genome,” Institute for Pure and Applied Mathematics, UCLA, Los Angeles, CA. January.

“Ultraconserved elements, living fossil transposons, distal enhancers, and mysterious RNA genes: reconstructing the detailed evolutionary history of the human genome,” Integrative Graduate Education and Research Traineeships, University of Arizona, Tucson, AZ. January.

2005 “Health, medicine, and biotechnology,” keynote address, World Technology Summit, San Francisco, CA. November.

“Using evolution to explore the human genome,” Computational and Genomic Biology Seminar Series, UCB, Berkeley, CA. November.

“Using evolution to explore the human genome,” honored speaker, European Bioinformatics Institute, Hinxton, Cambridge, UK. November.

“Using evolution to explore the human genome,” Evolutionary Genomics Meeting, The Stazione Zoologica Anton Dohrn, Naples, Italy. October.

“Using evolution to explore the human genome,” keynote address, Genome Informatics Conference, Cold Spring Harbor, NY. October.

“Using evolution to explore the human genome,” honored speaker, UC System-Wide Bioengineering Symposium, UCSC, Santa Cruz, CA. June.

“Using evolution to explore the human genome,” keynote address, IEEE Workshop on Computer Vision Methods for Bioinformatics, San Diego, CA. June.

“Computational reconstruction of an ancestral mammalian chromosome,” keynote address, Cold Spring Harbor Conference, Cold Spring Harbor, NY. May.

“Reconstructing an ancestral mammalian chromosome,” keynote address, Cold Spring Harbor Conference, Cold Spring Harbor, NY. May.

“Ultraconserved elements in the human genome,” European Human Genetics Conference, Prague, Czech Republic. May.

“Impact of human genome research: present and future,” Mervyn Young Memorial Lecture, University of Colorado, Boulder, Boulder, CO. April.

Short CV 20 Last Updated 12/22/2010 199

“Using evolution to explore the human genome,” Distinguished Engineering Alumni Award Seminar, University of Colorado, Boulder, Boulder, CO. April.

“Impact of human genome research: present and future,” honored speaker, Mervyn Young Memorial Lecture, University of Colorado, Boulder, Boulder, CO. April.

2004 “Using evolution to explore the human genome,” honored speaker, University of Washington, CSE Distinguished Lecture, Seattle, WA. December.

“Using evolution to explore the human genome,” National Academy of Science Sackler Colloquium, Stanford University, Palo Alto, CA. October.

“Comparative genomics to identify functional elements in the human genome,” Molecular Medicine Tri-Conference, San Francisco, CA. March.

“Comparing the human, chimp, mouse and rat genomes: using evolution to predict functional elements in the human genome,” Chemistry and Genomics Seminar, Stanford University, Palo Alto, CA. March.

“The power of multiple vertebrate genome sequences,” Keystone Symposia, Steamboat Springs, CO. March.

“Reconstructing an ancestral mammalian genome in silico,” Gordon Research Conference in Molecular Evolution, Ventura, CA. February.

“Comparing the human, chimp, mouse and rat genomes: using evolution to predict functional elements in the human genome,” Sali Labs, UCSF, San Francisco, CA. January.

2003 “Using comparative genomics to predict functional elements in the human genome,” Distinguished Speaker Series, Sloan- Swartz Center for Theoretical Neurobiology Seminar, Colorado State University, Ft. Collins, Fort Collins, CO. November.

“Using comparative genomics to predict functional elements in the human genome,” 2003-04 Distinguished Seminar Series, Department of Computer Science, University of British Columbia, Canada. November.

“Using comparative genomics to predict functional elements in the human genome,” XIX International Congress of Genetics, Melbourne, Australia. July.

“Identifying functional elements in the human genome by tracing the evolutionary history of the bases: a key challenge for comparative genomics,” Intelligent Systems for Molecular Biology, Brisbane, Australia. June.

“Bioinformatics, genome evolution and the challenge of identifying functional elements in the human genome,” The Genome of Homo Sapiens. Symposium on Quantitative Biology, Cold Spring Harbor, NY. May.

“Computational genomics on mammals: sequence, function, and evolution,” Intra- and Intercellular Communication Science Meeting, Howard Hughes Medical Institute, Washington, DC. April.

“Bioinformatics, genome evolution and the challenge of identifying functional elements in the human genome,” Distinguished Science Seminar, Affymetrix, Santa Clara, CA. April.

“Computational analysis of the human and other mammalian genomes,” International Conference on Artificial Intelligence and Statistics,” Key West, FL. January.

“Computational analysis of the human and other mammalian genomes,” Oncogenomics, Phoenix, AZ. January.

2002

Short CV 21 Last Updated 12/22/2010 200

“Computational analysis of the human and mouse genomes,” Conference on Signals, Systems, and Computers, Asilomar Conference Center, Pacific Grove, CA. November.

“The working drafts of the human and mouse genomes,” Osong International Bio Conference, South Korea. October.

“The working drafts of the human and mouse genomes,” IBC’s Post-Genomic Bioinformatics Conference, San Francisco, CA. June.

“Initial computational analysis of the public working drafts of the human and mouse genomes, and the long road ahead,” Workshop on Theory of Computation and the Sciences, Berkeley, CA. May.

“Assembly and initial analysis of the working draft of the human genome,” Clinical Ligand Assay Society, in conjunction with Boston Biomedica/CLAS Distinguished Scientist of the Year Award, 28th Annual Meeting, Houston, TX. May.

“Initial computational analysis of the public working drafts of the human and mouse genomes, and the long road ahead,” Genomes and Biology Conference, Cold Spring Harbor, NY. May.

“Status of the human and mouse working draft genomes, and some early comparisons,” Genes and Genomes in Health and Disease, Howard Hughes Medical Institute, Washington, DC. March.

“Status of the human genome working draft: map, assembly and web access,” Advances in Genome Biology & Technology, joint meeting with Automation in Mapping & DNA Sequencing, Marco Island, FL. February.

2001 “Overview of the human genome project and the construction of the working draft,” and “Exploring the working draft of the human genome,” NATO ASI on Artificial Intelligence and Heuristic Methods for Bioinformatics, San Miniato, Italy. October.

“Assembly and annotation of the public human genome working draft,” 13th International Genome Sequencing and Analysis Conference, San Diego, CA. October.

“The public working draft of the human genome,” keynote address, CHI Bioinformatics and Genome Research, San Francisco, CA. June.

“Assembly and annotation of the working draft of the human genome,” Gordon Research Conference on Human Molecular Genetics, Newport, RI. August.

“The public working draft of the human genome,” 33rd Annual Symposium on the Interface of Computer Science and Statistics, Costa Mesa, CA. May.

“Assembly and initial analysis of a working draft of the human genome,” New Frontiers in Structural and Computational Biology, Howard Hughes Medical Institute, Chevy Chase, MD. March.

“A working draft of the human genome,” Pacific Symposium on Biocomputing, Mauna Lani, HI. January.

2000 “A working draft of the human genome,” Biomedical Computation at Stanford, Stanford University, Palo Alto, CA. October.

“Hidden Markov models, Fisher kernels and support vector machines for biosequence analysis,” Bioinformatics, Elsinore, Denmark. April.

“Computational prediction of genes and gene function from high-throughput genomics data,” Association for the Advancement of Artificial Intelligence, Washington, D.C. February.

1999 “Hidden Markov models and Fisher kernels for biosequence analysis,” Learning, 13th Annual Workshop, Snowbird, UT. April.

Short CV 22 Last Updated 12/22/2010 201

“Combining discriminative classification methods with hidden Markov models for more effective biosequence analysis,” 8th Bioinformatics and Genome Research Conference, San Francisco, CA. June.

“Analysis of microarray gene expression data using support vector machines,” In Silico Biology: Sequence, Structure and Function, Atlanta, GA. November.

“Computational analysis of high-throughput genomics data using hidden Markov models and support vector machines,” keynote speaker, 10th Annual Genome Informatics Workshop, Tokyo. December.

1998 “Statistical methods in biosequence analysis: discriminative vs. generative models,” 2nd Annual Conference on Computational Genomics, Reston, VA. November.

“Models and methods in biosequence analysis,” International Conference on Problems in Biophysics, Moscow. June.

“Using hidden Markov models for biosequence analysis: recent tests and new methods,” Understanding the Genome: Technological and Mathematical Challenges, Mathematical Sciences Research Institute, Berkeley, CA. May.

“Hidden Markov models for protein families,” Structure-Function Based Genomics Symposium, London, England. April.

“A new discriminative methodology for detecting remote protein homologies,” 1st Annual Computational Structural Biology Research Meeting, Monterey, CA. December.

1997 “Design of the Genie genefinder,” Finding Genes: Computational Analysis of DNA Sequences, Cold Spring Harbor, NY. March.

“A brief look at some machine learning problems in genomics,” keynote lecture, 10th International Conference on Computational Learning Theory, Vanderbilt University, Nashville, TN. July.

“Statistical genome analysis: hidden Markov methods,” Newton Seminar, Isaac Newton Institute, Cambridge, England. October.

1996 “Using hidden Markov models for biosequence analysis,” keynote lecture, 4th International Conference on Intelligent Systems in Molecular Biology, St. Louis, MO. June.

“Hidden Markov Models for Biosequence Analysis,” Workshop on Theoretical and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA. August.

“VC dimension, covering numbers and worst-case prediction of individual sequences,” ICMS Workshop on the Vapnik- Chervonenkis Dimension, Edinburgh, Scotland. September.

1995 “Bounds on the mutual information between a parameter and a sequence of conditionally independent observations,” Workshop on Theory of Neural Networks, Pohang, Korea. February.

“Hidden Markov models for proteins,” DIMACS Workshop on Sequence Based Methods for Protein Folding, Rutgers, NJ. March.

“Hidden Markov models in biosequence analysis,” Workshop on Biosequence Analysis, Aspen Center for Physics, Aspen, CO. June.

“Prediction, data compression and metric dimension,” 11th ACM Symposium on Computational Geometry, Vancouver, Canada. June.

Short CV 23 Last Updated 12/22/2010 202

“Using hidden Markov models to search biosequence databases,” Workshop on Knowledge, Discovery and Database Mining, Montreal, Canada. August.

“Hidden Markov and related statistical models: how they have been applied to biosequence analysis,” Workshop on Uncertainty in Artificial Intelligence, Montreal, Canada. August.

1994 “Hidden Markov models for multiple alignments and database search for proteins,” Meeting on Critical Assessment of Techniques for Protein Structure Prediction, Asilomar Conference Center, Pacific Grove, CA. December.

“Using stochastic context-free grammars to fold, align and model homologous RNA sequences,” Workshop on the Fusion of Molecular Biology and Knowledge Information Processing, Tokyo, Japan. December.

1993 “Hidden Markov models and beyond,” Macromolecules, Genes and Computers: Chapter Three, Waterville, NH. August.

“On-line prediction: models from computational learning theory and statistics,” Learning Days in Jerusalem Conference, Jerusalem, Israel. May.

1992 “How to use expert advice,” 6th Conference on Neural Information Processing Systems, post-meeting workshop on Bayesian Methods, Vail, CO.

“Hidden Markov models for protein families,” 6th Conference on Neural Information Processing Systems, post-meeting workshop on hidden Markov Models, Vail, CO.

“Hidden Markov models for protein families” and “Bayes Methods for Prediction,” Workshop on Supervised Learning, Santa Fe, NM.

“How well do Bayes Methods work for on-line prediction of +1,-1 values?” 3rd NEC Symposium on Computation and Cognition, Princeton, NJ.

1991 “Uniting the VC and TLS theories of generalization,” Neural Networks for Computing, Snowbird, UT. April.

“Computational learning theory,” 3rd Woodward Conference on Modeling Complex Phenomena, San Jose, CA. April.

“How well do Bayes methods work?” 5th Conference on Neural Information Processing Systems, post-meeting workshop on Bayesian methods, Vail, CO.

“Information theory, VC dimension and the Bayesian approach to machine learning,” Workshop on Computational Learning Theory and Natural Learning Systems, Berkeley, CA. September.

1990 “Probably approximately correct learning,” National Conference, Association for the Advancement of Artificial Intelligence, Boston, MA. July.

“Learnability and the metric dimension: decision theoretic generalizations of the PAC learning model,” 1st International Workshop on Algorithmic Theory, Tokyo, Japan. October.

1989 “Generalization in neural networks: a computational learning theory perspective,” Annual Meeting of the American Association for the Advancement of Science, San Francisco, CA. January.

Short CV 24 Last Updated 12/22/2010 203

“Bounds on sufficient training set size when learning from random examples,” Neural Networks for Computing, Snowbird, UT. April.

“Probably approximately correct learning,” Discovery and Learning: Philosophical and Computational Perspectives, Pittsburgh, PA. April.

“Complexity issues in learning from random examples,” Annual Meeting of the Society for Industrial and Applied Mathematics, Mini-symposium on Neural Computing, San Diego, CA. July.

1988 “Theoretical results in machine learning,” 5th International Conference on Machine Learning, Ann Arbor, MI. June.

Books Edited Proceedings of the Fifth ACM Workshop on Computational Learning Theory, ACM, 1992.

Proceedings of the Second Workshop on Computational Learning Theory, Morgan Kaufmann, Los Altos, CA, 1989. (with R. Rivest and M. Warmuth)

Proceedings of the First Workshop on Computational Learning Theory, Morgan Kaufmann, Los Altos, CA, 1988 (with L. Pitt)

Journals Edited 2005- Associate Editor: Public Library of Science Computational Genomics

2001-2005 Editorial Board: Drug Discovery Today

1996- Associate Editor: Journal of Computational Biology

1996-2002 Editorial Board: Neural Computing Surveys

1995-2002 Editorial Board: Journal of Neurocomputing

1993-95 Editorial Board: Journal of Artificial Intelligence Research

1988-97 Associate Editor: Machine Learning

1988-97 Guest Editor: Machine Learning, special issue on recent theoretical directions in Machine Learning. Spring, 1988

Professional Service Review and Planning Panels 2010 Founding member of the Cancer Commons Computational Advisory Board (CAB). San Francisco, December

2010 Reviewer, Scientific Quinquennial Review (QQR) Review, Oxford

2010 Chair, Review Committee, Biomedical Informatics (BMI Degree Program), University of California, San Francisco. May

2010 Reviewer, Scientific Review, National Centers for Biomedical Computing. May.

2010 Participant, Informatics and Analysis Planning Meeting, National Human Genome Research Institute. April.

2010 Member, Scientific Review, Wellcome Trust Sanger Institute. March.

Short CV 25 Last Updated 12/22/2010 204

1/10- Member, Scientific Advisory Board, International Barcode of Life, Toronto, Ontario, Canada

2009 Member, Scientific Review, Wellcome Trust Sanger Institute. July

2008- Member, The Cancer Genome Atlas Steering Committee.

2007 Member, NAS Committee on Science Engineering and Public Policy

2006- Member, Board of Scientific Counselors, Eli & Edythe L. Broad Institute

2006- Panel Member, Computational Biology, RECOMB. April

2006 Panel Member, Life Sciences Division Review Committee, Lawrence Berkeley National Laboratory

2005 Committee Member, National Academies Keck Futures Initiative

2005 Member, Scientific Advisory Board, Ensembl genome browser project, European Bioinformatics Institute

2005 Reviewer, report on mathematical sciences funding to support biological aims, National Academy of Sciences

2004 Advisory Panel Member, PharmGKB NIGMS

2003 Committee Member, NIH Committee to Prioritize Sequencing Targets for NHGRI, to aid in better understanding the human genome

2003 NHGRI Council Meeting. September

2002 Organizing Committee Member, NHGRI 1% pilot project to recognize all functional elements in the human genome

2002 NHGRI Future of Genomics Planning Meeting. November

2001 Section Leader, Bioinformatics, NHGRI Future of Genomics Planning Meeting. December

1999 Member, NSF Panel (panel name is confidential)

1998 Member, NIH Review Panel. November

1996 Panel Member, DOE Human Genome Project, Informatics Section. September

1993 Panel Member, DOE Human Genome Project, Informatics Section. September

University Service UC System-wide Service 2000- Scientific Co-Director, California Institute for Quantitative Biosciences (QB3)

1998- Member, UC System-Wide Life Science Informatics Working Group

Special UCSC Campus-wide Service 2005- Director, Training Program in the Systems Biology of Stem Cells, UC Santa Cruz

1999- Director, UCSC Center for Biomolecular Science and Engineering

Short CV 26 Last Updated 12/22/2010 205

1997-98 Member, Chancellor’s Millennium Committee

Short CV 27 Last Updated 12/22/2010 206

PAUL B. THOMPSON Department of Philosophy, 503 South Kedzie Hall 1611 Osborn Road MichiganStateUniversity Lansing, MI48915 East Lansing, MI48824-1032 (517) 230 5821 (517) 432-0316 FAX (517) 432-1320 [email protected] Personal Data: Born July 22, 1951, Springfield, MO; Married March 28, 1975; 2 children.

Education: Ph.D. 1980 StateUniversity of New York at Stony Brook - Philosophy Major Professor: Don Ihde Dissertation: The Concept of Risk M. A. 1979 State University of New York at Stony Brook - Philosophy B. A. 1974 EmoryUniversity – Major: Philosophy 1971 - 1973 Georgia Institute of Technology – Major: Mathematics 1969 - 1971 University of Northern Colorado – Major: Mathematics Diploma 1969 George Washington High School, Denver, CO

Professional Experience: August 2003-present: Endowed Professor of Philosophy, Agriculture, Food and Resource Economics and Community, Agriculture, Recreation and Resource Studies, MichiganStateUniversity July 1997 to August 2003: Distinguished Professor of Philosophy, PurdueUniversity. July 1999 to August 2003: Director, Center for Food Animal Productivity and Well-Being, PurdueUniversity Sept. 1992 to July 1997: Professor of Philosophy and Agricultural Economics, TexasA&MUniversity Sept. 1990 to July 1997: Director, Center for Science and Technology Policy and Ethics (formerly Center for Biotechnology Policy and Ethics), Institute for Biosciences and Technology, TexasA&MUniversity Sept. 1987 to Aug. 1992: Associate Professor of Philosophy and Agricultural Economics, TexasA&MUniversity Sept. 1986 to Aug. 1987: Visiting Scholar, U.S. Agency for International Development, Washington D. C. Sept. 1982 to Aug. 1986: Assistant Professor of Philosophy and Agricultural Economics, TexasA&MUniversity Sept. 1981 to June 1982: Visiting Assistant Professor of Philosophy, TexasA&MUniversity Sept. 1975 to June 1980: Graduate Council Fellow, Department of Philosophy, SUNY Stony Brook

Academic Honors: W. K. Kellogg Professor of Agricultural, Food and Community Ethics, MichiganStateUniversity, 2003— Fellow, The HastingsCenter, Garrison, NY, 2000— Joyce and Edward E. Brewer Professor of Applied Ethics, PurdueUniversity, 1997—2003 YaleUniversity, Postdoctoral Fellow, Program on Agrarian Studies, 1994-95. New Mexico State University, 1993-94 Visiting Distinguished Professor. American Agricultural Economics Association Award for Professional Excellence in Communication for Sacred Cows and Hot Potatoes, 1993. American Agricultural Economics Association Award for Professional Excellence in Communication for contributions to Agricultural Biotechnology: Issues and Choices, 1992. Maria Julia and George R. Jordan, Jr. Term Professorship in Public Policy, Texas A&M University, 1990-92. National Endowment for the Humanities Summer Seminars Participant, SyracuseUniversity, 1988. Council on Foreign Relations International Affairs Fellow, 1986-87. NationalCenter for Food and Agricultural Policy, Resources for the Future, Resident Fellow, 1986-87. National Endowment for the Humanities Summer Seminars Participant, TrinityUniversity, San Antonio, TX, 1983. SUNY Doctoral Exchange Fellow, 1977-78. SUNY Stony Brook Graduate Council Fellow, 1975-79.

Related Experience: Chair, Council on Agricultural Science and Technology Working Group on Ethics and Animal Agricultural Biotechnology, 2006—2010

207 Paul B. Thompson Vita 2/7/2011

Member, Advisory Committee on Biotechnology, Board of Agriculture and Natural Resources, National Research Council, Washington, D.C. 2002— Member, Scientific Advisory Committee, The Mansholt Graduate School, Wageningen University and Research Institute, The Netherlands, 1996—2010 Member, Steering Committee, University of Texas Center on Sustainable Development, Austin, TX, 2002—2004 Member, Science and Industry Advisory Committee, Genome Canada, 2004—2008 Member, Executive Committee, Institutional and Behavioral Economics Section, American Agricultural Economics Association, 2006-2008; 2008-2010. Member, Scientific Advisory Committee, Genome Alberta, 2005—2007 Member Scientific Advisory Committee, Genome Prairie Research Project, Alberta, Canada, 2002—2005. Consultant to the Food and Agricultural Organization of the United Nations on ethics and food safety, 2002. Member, Subcommittee on Environmental Consequences from Commercialization of Transgenic Crops, National Research Council, 2000—2001. Member, Council on Agricultural Science and Technology Task Force on Urban Agriculture, 2000—2001. Faculty, Foundation for American Communications Workshop, The Biotech Food Fight, April 28-30, 2000, Minneapolis, MN. Member, Ecological Standards Workgroup, Public Policy Dialog Committee, U. S. Environmental Protection Agency, June 1997—May 1998. Member, U. S. Government Agricultural Biotechnology Research Advisory Committee (ABRAC), October 1994 - January 1996. Graduate Faculty of the GeorgeBushSchool for Public Leadership, Texas A&M University, 1996-97. Graduate Faculty, Speech Communication and Theater Arts, Texas A&M University, 1992-1997. Instructor and Associate Producer, AG*SAT course on Agricultural Ethics, interactive satellite broadcast, Spring 1992. Member, Council on Agricultural Science and Technology Task Force on Animal Well Being, 1991-97. Organizer and Coordinator, Curriculum and research workshops on ethics in agriculture at University of Florida, University of Kentucky, University of Minnesota, Michigan State University, Oregon State University, Purdue University, Pennsylvania State University, Rutgers University, Texas A&M University, 1984-1998. Director of Graduate Studies, Department of Philosophy, Texas A&M University, 1989-1990. Visiting Fellow, U.S. Agency for International Development, Bureau of Science & Technology, Office of Agriculture, Washington, DC. 1986 - 87. Member, Editorial Advisory Board: Environmental Values,2000-2006; Environmental Ethics, since 2007; Journal of Agricultural and Environmental Ethics, since 1988; Agriculture and Human Values, since 1985. Coordinator, Agriculture and Liberal Arts Project, Texas A&M University, 1985-1989. Risk Quantification Consultant, Oconee Probabilistic Risk Assessment, Nuclear Safety Analysis Center and the Duke Power Company, Charlotte, NC, 1981. Writer and Producer for a pilot episode of a TV program to teach logic, SUNY Stony Brook, 1979.

Books and Monographs: 1. P. B. Thompson, The Agrarian Vision: Sustainability and Environmental Ethics. Lexington, KY: The University Press of Kentucky, 2010. 2. P. B. Thompson, Ed. The Ethics of Intensification: Agricultural Development and Cultural Change.Dordrecht, NL: Springer, 2008. 3. K. David and P. B. Thompson, Eds. What Can Nanotechnology Learn from Biotechnology? Social and Ethical Lessons for Nanoscience from the Debate over Agrifood Biotechnology and GMOs.Burlington, MA: Academic Press, 2008. 4. J. B. Callicott and R. Frodeman, Eds-in-Chief; V. Davion, B. Norton, C. Palmer and P. B. Thompson, Assoc. Eds. Encyclopedia of Environmental Ethics and Philosophy Farmington Hills, MI: 2008, Gale- Cengage Learning. 5. P. B. Thompson, Food Biotechnology in Ethical Perspective 2nd Edition, Dordrecht, NL: Springer, 2007. 6. Committee on Environmental Impacts Associated with Commercialization of Transgenic Plants, Board on Agriculture and Natural Resources, (12 individuals). Environmental Effects of Transgenic Plants: The Scope and Adequacy of Regulation.Washington, DC: 2002, The National Research Council. 7. P. B. Thompson and T. C. Hilde, Eds. The Agrarian Roots of Pragmatism. Nashville, TN: VanderbiltUniversity Press, 2000.

2 208 Paul B. Thompson Vita 2/7/2011

8. P. B. Thompson, Agricultural Ethics: Research, Teaching and Public Policy, Ames, IA: Iowa State University Press, 1998. 9. P.B. Thompson, Food Biotechnology in Ethical Perspective, London: Chapman and Hall (Blackie Academic and Professional), 1997. 10. P.B. Thompson, The Spirit of the Soil: Agriculture and Environmental Ethics, New York and London: Routledge Publishing Co., 1995. 11. P.B. Thompson, R. Matthews, E.O. van Ravenswaay, Ethics, Public Policy, and Agriculture, New York: Macmillan, 1994. 12. P.B. Thompson, The Ethics of Aid and Trade: U.S. Food Policy, Foreign Competition and the Social Contract, New York: CambridgeUniversity Press, 1992. 13. W. Browne, J. Skees, L. Swanson, P.B. Thompson, and L. Unnevehr, Sacred Cows and Hot Potatoes: Agrarian Myths and Policy Realities, Boulder, CO: Westview Press, 1992. 14. P.B. Thompson and B. A. Stout, Eds. Beyond the Large Farm: Ethics and Research Goals for Agriculture, Boulder, CO: Westview Press, 1991.

Selected Refereed Journal Articles: 1. P. B. Thompson, ―Food Aid and the Famine Relief Argument (Brief Return),‖ The Journal of Agricultural and Environmental Ethics 23(2010): 209-227. 2. P. B. Thompson, ―Animal Ethics and Public Expectations: The North American Outlook,‖ Journal of Veterinary Medical Education 37(2010): 13-21. 3. P. B. Thompson, ―Why Using Genetics to Address Welfare May Not Be a Good Idea,‖ Poultry Science 89(2010): 814-821. 4. P. B. Thompson, ―The Opposite of Human Enhancement: Nanotechnology and the Blind Chicken Problem,‖ NanoEthics2(2008): 305-316. 5. P. B. Thompson, ―Agrarian Philosophy and Ecological Ethics,‖ Science and Engineering Ethics 14(2008): 527- 544. 6. P. B. Thompson, ―The Agricultural Ethics of Biofuels: A First Look,‖ Journal of Agricultural and Environmental Ethics 21(2008):183-198. 7. W. Hannah and P. B. Thompson, ―Nanotechnology, Risk and the Environment: A Review,‖ Journal of Environmental Monitoring 10(2008):291-300. 8. P. B. Thompson and W. Hannah. ―Food and Agricultural Biotechnology: A Summary and Analysis of Ethical Concerns,‖ Advances in Biochemical Engineering and Biotechnology 111(2008): 229-264. 9. P. B. Thompson, ―Current Ethical Issues in Animal Biotechnology,‖ Reproduction, Fertility and Development, 20 (2008): 67–73. 10. P. B. Thompson,―Animal Biotechnology: How Not to Presume,‖ The American Journal of Bioethics, 8:6, (2008) 49-50. DOI: 10.1080/15265160802248278.URL: http://dx.doi.org/10.1080/15265160802248278 11. P. B. Thompson, ―Borgmann on Commodification: A Comment on Real American Ethics,‖ Journal of Agricultural and Environmental Ethics 21 (2008): 75-84, (published with a reply by Borgmann, pp. 85-96). 12. A. J. Knight, M. R. Worosz, M. K. Lapinski, T. A. Ten Eyck, C. K. Harris, L. D. Bourquin, T. M. Dietz, P. B. Thompson, and E. C. Todd. ―Consumer Perceptions of the Food Safety System: Implications for Food Safety Educators and Policy Makers.‖ Food Protection Trends 28(6)(2008): 27-32. 13. P. B. Thompson, ―Theorizing Technological and Institutional Change: Alienability, Rivalry and Exclusion Cost,‖ Technè 11(1)(Fall 2007): 19-31. 14. P. B. Thompson, ―Agricultural Sustainability: What It Is and What It Is Not,‖ International Journal of Agricultural Sustainability 5 (2007): 5-16. 15. P. B. Thompson, ―Agriculture and Working-Class Political Culture: A Lesson from The Grapes of Wrath,‖ Agriculture and Human Values24(2007): 165-177. 16. P. B. Thompson, C. Harris, D. Holt and E.A. Pajor. ―Livestock Welfare Product Claims: The Emerging Social Context,‖ Journal of Animal Science 85 (2007): 2354—2361. 17. P. B. Thompson, ―Norton’s Sustainability: Some Comments on Risk and Sustainability,‖ Journal of Agricultural and Environmental Ethics 20(2007): 375-386 (published with a Reply by Norton, pp. 387-405). 18. P. B. Thompson, ―Mark Sagoff’s Kantian Environmental Philosophy,‖ Ethics, Place and Environment 9(2006): 344-350 (published with a Reply from Sagoff, pp. 365-372). 19. P. B. Thompson, ―Should We Have GM Crops?‖ Santa Clara Journal of International Law 4(2006): 75-95. http://www.scu.edu/scjil/archive/v4_ThompsonAbstract.shtml

3 209 Paul B. Thompson Vita 2/7/2011

20. P. B. Thompson, ―Ecological Risks of Transgenic Crops: A Framework for Assessment and Conceptual Issues,‖ Sustainability in Agriculture, R.E. Hester and R. M. Harrison, Eds. Issues in Environmental Science and Toxicology, Vol. 21, Cambridge, UK: 2005, Royal Society of Chemistry, pp. 16-30. 21. P. B. Thompson, ―Value Judgments and Risk Comparisons: The Case of Genetically Engineered Crops,‖ Plant Physiology 132(2003): 10-16. http://www.plantphysiol.org/cgi/content/full/132/1/10 Republished in Maarten J. Chrispeels, Ed. Agricultural Ethics in a Changing World.Rockville, MD: 2004, American Society of Plant Biologists, pp. 40-46; Republished in Craig Hanks, Technology and Values: Essential Readings Malden, MA: 2010, Wiley-Blackwell, pp. 347-355. 22. K.K. Schillo and P. B. Thompson, ―Postmodernism for Animal Scientists,‖ Journal of Animal Science 80(E. Suppl. 2)[2003]: E189-E194. 23. P. B. Thompson, ―Crossing Species Boundaries Is Even More Controversial than You Think,‖ The American Journal of Bioethics 3(3)[2003]: 14-15. 24. P. B. Thompson, ―The Reshaping of Conventional Farming: A North American Perspective,‖ Journal of Agricultural and Environmental Ethics 14 (2001): 217-229. 25. P. B. Thompson, ―Risk, Consent and Public Debate: Some Preliminary Considerations for the Ethics of Food Safety,‖ International Journal of Food Science and Technology36 (2001): 833-843. 26. P. B. Thompson, ―Animal Welfare and Livestock Production in a Postindustrial Milieu,‖ Journal of Applied Animal Welfare Science 4(3) [2001]: 191-205. 27. P. B. Thompson, ―Privacy, Secrecy and Security,‖ Ethics and Information Technology 3(2001): 13-19. 28. P. B. Thompson, ―Grades and Standards in the Context of International Trade: Some Ethical Considerations,‖ Cahiers d’Economie et SociologieRurales 55-56(2000): 53-70. 29. P. B. Thompson, ―Food and Agricultural Biotechnology: Ethical Issues Behind the Research Choices,‖ The IPTS Report, 50 (December 2000): http://www.jrc.es/iptsreport (Simultaneously published in English, French, Spanish and German). 30. P. B. Thompson, ―The Ethics of Truth-Telling and the Problem of Risk,‖ Science and Engineering Ethics 5(4)[1999]: 489-511.

Selected Book Chapters and Invited Papers: 1. P. B. Thompson, ‖Agrifood Nanotechnology: Is This Anything?‖ in Understanding Nanotechnology: Philosophy, Policy and Publics, U. Fiedeler, C. Coenen, S. R. Davies and A. Ferrari, eds. Heidelberg, Germany: 2010, Akademische Verlagsgesellshchaft AKA GmbH, pp. 157-170. 2. P. B. Thompson, ―Sustainability: What It Is and What It Is Not,‖ in Pragmatic Sustainability: Theoretical and Practical Tools, S. E. Moore, ed. London: Routledge, pp. 16-29. 3. ―Everything Must Go,‖ in Kathleen Dean Moore and Michael P. Nelson, Eds. Moral Ground: Ethical Action for a Planet in Peril, San Antonio, TX: 2010, Trinity University Press, pp. 4. P. B. Thompson, ―Land,‖ in Life Science Ethics G. Comstock, Ed. Ames, IA: 2002, Iowa State Press, pp. 169- 190; revised and republished in Life Science Ethics 2nd Ed. G. Comstock Ed., 2010, Dordrecht, NL: Springer, pp. 123-144. 5. P. B. Thompson, ―Convergence in an Agrarian Key,‖ in Nature in Common? Environmental Ethics and the Contested Foundations of Environmental Policy. Ben Minteer, Ed. Philadelphia, PA: 2009, TempleUniversity Press, pp. 167-184. 6. P. B. Thompson, ―Of Biotechnology and Blind Chickens,‖ in Emerging Technologies: From Hindsight to Foresight, Edna Einseidel, Ed. Vancouver:2009, University of British Columbia Press, pp. 69-80. 7. P. B. Thompson, ―Animal Welfare in Livestock Production: Implications for Producers, Consumers and Public Health,‖ in Food Security in a Global Economy: Veterinary Medicine and Public Health, Gary Smith and Alan M. Kelly, Eds. Philadelphia: 2009, University of Pennsylvania Press, pp. 51-60. 8. P. B. Thompson, ―Ethical Perspectives on Food Biotechnology,‖ in Acceptable Genes: Religious Traditions and Genetically Modified Foods, Conrad G. Brunk and Harold Coward, Eds. Albany, NY: SUNY Press, pp. 39-62. 9. P. B. Thompson, ―Alienability, Rivalry and Exclusion Cost: Three Institutional Factors for Design,‖ in Philosophy and Design: From Engineering to Architecture, Pieter E. Vermaas, Peter Kroes, Andrew Light and Steven A. Moore, Eds. Dordrecht, NL: Springer, 2008, pp. 131-140. 10. P. B. Thompson, ―The Presumptive Case for Nanotechnology,‖ in Nanotechnology & Society: Current and Emerging Issues, Fritz Allhoff and Patrick Lin, Eds. Dordrecht, NL: Springer, 2008, pp. 39-54.

4 210 John D. McPherson, Ph.D. (Date prepared August 2010)

CURRICULUM VITAE

BIOGRAPHICAL INFORMATION

Education

B.Sc., Honours/Biochemistry September 1979 to May 1983, degree received June 4, 1983 Queen's University at Kingston Kingston, Ontario Canada K7L 3N6

Ph.D., Biochemistry May 1983 to October 1988, degree received May 26, 1989 Queen's University at Kingston Kingston, Ontario Canada K7L 3N6

Thesis Title: Nonenzymatic Glycation: A Study of the Post-translational Modification of Proteins by the Nonenzymatic, Covalent Attachment of Glucose and Fructose.

Postdoctoral Fellow: University of California at Irvine, February 1990 to February 1992. Principle investigator: Dr. J.J. Wasmuth, Ph.D., Department of Biological Chemistry.

Postdoctoral Fellow: University of California at Irvine, March 1988 to January 1990. Principle investigator: Dr. M. Smith, M.D., Ph.D., Department of Pediatrics.

Employment:

Current Appointments

Director, Cancer Genomics, Ontario Institute for Cancer Research, July 2007 – present.

Professor University of Toronto, July 2009 – present. Department of Medical Biophysics

Past Appointments Associate Professor: Baylor College of Medicine, May 2003 to June 2007. Tenure granted October 2003. Primary appointment: Department of Molecular and Human Genetics Joint appointment: Human Genome Sequencing Center

Associate Professor: Washington University School of Medicine, July 2000 to April 2003. Tenure granted October 2000. Primary appointment: Division of Biology and Biomedical Sciences, Department of Genetics Joint appointment: Genome Sequencing Center

Assistant Professor: Washington University School of Medicine, December 1995 to June 2000

Co-Director, Genome Sequencing Center: Washington University School of Medicine, December 1999 to April 2003 (Assistant Director, December 1996 – November 1999).

Assistant Professor: University of California at Irvine, October 1994 to December 1995. Primary appointment: Department of Biological Chemistry. Joint appointment: Department of Psychiatry and Human Behavior

Co-Director, National Human Genome Research Center at UCI: University of California at Irvine, October, 1993 to 1996.

1

211 John D. McPherson, Ph.D.

Assistant Researcher: University of California at Irvine, March 1992 to September 1994.

Founder: Orion Genomics, LLC, St. Louis, MO. (www.oriongenomics.com) Orion Genomics was founded in 1998 and is an agricultural research company using state-of-the-art physical mapping, sequencing and bioinformatics to identify genes associated with important crop and animal traits. A primary target was to exploit DNA methylation differences between the gene space and repetitive DNA in plants. The experience gained in DNA methylation has led to the development of methods for large-scale analysis of methylation states and the application of these platforms for the discovery of biomarkers differentiating tumor and normal tissues. The other Founders are Drs. W. Richard McCombie, Robert Martienssen and Richard K. Wilson.

Honours and Awards

Queen's Graduate Award, Queen's University at Kingston, 1984-1985. R.S. McLaughlin Fellowship, Queen's University, 1985-1988. Biotechnology Training Grant Fellowship, University of California at Irvine, 1988-1991.

Service on Committees

Member: Provincial Expert Panel: Pharmacogenetic Tests, Ontario Ministry of Health, Ontario Canada, 2010 – present.

Member: Soymap II Advisory Committee National Science Foundation USA, 2010 – present.

Member: Technology Development Advisory Group (TDAG), International Barcode of Life (iBOL) Project, 2009 - present

Member: Scientific Advisory Board for the Medicago Hapmap Project, National Science Foundation USA, 2009.

Invited Participant: ―Workshop on the Future of the NHGRI Large-Scale Sequencing Program‖, National Human Genome Research Institute, NIH USA, March 2009.

Ad hoc Member: Genome Study Section, Genomics, Computational Biology and Technology, National Institutes of Health USA, October 2008.

Member: Grant Review Committee – Cancer Genetics Panel, National Cancer Institute of Canada (NCIC), 2008 – Present.

Member: Grant Review Committee – Genomics Panel, Canadian Institutes of Health Research (CIHR), 2008 – Present.

Chair: Maize Genome Advisory Committee, National Science Foundation USA, 2008.

Member: Advisory Panel for the Plant Genome FY08, National Science Foundation USA, April 2008.

Steering Committee Member: Canada-California Cancer Stem Cell Workshop, March 2008.

Member: Site Visit Review Committee - National Human Genome Research Institute, Genome Technology Branch, National Institutes of Health USA, June 2007.

Member, Genome Study Section, Genomics, Computational Biology and Technology, National Institutes of Health USA, June 2004 – June 2007.

Chair: Canada Foundation For Innovation - 2006 New Initiatives and Leading Edge Fund, Review Committee 2 – Genomics, Proteomics, Stem Cells, Disease Models, June 2006.

Invited Participant: ―Workshop on the Future of the NHGRI Large-Scale Sequencing Program‖, National Human Genome Research Institute, NIH USA, June 2005.

Invited Participant: Workshop ―Toward the Comprehensive Genomic Analysis of Cancer‖, National Human Genome Research Institute (NIH USA) and National Cancer Institute USA, June 2005.

Chair, SoyMap Advisory Committee, National Science Foundation USA, 2005 – 2008.

Member: Special Emphasis Panel: SBIR review National Cancer Institute USA, April 2004.

2

212 John D. McPherson, Ph.D.

Member: Plant Genome Research Advisory Panel, National Science Foundation USA, April 2004.

Member: Review Committee ―Resequencing of Mouse Genomes‖, National Institute of Environmental Health Sciences, May 2004.

Invited Participant: ―New Directions for Sickle Cell Therapy in the Genome Era‖, National Institutes of Health USA, November 2003.

Ad hoc Member, Genome Study Section, National Institutes of Health USA, October 2003, February 2004.

Member: Special Emphasis Panel: ENCODE (Encyclopedia of DNA elements) Determination and Technology National Human Genome Research Institute, July 2003, June 2004.

Member: Preliminary Review: Competition in Applied Genomics and ProteomicsResearch in Human Health, Genome Canada, 2003.

Member: Expert Committee on Genomics and Proteomics, Canadian Foundation for Innovation March 2003.

Program Committee Member: American Society of Human Genetics Annual Meeting, 2002 – 2006.

Organizer and Chairperson: Workshop: ―The New Era of Positional Cloning‖, American Society of Human Genetics Annual Meeting, October 2002.

Member: Special Emphasis Panel: ―Computational Gene Identification and Genome Structure‖, National Institutes of Health USA, August 2002.

Member: Special Emphasis Panel: Specialized Programs in Research Excellence for Gynecological Cancer, National Cancer Institute USA, June 2002.

Organizer and Chairperson: Workshop: ―Comparing Genome Sequences in Vertebrates‖, American Society of Human Genetics Annual Meeting, October 2001.

Member: Expert Committee on Genomics and Proteomics, Canadian Foundation for Innovation September 2001.

Invited Participant: Gynecological Cancers Progress Review Group Roundtable, National Cancer Institute USA, June 2001.

Member: Advances in Genome Biology and Technology Conference Advisory Board, 1999 – 2001.

Invited Participant: Mouse Genome Advisory Meeting, National Institutes of Health USA, May 2000.

Member: SBIR/STTR Study Section in Genetic Sciences, National Institute of Health USA, November 1999.

Invited Reviewer: Special Emphasis Panel-03: RFA HG-98001, ―Methods for Discovering and Scoring Single Nucleotide Polymorphisms‖, National Institute of Health USA, March 1999. ad hoc Member: Genome Study Section, National Institute of Health USA, February 1999.

Member: Arrayed BAC clones for Fish Mapping of the Human Genome Review Committee, National Cancer Institute USA, June 1998.

Invited Participant: Committee to Establish Resource and Research Priorities for the Mouse, National Institute of Health USA, March 1998.

Member: Rat Genome Project Advisory Committee, National Institute of Health USA, 1996 to 1999.

Senior Database Editor, Chromosome 5, Human Genome DataBase, 1992 to 2000. ad hoc reviewer: Genome Research, Nature, PLoS One, Science

3

213 John D. McPherson, Ph.D.

ACADEMIC ACTIVITIES

Research Statement Prior to joining the Ontario Institute for Cancer Research as Director, Cancer Genomics, my career spanned three Genome Centers. Shortly after completing post -doctoral studies at the University of California, Irvine I attained a faculty position and established, as Co -Director, the National Human Genome Research Center Chromosome 5 Genome Center (1993 -1996). The UCI Genome Center constructed a physical map of human chromosome 5 in preparation for complete human genome sequencing. In addition, I participated in a number of collaborative positional cloning efforts associated with this chromosome including an international consortium to identify the gene responsible for spinal muscular atrophy. I was then recruited to the Washington University Genome Sequencing Center (GSC) where as Co -Director I played a significant role in the Human Genome Project (1996 -2003). During this time I pioneered many large -scale mapping and sequencing technologies and was the lead author on the human genome physical map. I was the lead Principal Investigator for the GSC contribution to the mouse genome and oversaw the initial mapping of the chicken genome. Throughout this time I was an active member of the senior scientific management of the Human Genome Project participating at many levels in this international collabo rative effort with weekly participation in steering meetings and both attending and organizing various meetings to review progress and chart courses. As the Genome Centers took on a wide variety of genomes spanning the Tree of Life, I chose to remain clos er t o my human genome roots and accepted an offer to join the Human Genome Sequencing Center at the Baylor College of Medicine (2003 -2007). There I established a high -throughput resequencing pipeline with a peak capacity of one million sequences per month of PCR amplified genome targets. The primary objective of this pipeline was the sequencing of all ion channel genes (~250) in 500 sporadic epilepsy patients and controls. This same pipeline was also used to examine lung adenocarcinomas and glioblastomas as part of trans Genome Center collaborations, the Tumor Sequencing Project and the Cancer Genome Atlas, respectively. These projects laid the groundwork at BCM-HGSC for further large -scale efforts at utilizing high -throughput genomic technologies to unra vel the cancer genome. Collectively these activities have made significant contributions to the availability of methodologies and accessible data sets that have benefited countless researchers around the world and provided the foundation for a movement of m y ca r eer focus to cancer genomics. Recently I have joined the Ontario Institute for Cancer Research as Director, Cancer Genomics (July 2007). In the time since relocating to OICR, I have assembled and trained a team and established a next -generation sequ encing platform. With a fleet of 15 sequencers, the sequencing capacity of this group places it in a small elite class centers with mega -scale throughput. The OICR is one of the founder members of the International Cancer Genome Consortium and I am leadin g the OICR effort to sequence 375 pancreatic adenocarcimomas and matched normal DNA. This project utilizes xenograft generation to not only provide enriched tumor material but to also provide pre -clinical models for future hypotheses testing. Through deep sequencing of germline and tumor DNA and RNA, the immediate goal of my research is to generate a comprehensive catalog of somatic alterations and to correlate these DNA and RNA changes to causative and supportive roles in tumor predisposition, initiation a nd maintenance. By gaining insight into the underlying mechanisms driving tumor formation, essential pathways will be elucidated to provide targets for therapy. Once identified, the xenograft models provide ready models for testing new therapeutic interven tions. Through multiple collaborations in the Toronto area, further tumor types are also undergoing investigation.

4

214 John D. McPherson, Ph.D.

An important extension of this work is the application of new sequencing technologies to the characterization of individual patient tumors to provide guidance for therapeutic intervention – a personalized medicine approach. Great challenges must be overcome to make this a reality, including the logistics of obtaining suitable biopsy material, rapid and comprehensive sequencing from the limited biopsy material, and interpretation of the potentially overwhelming amount of data that can be generated. Programs are being initiated with UHN clinical researchers to pilot this approach with a goal of making this routine within one to two years.

Current Research Support

Title of award: Functional Genomics of Solid Tumors for Discovery and Development of New Biologics and Biomarkers. Source: Ontario Research Fund Award: CAN$10,109,310 Dates of approved project: 04/2010-03/2014 Name of P.I: Bradley Wouters and Benjamin Neel Role: Co-Investigator The major goals of this project are: To rapidly develop novel, individualized cancer therapeutics that exploit tumor vulnerabilities for pathways that they have become unusually dependent upon or ―addicted‖ to.

Title of award: Pancreatic Cancer Genome Project and Data Coordination Centre for the International Cancer Genome Consortium Source: Canadian Foundation for Innovation Award: CAN$12,503,208 Dates of approved project: 10/2009-09/2012 Name of P.I: Tom Hudson Role: Co-P.I. The major goals of this project are: Infrastructure request to support a pancreatic cancer genome sequencing project as a contribution to the International Cancer Genome Consortium.

Title of award: Pancreatic Cancer Genome Project Source: Ontario Institute for Cancer Research Award: CAN$15,739,250 Dates of approved project: 07/2009-06/2013 Name of P.I.: John McPherson Role: P.I. The major goals of this project are: The Ontario Institute for Cancer Research (OICR) is a new centre of excellence in cancer research at the forefront of discovery and innovation. The Cancer Genomics Platform uses state-of-the-art technologies, including next-generation sequencing platforms to analyze tumors and other genomic samples. A primary focus of the Cancer Genomics Program research will be pancreatic cancer with additional capacity used to support the OICR objectives.

Title of award: Cancer Genomics Program and Platform, Ontario Institute for Cancer Research Source: Ontario Institute for Cancer Research Award: CAN$4,077,305 Dates of approved project: 07/2009-06/2013 Name of P.I.: John McPherson (OICR P.I.: Tom Hudson; $82,000,000 per year total award for all OICR Platforms and Programs; Ministry of Research and Innovation, Ontario Provincial Government) Role: Director, OICR Cancer Gen o m ics The major goals of this project are: The Ontario Institute for Cancer Research (OICR) is a new centre of excellence in cancer research at the forefront of discovery and innovation. The key elements of the OICR strategy for meeting the cancer challenge include: The Ontario Cancer Cohort designed to bring more effective prevention strategies to the population; The One Millimetre Cancer Challenge which aims to facilitate early diagnosis and cure for cancer through the development of sensitive biomarkers and imaging technologies that will detect millimetre size tumours; The Cancer Stem Cell Project to develop approaches that will target therapies that are unique to cancer stem cells, with the goal of preventing recurrence and lessening toxicity. These projects will be integrated with four platforms that will develop state-of-the-art knowledge and technologies in the following disciplines: 1. Imaging and Interventions; 2. Bio-repositories and Pathology; 3. Genomics and High-Throughput Screening (HTS); 4. Informatics and Bio-computing. The Cancer Genomics Platform uses state-of-the-art technologies, including next-generation sequencing platforms to analyze tumors and other genomic samples. A primary focus of the Cancer Genomics Program research will be pancreatic cancer with additional capacity used to support the OICR objectives. In addition, many local collaborative projects are underway.

Title of award: OICR Investigator Award

5

215 John D. McPherson, Ph.D.

Source: Ontario Institute for Cancer Research Award: CAN$415,975 Dates of approved project: 07/2009-06/2013 Name of P.I: John McPherson Role: P.I. The major goals of this project are: Support for independent research into development of genomic technologies and the role of mitochondria in cancer phenotypes.

Title of award: POP-CURE Source: Pfizer Inc. (USA) Name of P.I: Bradly Wouters (PI) Dates of approved project: 04/2009-03/2012 Award: US$5,332,054 Role: Co-Investigator The major goals of this project are: This award is for the genomic characterization of 80 colon cancer xenografts.

Past Research Support a. 1U01HG003273 Gibbs (PI) Role: Co-Investigator 11/01/06 to 10/30/09 NIH/NHGRI US$110,000,000 (NOTE: I no longer have a role in this project after leaving BCM, July 2007) Large Scale Sequencing at BCM-HGSC: The major goals of this project are to continue large scale sequencing of several mammalian genomes as well as resequencing human genes to establish a genome-wide catalog of rare variants within the population. Resequencing efforts are also directed towards tumor samples as part of the Cancer Genome Atlas Project. b. 0547567 McPherson (PI) Role: PI 09/15/05 to 12/31/06 NSF US$200,000 Physical Mapping Using Short Sequence Connectors: This project aims to develop a physical mapping method using large-insert clones and the 454 Genome Sequencer 20 sequencing platform. c. 24XS055 Gibbs (PI) Role: Co-Investigator 05/01/04 to 04/30/07 NCI US$2,300,000 Large Scale RT-PCR Clone Rescue: This project is directed at providing clones and sequenced full length open reading frames in support of the Mammalian Gene Collection goal of archiving all human and mouse genes. d. 1U01HG003273 Gibbs (PI) Role: Co-Investigator 11/01/03 to 10/30/06 NIH/NHGRI US$115,000,000 Large Scale Sequencing at BCM-HGSC: The major goal of this project is to produce draft sequences of large and small genomes and extract maximal biological information from these data. Another major activity is the resequencing of human genes for studying variation as it relates to human disease has been established. e. 1U01HG02042 Waterston (PI) Role: Co-PI 03/01/99 to 10/31/03 NIH/NHGRI US$140,000,000 Sequencing the Human Genome: The goal of this project is to provide fingerprint data for BAC clones covering the entire human genome in the first year; to position the fingerprint contigs onto chromosomes during years 1 & 2; and to sequence 1/3 of the genome over the first 3 years of the project, in order to contribute to the placement of 95% of the human sequence in the public domain by 2001. f. 1U01HG02155 McPherson (PI) Role: PI 09/30/99-10/31/03 NIH/NHGRI US$26,500,000 Sequencing the Mouse Genome: The goal of this project is to provide map data for the entire mouse genome, working draft sequence for half the mouse genome, and 115 Mb of finished mouse genome sequence to the mouse research community as a tool for gene discovery and annotation of the mouse genome. g. 1R01DK55379 Johnson (PI) Role: Co-Investigator 09/30/98-8/31/03 NIH/NIDDK US$2,140,000 An Integrated Approach to Zebrafish Genomic Resource Development: This project will develop genomic resources to be used in the identification of zebrafish genes. h. 1U01AI50934 Mardis (PI) Role: Co-Investigator 9/30/01 to 08/31/03 NIH/NIAID US$1,900,000

6

216 John D. McPherson, Ph.D.

Genomic Resources for Histoplasma capsulatum: The goal of this proposal is to produce comprehensive genomic resources for the fungal pathogen Histoplasma capsulatum. i. 1P01HG001845 McPherson (PI) Role: PI 09/01/96 to 08/31/99 NIH/NHGRI US$6,500,000 Physical Mapping Component for HGP: The goal of this proposal was to provide a sequence-ready BAC and/or PAC contig map at a rate that would sustain the sequencing effort at the Washington University Genome Sequencing Center with an uninterrupted flow of well characterized clones. j. 1P01HG001845 Waterston (PI) Role: Co-PI 04/11/96 to 06/30/99 NIH/NHGRI US$115,000,000 Human Genome Sequence – A Pilot Project: The goal of this proposal was to establish the methods and begin to sequence chromosome 7 as initial efforts towards the Human Genome Project. k. 1R13HG001570 McPherson (PI) Role: PI 09/30/96 to 09/29/97 NIH/NHGRI US$55,000 Fourth International Workshop on Human Chromosome 5: These funds supported a workshop of International researchers with common interests in genomic intervals on human chromosome 5 to coordinate research efforts and resources. l. 1P01HG000834 Wasmuth (PI) Role: Co-PI and Center Co-Director 02/01/93 to 1/31/96 NIH/NHGRI US$2,400,000 Physical Map of Chromosome 5: The long-term objective of this proposal was to develop a high resolution, contiguous physical map of human chromosome 5. The map was constructed using several different but complementary approaches, including: natural deletion mapping; radiation hybrid mapping; multicolor fluorescence in situ hybridization; and the establishment of many overlapping segments of cloned DNA in the form of cosmid contigs. m. Muscular Dystrophy Association Research Award McPherson (PI) Role: PI 09/30/93 to 09/29/95 MDA US$200,000 Positional Cloning of a Limb Girdle Muscular Dystrophy Locus on Chromosome 5: The goal of this proposal was to generate new polymorphic markers within an interval linked to a recessive form of LGMD to further narrow the region and then to identify and characterize genes in a minimal interval.

Patents

United States Patent No.: 6,211,340 B1; delta-Sarcoglycan Antibodies Inventors: Kevin P. Campbell, Daniel Jung, Franck Duclos, Volker Straub and John McPherson Assignees: University of Iowa Research Foundation and Washington University at St. Louis

PUBLICATIONS

Peer-Reviewed

1. The International Cancer genome Consortium (2010). International Network of Cancer Genome Projects. Nature 465: 993-998 . (PA)

2. Cole SA, Butte NF, Voruganti VS, Cai G, Haack K, Kent JW Jr, Blangero J, Comuzzie AG, McPherson JD, Gibbs RA (2010). Evidence that multiple genetic variants of MC4R play a functional role in the regulation of energy expenditure and appetite in Hispanic children. Am J Clin Nutr. 91:191-199. (Co-PA)

3. Angly E, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, T McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. (2009). The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput. Biol. 5:e1000593. (CA)

4. Diamandis E, Voelkerding K, Drmanac R, Agus D, McPherson J (2009). Next-Generation Sequencing: A New

7

217 John D. McPherson, Ph.D.

Revolution in Molecular Diagnostics? Clin. Chem. 55: 1-5. (Co-PA)

5. McPherson JD (2009). Next-Generation Gap. Nature Meth. Supplement, Next-generation sequencing data analysis. Volume 6, No.11s:S2-S5. (SRA)

6. Toronto International Data Release Workshop Authors, Ewan Birney, Thomas J Hudson, Eric D Green, Chris Gunter, Sean Eddy, Jane Rogers, Jennifer R Harris, S Dusko Ehrlich, Rolf Apweiler, Christopher P Austin, Lisa Berglund, Martin Bobrow, Chas Bountra, Anthony J Brookes, Anne Cambon-Thomsen, Nigel P Carter, Rex L Chisholm, Jorge L Contreras, Robert M Cooke, William L Crosby, Ken Dewar, Richard Durbin, Stephanie O M Dyke, Joseph R Ecker, Khaled El Emam, Lars Feuk, Stacey B Gabriel, John Gallacher, William M Gelbart, Antoni Granell, Francisco Guarner, Tim Hubbard, Scott A Jackson, Jennifer L Jennings, Yann Joly, Steven M Jones, Jane Kaye, Karen L Kennedy, Bartha Maria Knoppers, Nikos C Kyrpides, William W Lowrance, Jingchu Luo, John J MacKay, Luis Martín-Rivera, W Richard McCombie, John D McPherson, Linda Miller, Webb Miller, Don Moerman, Vincent Mooser, Cynthia C Morton, James M Ostell, B F Francis Ouellette, Julian Parkhill, Parminder S Raina, Christopher Rawlings, Steven E Scherer, Stephen W Scherer, Paul N Schofield, Christoph W Sensen, Victoria C Stodden, Michael R Sussman, Toshihiro Tanaka, Janet Thornton, Tatsuhiko Tsunoda, David Valle, Eero I Vuorio, Neil M Walker, Susan Wallace, George Weinstock, William B Whitman, Kim C Worley, Cathy Wu, Jiayan Wu, Jun Yu (2009). Opinion: Prepublication Data Sharing. Nature 461: 168-170. (Co-PA)

7. The MGC Project Team, G Temple, D Gerhard, R Rasooly, E Feingold, P Good, C Robinson, A Mandich, J Derge, J Lewis, D Shoaf, F Collins, W Jang, L Wagner, C Shenmen, L Misquitta, C Schaefer, K Buetow, T Bonner, L Yankie, M Ward, L Phan, A Astashyn, G Brown, C Farrell, J Hart, M Landrum, B Maidak, M Murphy, T Murphy, B Rajput, L Riddick, D Webb, J Weber, W Wu, K Pruitt, D Maglott, A Siepel, B Brejova, M Diekhans, R Harte, R Baertsch, J Kent, D Haussler, M Brent, L Langton, C Comstock, M Stevens, C Wei, M van Baren, K Salehi-Ashtiani, R Murray, L Ghamsari, E Mello, C Lin, C Pennacchio, K Schreiber, N Shapiro, A Marsh, E Pardes, T Moore, A Lebeau, M Muratet, B Simmons, D Kloske, S Sieja, J Hudson, P Sethupathy, M Brownstein, N Bhat, J Lazar, H Jacob, C Gruber, M Smith, J McPherson, A Garcia, P Gunaratne, J Wu, D Muzny, R Gibbs, A Young, G Bouffard, R Blakesley, J Mullikin, E Green, M Dickson, A Rodriguez, J Grimwood, J Schmutz, R Myers, M Hirst, T Zeng, K Tse, M Moksa, M Deng, K Ma, D Mah, J Pang, G Taylor, E Chuah, A Deng, K Fichter, A Go, S Lee, J Wang, M Griffith, R Morin, R Moore, M Mayo, S Munro, S Wagner, S Jones, R Holt, M Marra, S Lu, S Yang, J Hartigan, M Graf, R Wagner, S Letovksy, J Pulido, K Robison, D Esposito, J Hartley, V Wall, R Hopkins, O Ohara, S Wiemann (2009). The Completion of the Mammalian Gene Collection (MGC). Genome Res. 12:2324-2333. (Co-PA)

8. Pan S, Huang L, McPherson J, Muzny D, Rouhani F, Brantly M, Gibbs R, Sifers RN (2009). SNP-mediated translational suppression of ERManI modifies the onset of end-stage liver disease in alpha1-antitrypsin deficiency. Hepatology 50: 275-281; early online access march 19, 2009. (Co-PA)

9. Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, Ordway JM, McCombie WR, Leon J, Jeddeloh JA, McPherson JD (2008). Massively parallel bisulphate pyrosequencing reveals the molecular complexity of breast cancer associated cytosine methylation patterns obtained from tissue and serum DNA. Genome Res. 18:19-29. (SRA)

10. Ordway JM, Budiman MA, Korshunova Y, Maloney RK, Bedell JA, Citek RW, Bacher B, Peterson S, Rohlfing T, Hall J, Brown R, Lakey N, Doerge RW, Martienssen RA, Leon J, McPherson JD, Jeddeloh JA (2007). Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS One 2:e1314. (PA)

11. Holemon H, Korshunova Y, Ordway JM, Bedell JA, Citek RW, Lakey N, Leon J, Finney M, McPherson JD, Jeddeloh JA (2007). MethylScreen: DNA methylation density monitoring using quantitative PCR. Biotechniques 43:683-693. (PA)

12. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao MS, Twomey D, Verhaak RG, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M. (2007). Characterizing the cancer genome in lung adenocarcinoma. Nature 450:893-898. (Co-PA)

8

218 John D. McPherson, Ph.D.

13. Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD (2007). Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 316:240-3. (CA)

14. Ordway JM, Bedell JA, Citek RW, Nunberg A, Garrido A, Kendall R, Stevens JR, Cao D, Doerge RW, Korshunova Y, Holemon H, McPherson JD, Lakey N, Leon J, Martienssen RA, Jeddeloh JA (2006). Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 27:2409-2423. (Co-PA)

15. Lalani SR, Safiullah AM, Fernbach SD, Harutyunyan KG, Thaller C, Peterson LE, McPherson JD, Gibbs RA, White LD, Hefner M, Davenport SL, Graham JM, Bacino CA, Glass NL, Towbin JA, Craigen WJ, Neish SR, Lin AE, Belmont JW (2006). Spectrum of CHD7 Mutations in 110 Individuals with CHARGE Syndrome and Genotype-Phenotype Correlation. Am. J. Hum. Genet. 78:303-14. (Co-PA)

16. Naviaux RK, Good B, McPherson JD, Steffen DL, Markusic D, Ransom B, Corbeil J (2005). Sand DNA—A Genetic Library of Life at the Water’s Edge. Marine Ecology Progress Series 301: 9-22.

17. Horvath JE, Gulden CL, Vallente RU, Eichler MY, Ventura M, McPherson JD, Graves TA, Wilson RK, Schwartz S, Rocchi M, Eichler EE (2005). Punctuated duplication seeding events during the evolution of human chromosome 2p11. Genome Res. 15:914-927. (CA)

18. Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK. (2005). Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434:724-731. (PA)

19. Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P, Johnson ME, Eichler MY, McPherson JD, Zhao S, Paabo S, Eichler EE (2005). Lineage-specific expansions of retroviral insertions within the genomes of African Great Apes but not Humans and Orangutans. PLoS Biol. 4: 1-11. (Co-PA)

20. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team (2004). The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 14: 2121-2127. (Co-PA)

21. International Chicken Genome Sequencing Consortium Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Genomefingerprint map, sequence and assembly: Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang S-P, Mapping: Michael N. Romanov MN, Catherine M. Rondelli CM, 9

219 John D. McPherson, Ph.D.

Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, cDNAsequencing:, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde J-M, Wilson SA, Othersequencing and libraries: Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK-S, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, deJong PJ, Analysisand annotation:, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Brian Raney B, Adam Siepel A, W. James Kent WJ, Haussler D, Eyras E, Castelo R, Abril JP, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Projectmanagement:, Fulton LA, Mardis ERand Wilson RK (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716. (Co-PA)

22. Wallis JW, Aerts J, Groenen MA, Crooijmans RP, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang SP, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, de Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, Warren WC (2004). A physical map of the chicken genome. Nature 432: 761-764. (Co-PA)

23. Liao G, Wang J, Guo J, Allard J, Cheng J, Ng A, Shafer S, Puech A, McPherson JD, Foernzler D, Gary Peltz, and Usuka J (2004). In Silico Genetics: Identification of a Functional Element Regulating H2-E Gene Expression. Science 306: 609-695. (Co-PA)

24. Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK (2004). The human genome: genes, pseudogenes, and variation on chromosome 7. Cold Spring Harb Symp Quant Biol. 2003;68:13-22. (PA)

25. Magrini V, Warren WC, Wallis J, Goldman WE, Xu J, Mardis ER, McPherson JD (2004). Fosmid-Based Physical Mapping of the Histoplasma capsulatum.Genome. Genome Res. 14:1603-1609. (SRA)

26. Wu JQ, Garcia AM, Hulyk S, Sneed A, Kowis C, Yuan Y, Steffen D, McPherson JD, Gunaratne PH, Gibbs RA (2004). Large-scale RT-PCR recovery of full-length cDNA clones. Biotechniques 690: 698-700. (PA)

27. Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hübner N, Jones S, Marra M, Schein J. (2004). Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 14:766-779. (PA)

28. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, U, Wingrove J, Camara F, Mar Albà M,

10

220 John D. McPherson, Ph.D.

Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521. (PA)

29. Chang YT, Sharma R, Marsh JL, McPherson JD, Bedell JA, Knust A, Brautigam C, Hoffmann GF, Hyland K. (2004). Levodopa-Responsive aromatic L-amino acid decarboxylase deficiency. Ann Neurol. 55:435-438. (Co-PA)

30. Rao C, Foernzler D, Loftus SK, Liu S, McPherson JD, Jungers KA, Apte SS, Pavan WJ, Beier DR (2003). A defect in a novel ADAMTS family member is the cause of the belted white-spotting mutation. Development 130, 4665-4672. (CA)

31. Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. (2003). The DNA sequence of human chromosome 7. Nature 424, 157-164. (Co-PA)

32. Horvath JE, Gulden CL, Bailey JA, Yohn C, McPherson JD, Prescott A, Roe BA, De Jong PJ, Ventura M, Misceo D, Archidiacono N, Zhao S, Schwartz S, Rocchi M, Eichler EE (2003). Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. Mol Biol Evol. 9, 1463-1479. (CA)

33. Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC (2003). The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 6942, 825-837. (CA)

34. Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJ, Marra MA (2003). Software for automated analysis of DNA fingerprinting gels. Genome Res. 5, 940-953. (PA)

35. Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A, Pelletier E, Vico V, Anthouard V, Rowen L, Madan A, Qin S, Sun H, Du H, Pepin K, Artiguenave F, Robert C, Cruaud C, Brüls T, Jaillon O, Friedlander L, Samson G, Brottier P, Cure S, Ségurens B, Anière F, Samain S, Crespeau H, Abbasi N, Aiach N, Boscus D, Dickhoff R, Dors M, Dubois I, Friedman C, Gouyvenoux M, James R, Madan A, Mairey-Estrada B, Mangenot S, Martins N, Ménard M, Oztas S, Ratcliffe A, Shaffer T, Trask B, Vacherie B, Bellemere C, Belser C, Besnard-Gonnet M, Bartol-Mavel D, Boutard M, Briez-Silla S, Combette S, Dufossé-Laurent V, Ferron C, Lechaplais C, Louesse C, Muselet D, Magdelenat G, Pateau E, Petit E, Sirvain-Trukniewicz P, Trybou A, Vega-Czarny N, Bataille E, Bluet E, Bordelais I, Dubois M, Dumont C, Guérin T, Haffray S, Hammadi R, Muanga J, Pellouin V, Robert D, Wunderle E, Gauguet G, Roy A, Sainte-Marthe L, Verdier J, Verdier-Discala C, Hillier L, Fulton L, McPherson J, Matsuda F, Wilson R, Scarpelli C, Gyapay G, Wincker P, Saurin W, Quétier F, Waterston R, Hood L,

11

221 John D. McPherson, Ph.D.

Weissenbach J. (2003). The DNA sequence and analysis of human chromosome 14. Nature 421, 601-607. (Co-PA)

36. Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562. (PA)

37. Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu A-L, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanesek JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR (2002). A physical map of the mouse genome. Nature 419, 743-750. (PA)

38. Lindblad-Toh K, Lander ES, McPherson JD, Waterston RH, Rodgers J, Birney E (2002). Progress in sequencing the mouse genome. Genesis 31, 137-141. (Co-PA)

39. Hukriede N, Fisher D, Epstein J, Joly L, Tellis P, Zhou Y, Barbazuk B, Cox K, Fenton-Noriega L, Hersey C, Miles J, Sheng X, Song A, Waterman R, Johnson SL, David IB, Chevrette M, Zon LI, McPherson J, Ekker M (2001). The LN54 radiation hybrid map of zebrafish expressed sequences. Genome Res. 12, 2127-2132. (Co-PA)

40. Montgomery KT, Lee E, Miller A, Lau S, Shim C, Decker J, Chiu D, Emerling S, Kim R, Lenz J, Han J, Yang R, Ioshikhes I, Renault B, Marondel I, Yoon S-JK, Song K, Murty VVVS, Scherer S, McPherson J, Gibbs R, Kucherlapati R (2001). A high resolution STS-content based map of human chromosome 12. Nature 409, 945-946. (Co-PA)

41. Tilford CA, Kuroda-Kawaguchi T, Skaletsky H, Rosen S, Brown LG, Rosenberg M, McPherson JD, Wylie K, Sekhon M, Kucaba TA, Waterston RH, Page DC (2001). A physical map of the human Y chromosome. Nature 409, 943-945. (Co-PA)

42. International Human Genome Mapping Consortium McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E,

12

222 John D. McPherson, Ph.D.

Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H (2001). A physical map of the human genome. Nature 409, 934-941. (SRA)

43. International SNP Map Working Group Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D. (2001). A map of human genome sequence variation containing 1.4 million single nucleotide polymorphisms. Nature 409, 928-933. (PA)

44. International Human Genome Sequencing Consortium Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ. (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921. (PA)

45. Barbazuk WB, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell JA, McPherson JD, Johnson SL (2000). The syntenic relationship of the zebrafish and human genomes. Genome Res. 10, 1351-1358. (PA)

46. Hukriede NA, Joly L, Tsang M, Miles J, Tellis P, Epstein JA, Barbazuk WB, Li FN, Paw B, Postlethwait JH, Hudson TJ, Zon LI, McPherson JD, Chevrette M, Dawid IB, Johnson SL, Ekker M (1999). Radiation hybrid mapping of the zebrafish genome. Proc. Natl. Acad. Sci. USA 17, 9745-9750 (Co-PA)

47. Monani UR, McPherson JD, Burghes AH (1999). Promoter analysis of the human centromeric and telomeric survival motor neuron genes (SMNC and SMNT). Biochim. Biophys. Acta. 1445, 330-336. (Co-PA)

48. Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gund C, McCombie WR, MacDonald K, McPherson J, Mudd N, Parnell L, Schein J, Seim R, Shelby P, Waterston R, Wilson R (1999). A map for sequence analysis of the Arabidopsis thaliana genome. Nature Genetics 22, 265-270. (Co-PA)

49. Monani UR, Lorson CL, Parsons DW, Prior TW, Androphy EJ, Burghes AHM, and McPherson JD (1999). A single nucleotide difference that alters splicing patterns distinguishes the SMA gene SMN1 from the copy gene SMN2. Hum.

13

223 John D. McPherson, Ph.D.

Molec. Genet. 8,1177-1183. (SRA)

50. Ellsworth RE, Ionasescu V, Searby C, Sheffield VC, Braden VV, Kucaba TA, McPherson JD, Marra MM, Green ED (1999). The CMT2D locus: refined genetic position and construction of a bacterial clone-based physical map. Genome Res. 9, 568-574. (Co-PA)

51. Wu Y-Q, Heilstedt HA, Bedell JA, May KM, Starkey DE, McPherson JD, Shapira SK, Shaffer LG (1999). Molecular refinement of the 1p36 deletion syndrome reveals size diversity and a preponderance of maternally derived deletions. Hum. Molec. Genet. 8, 313-321. (Co-PA)

52. The Sanger Centre and The Washington University Sequencing Center (1998). Toward a complete human genome sequence. Genome Res. 8, 1097-1108. [This article was written by the Senior Management at the two Genome Centres, including McPherson JD but with a decision to only list the Centre names as authors.] (PA)

53. Jaju RJ, Boultwood J, Oliver FJ, Kostrzewa M, Fidler C, Parker N, McPherson JD, Morris SW, Muller U, Wainscoat JS, Kearny L (1998). Molecular cytogentic delineation of the critical deleted region in 5q- syndrome. Genes Chromosomes Cancer 22, 251-256. (Co-PA)

54. Simmons AD, Puschel AW, McPherson JD, Overhauser J, Lovett M (1998). Molecular cloning and mapping of human semaphorin F from the Cri-du-chat candidate interval. Biochem. Biophys. Res. Commun. 242, 685-691. (Co-PA)

55. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH (1997). High throughput fingerprint analysis of large-insert clones. Genome Res., 7, 1072-1084. (PA)

56. McPherson JD, Apostol B, Wagner-McPherson CB, Hakim S, Del Mastro RG, Aziz N, Baer E, Gonzales G, Krane MC, Markovich R, Masny P, Ortega M, Vu J, Vujicic M, Church DM, Segal A, Grady DL, Moyzis RK, Spence A, Lovett M, Wasmuth JJ (1997). A Radiation Hybrid Map of Human Chromosome 5 with Integration of Cytogenetic, Genetic and Transcript Maps. Genome Res., 7, 897-909. (SRA)

57. McPherson JD, Krane MC, Wagner-McPherson CB, Kos CH, Tennenhouse HS (1997). High resolution mapping of the renal sodium-phosphate cotransporter gene (NPT2) confirms its localization to human chromosome 5q35. Pediatr. Res., 41, 632-634. (SRA)

58. Jung D, Duclos F, Apostol B, Straub V, Lee JC, Allamand V, Venzke DP, Sunada Y, Moomaw CR, Leveille CJ, Slaughter CA, Crawford TO, McPherson JD, Campbell KP (1996). Characterization of delta-Sarcoglycan, a Novel Component of the Oligomeric Sarcoglycan Complex Involved in Limb-Girdle Muscular Dystrophy. J. Biol. Chem. 271, 32321-32329. (PA)

59. Feldblyum TV, Maglott DR, McPherson JD, Adams M, Apostol BL, Durkin AS, Wasmuth JJ, Nierman WC (1996). Regional Assignment and Tissue-Specific Patterns of Expression of Twenty-one Expressed Sequence Tags (ESTs) on Human Chromosome 5. Genomics 33, 128-130. (Co-PA)

60. Grady DL, Robinsom DL, Gersh M, Nickerson E, McPherson J, Wasmuth JJ, Overhauser J, Deaven LL, Moyzis RK (1996). The Generation and Regional Localization of 303 New Chromosome 5 Sequence-Tagged Sites. Genomics 32 32, 91-96. (Co-PA)

61. Del Mastro RG, Wang L, Simmons AD, Gallardo TD, Clines GA, Ashley JA, Hillard CJ, Wasmuth JJ, McPherson JD, M Lovett (1995). Human Chromosome-Specific cDNA Libraries: New Tools for Gene Identification and Genome Annotation. Genome Res. 2, 185-194. (Co-PA)

62. Spicer AP, Roller ML, Camper SA, McPherson JD, Wasmuth JJ, Hakim S, Wang C, Turley E, McDonald JA (1995). The Human and Mouse Receptors for Hyaluronan-Mediated Motility, RHAMM, Genes (HMMR) Map to Human Chromosome 5q33.2-qter and Mouse Chromosome 11. Genomics 30, 115-117. (CA)

63. Abrams WR, Ma R-I, Kucich U, Bashir MM, Decker S, Tsipouras P, McPherson JD, Wasmuth JJ, Rosenbloom J (1995). Molecular Cloning of the Microfibrillar Protein MFAP3 and Assignment of the Gene to Human Chromosome 5q32-q33.2. Genomics 26, 47-54. (Co-PA) 14

224 John D. McPherson, Ph.D.

64. Vamakopoulos NC, Sioutopoulou TO, Durkin SA, Nierman WC, Wasmuth JJ, McPherson JD (1995). Mapping the Human Corticotrophin Releasing Hormone Binding Protein Gene (CRHBP) to the Long Arm of Chromosome 5 (5q11.2-q13.3). Genomics 25, 325-327. (PA)

65. Didonato CJ, Morgan K, Carpten JD, Feurst P, Ingram SE, Prescott G, McPherson JD, Wirth B, Zerres K, Hurko O, Wasmuth JJ, Mendell J, Burghes AHM, Simard L (1994). Association Between Ag-1CA Alleles and Severity of Childhood-onset Spinal Muscular Atrophy. Am. J. Hum. Genet. 55, 1218-1229. (Co-PA)

66. Loftus SK, Shiang R, Warrington JA, Bengtsson U, McPherson JD, Wasmuth JJ (1994). Genes Encoding Adrenergic Receptors Are Not Clustered on the Long Arm of Human Chromosome 5. Cytogenet. and Cell Genet. 67, 69-74. (PA)

67. Burghes AHM, Ingram SE, McLean M, Thompson TG, McPherson JD, Kote-Jarai Z, Carpten JD, DiDonato CJ, Ikeda J-E, Surh L, Wirth B, Sargent CA, Ferguson-Smith MA, Fuerst P, Moyzis RK, Grady DL, Zerres K, Korneluk R, MacKenzie A, Wasmuth JJ (1994). A Multicopy Dinucleotide Marker that Maps Close to the Spinal Muscular Atrophy Gene. Genomics 21, 394-402. (Co-PA)

68. Clermont O, Burlet P, Burglen L, Lefebvre S, Pascal F, McPherson J, Wasmuth JJ, Cohen D, Le Paseller D, Weissenbach J, Lathrop M, Munnich A, Melki J (1994). Use of Genetic and Physical Mapping to Locate the Spinal Muscular Atrophy Locus Between Two New Highly Polymorphic DNA Markers. Am. J. Hum. Genet. 54, 687-694. (Co-PA)

69. McPherson JD, Morton RA, Ewing CM, Wasmuth JJ, Overhauser J, Nagafuchi A, Tsukita S, Isaacs WB (1994). -q22.Genomics 19, 188-190. (PA)

70. McPherson JD, Wasmuth JJ, Kurys G, Pietruszko R (1994). Human Aldehyde Dehydrogenase:Chromosomal 93, 211-212. (PA)

71. Clark CC, Cohen I, Eichstetter I, Cannizzaro LA, McPherson JD, Wasmuth JJ, Iozzo RV (1993). Molecular Cloning of the Human Proto-oncogene Wnt-5A and Mapping of the Gene (WNT5A) to Chromosome 3p14-p21. Genomics 18, 249-260. (Co-PA)

72. Thompson TG, Morrison KE, Kleyn P, Bengtsson U, Gilliam TC, Davies K, Wasmuth JJ, McPherson JD (1993). High Resolution Physical Map of the Region Surrounding the Spinal Muscular Atrophy Gene. Hum. Mol. Genet. 2, 1169-1176. (SRA)

73. Francis MJ, Morrison KE, Campbell I, Grewal PK, Christodoulou Z, Daniels RJ, Monaco AP, Frischauf A-M, McPherson J, Wasmuth J, Davies KE (1993). A Contig of Non-chimaeric YACs containing the Spinal Muscular Atrophy Gene in 5q13. Hum. Mol. Genet. 2, 1161-1167. (Co-PA)

74. Bernard LE, McPherson JD, Wasmuth JJ, Kreklywich CN, Brzustowicz L, Wood S (1993). Linkage Mapping Detects 2 Secondary Microdeletions in Cell Hybrid HHW1064, Used to Isolate DNA Probes From Within 5q11.2-q13.3. Cytogenet. Cell Genet. 64, 46-48. (Co-PA)

75. Brant SR, Bernstein M, Wasmuth JJ, Taylor EW, McPherson JD, Li X, Walker S, Pouyssgur J, Donowitz M, Tse C-M and Jabs EW (1993). Physical and Genetic Mapping of a Human Apical Epithelial NA+/H+ Exchanger (NHE3) Isoform to Chromosome-5p15.3. Genomics 15, 668-672. (CA)

76. Sun W, McPherson JD, Wasmuth JJ, Hoang DQ, Evans GA, Montal M (1992). Mapping of a Human Brain Voltage-gated Calcium Channel to Human Chromosome 12p13-pter. Genomics 14, 1092-1094. (Co-PA)

77. Iozzo RV, Naso MF, Cannizzaro LA, Wasmuth JJ, McPherson JD (1992). Mapping of the Versican Proteoglycan Gene (CSPG2) to the Long arm of Human Chromosome 5 (5q12-5q14). Genomics 14, 845-851. (PA)

78. Grissmer S, Ghanshani S, Dethlefs B, McPherson JD, Wasmuth JJ, Gutman GA, Cahalan MD, Chandy KG (1992). The Shaw-Related Potassium-Channel Gene, Kv3.1, on Human Chromosome 11, Encodes the Typel K+ Channel in T Cells. J. Biol. Chem. 267, 20971-20979. (Co-PA)

15

225 John D. McPherson, Ph.D.

79. Ahmed CMI, Ware DH, Lee SC, Patten CD, Ferrer-Montal AV, Schnider AF, McPherson JD, Wagner-McPherson CB, Wasmuth JJ, Evans GA, Montal M (1992). Primary Structure, Chromosomal Localization, and Functional Expression of a Voltage-Gated Sodium Channel from Human Brain. Proc. Natl. Acad. Sci. USA 89, 8220-8224. (Co-PA)

80. McNamara JO, Eubanks JH, McPherson JD, Wasmuth JJ, Evans GA, Heinemann SF (1992). Chromosomal Localization of Human Glutamate Receptor Genes. J. Neuroscience 12, 2555-2562. (Co-PA)

81. Peddada L, McPherson JD, Law R, Wasmuth JJ, Youderian P, Deans RJ (1992). Somatic Cell Mapping of the Human Cyclophilin B Gene (PPIB) to Chromosome 15. Cytogenet. Cell Genet. 60, 219-221. (Co-PA)

82. Scherer LJ, McPherson JD, Wasmuth JJ, Marsh JL (1992). Human Dopa Decarboxylase: Localization to Human Chromosome 7p11 and Characterization of Hepatic cDNAs. Genomics 13, 469-471. (Co-PA)

83. Liptay S, Schmid RM, Perkins ND, Meltzer P, Altherr MR, McPherson JD, Wasmuth JJ and Nabel GJ (1992). Related subunits of NF-kB Map to Two Distinct Loci Associated with Translocations in Leukemia, NFKB1 and NFKB2. Genomics 13, 287-292. (Co-PA)

84. Eubanks JH, Altherr M, Wagner-McPherson C, McPherson JD, Wasmuth JJ, Evans GA (1992). Localization of the D5 Dopamine Receptor gene to Human Chromosome 4p15.1-p15.3, Centromeric to the Huntington's Disease Locus. Genomics 12, 510-516. (Co-PA)

85. Ghanshani S, Pak M, McPherson JD, Strong M, Dethlefs B, Wasmuth JJ, Salkoff L, Gutman GA, Chandy KG (1992). Genomic Organization, Nucleotide Sequence, and Cellular Distribution of a Shaw-related Potassium Channel Gene, Kv3.3, and Mapping of KV3.3 and KV3.4 to Human Chromosomes 19 and 1. Genomics 12, 190-196. (Co-PA)

86. Weber JL, Polymeropoulos MH, May PE, Kwitek AE, Xiao H, McPherson JD, Wasmuth JJ (1991). Mapping of Human Chromosome 5 Microsatellite DNA Polymorphisms. Genomics 11, 695-700. (PA)

87. Joslyn G, Carlson M, Thilveris A, Albertsen H, Gelbert L, Samonwitz W, Groden J, Stevens J, Spiro L, Robertson M, Sargeant L, Krapcho K, Wolff E, Burt R, Hughes JP, Warrington J, McPherson J, Wasmuth J, Le Paslier D, Adberrahim H, Cohen D, Leppert M, White R (1991). Identification of Deletion Mutations and Three New Genes at the Familial Polyposis Locus. Cell 66, 601-613. (Co-PA)

88. Groden J, Thliveris A, Samonwitz W, Carlson M, Gelbert L, Albertson H, Joslyn G, Stevens J, Spiro L, Robertson M, Sargeant L, Krapcho K, Wolff E, Burt R, Hughes JP, Warrington J, McPherson J, Wasmuth J, Le Paslier D, Abderrahim H, Cohen D, Leppert M, White R (1991). Identification and Characterization of the Familial Adenomatous Polyposis Gene. Cell 66, 589-600. (Co-PA)

89. Tabas JA, Zasloff M, Wasmuth JJ, Emanuel BS, Altherr MR, McPherson JD, Wozney JM, Kaplan FS (1991). Bone Morphogenetic Protein: Chromosomal Localization of Human Genes for BMP1, BMP2 and BMP3. Genomics 9, 283-289. (Co-PA)

90. McPherson JD, Shilton BH, Walton DJ (1988). Evidence for Glycation of Horse Liver Alcohol Dehydrogenase In Vivo. Biochem. Biophys. Res. Comm. 152, 711-716. (PA)

91. McPherson JD, Shilton BH, Walton DJ (1988). Role of Fructose in Glycation and Cross-linking of Proteins. Biochemistry 27, 1901-1907. (PA)

92. Walton DJ, McPherson JD (1987). Analysis of Glycated Amino Acids by High-Performance Liquid Chromatography of Phenylthiocarbamyl Derivatives. Anal. Biochem. 164, 547-553. (PA)

93. Walton DJ, McPherson JD, Hvidt T, Szarek WA (1987). Synthetic Routes to N-(1-Deoxyfructos-1-yl)amino Acids by Way of Reductive Amination of Hexosuloses. Carbohydr. Res. 161, 123-130. (PA)

94. Walton DJ, McPherson JD (1986). Non-enzymic Glycation of Proteins; Analysis of N-(1-Deoxyhexitol-1-yl)amino Acids by High-Performance Liquid Chromatography. Carbohydr. Res. 153, 285-293. (PA)

16

226 John D. McPherson, Ph.D.

Book Chapters

95. Ross MT, LaBrie S, McPherson J, Stanton VP (1999). Screening Large-Insert Libraries by Hybridization. In Current Protocols in Human Genetics, eds. N.C. Dracopoli, J.L. Haines, B.R. Korf, D.T. Moir, C.C. Morton, C.E. Seidman, J.G. Seidman, D.R. Smith. pp. 5.6.1-5.6.52 John Wiley and Sons, New York

96. Mattise TC, Wasmuth JJ, Meyers RM, McPherson JD (1999). Somatic cell genetics and radiation hybrid mapping.In Genome Analysis: A Laboratory Manual, Volume 4: Mapping Genomes, eds. B. Birren, E. D. Green, P. Hieter, S. Klapholz, R.M. Meyers, H. Riethman and J. Roskams. pp. 259-302 Cold Spring Harbor Laboratory Press, New York.

97. Walton DJ, McPherson JD, Shilton BH (1989). Fructose Mediated Crosslinking of Proteins.In Progress in Clinical and Biological Research, Vol. 304: The Maillard Reaction in Aging, Diabetes and Nutrition.Eds. Baynes, J.W. and Monnier, V.M.Alan R. Liss Inc., New York, NY, 163-170.

Reviews

98. Klein SL, Gerhard DS, Wagner L, Richardson P, Schriml LM, Sater AK, Warren WC, McPherson JD (2006). Resources for genetic and genomic studies of Xenopus. Methods Mol Biol. 322:1-16.

99. Mardis E, McPherson J, Martienssen R, Wilson RK, McCombie WR (2002). What is finished, and why does it matter. Genome Res. 12, 669-671.

100. McPherson JD (1997). Sequence Ready - or Not? Genome Res., 7, 1111-1113.

No n -Refereed

101. Gibson-Brown, J, Osoegawa, K, McPherson, JD, Waterston, RH, de Jong, PJ, Rokhsar, DS, Holland, LZ (2003). A proposal to sequence the amphioxus genome submitted to the Joint Genome Institute of the US Department of Energy. J. Exper. Zoology 300, 5-22.

102. McPherson JD, Le Beau M (1994). Report of the Committee on the Genetic Constitution of Chromosome 5. Genome Priority Reports.

103. McPherson JD, Deaven LL (1993). Report of the Committee on the Genetic Constitution of Chromosome 5. Genome Priority Reports 1, 249-268.

104. Westbrook CA, Neuman WL, McPherson J, Camper S, Wasmuth J, Plaetke R, Williamson R (1992). Report of the Second International Workshop on Human Chromosome 5 Mapping. Cytogenet. Cell Genet. 61, 226-231.

PRESENTATIONS AND LECTURES

Ohio State University Comprehensive Cancer Center Annual Scientific Meeting -Targeted Cancer Therapies: Discovery to Personalized Medicine. February 2010, Columbus Ohio ―High Throughput Sequencing and Cancer Genomics‖.

Symposium - Advanced Analytical Technologies: Diagnostic and Therapeutic Applications November, 2009 Department of Lab Medicine and Pathobiology, University of Toronto. ―High-Throughput Gene Sequencing‖.

Alberta Cancer Board and the International Agency for Research on Cancer: Cohorts and Consortia: From Biotechnology to Populations, June 2009, Banff, Alberta. ―Incorporating Latest Technology into Molecular Epidemiologic Studies‖.

American Association for the Advancement of Science: Science Magazine Webinar Series (http://www.sciencemag.org/webinar/) Invited Speaker. ―Advances in Cancer Genomics‖. April 2009.

American Association of Cancer Researchers: Annual Meeting - Methods Workshop. Single Molecule Sequencing Approaches, Methods, and Applications ―High-throughput sequencing applications in cancer genomics‖, April 2009.

17

227 John D. McPherson, Ph.D.

Genome Quebec and Cambridge Healthtech Institute: Pharmacogenomics Now - Re-sequencing of Human Genes Workshop, November 2008, Montreal , Quebec. ―Cancer Genomics Applications of Human Genome Resequencing‖.

National Research Council of Canada, Biotechnology Research Institute, October 2008, Montreal, Quebec ―Cancer Genomics at the Ontario Institute for Cancer Research‖.

National Science Foundation IBDR: Workshop on Transformative Instrumentation for Biological Research – A vision for the Future, September 2008, Arlington, Virginia. ―"Future Directions and Opportunities for Genomics in Biological Research"

Intelligent Systems for Molecular Biology Annual International Conference, Special Interest Group on Algorithms for Next Generation Sequencing Technologies, July 2008, Toronto, Ontario. Keynote Speaker, ―Cancer Genomics at the Ontario Institute for Cancer Research – Opportunities for Software Development‖.

Applied Biosystems R&D Seminar Series, June 2008, Foster City, California. ―Impact of Next-generation Sequencing on Cancer Genomics‖

Plant, Animal and Microbe Genomes X Conference, January 2002, San Diego, CA. ―Integrated Whole Genome BAC Maps Utilizing Restriction Digest Fingerprinting and Overgo Hybridization‖.

Fifth International Scientific Meeting of the Cassava Biotechnology Network, November 2001, St. Louis, MO. ―Large-scale Mapping and Sequencing‖.

International Mouse Genome Conference, October 2000, Edinburgh, UK. ―Mapping and Sequencing the Mouse Genome‖.

Genome Sequencing Course, National Academy of Sciences sponsorship, October 2000, Buenos Aires, Argentina. ―The Human Genome Project‖.

Advances in Genome Biology and Technology, February 1999, Marco Island, FL. ―Sequencing the Mouse Genome‖.

American Society of Human Genetics Annual Meeting, October 1998, Denver, MO. ―Mapping and Sequencing the Human Genome‖.

Meetin g Presentations* and Posters

Refereed

The Biology of Genomes, May 2009, Cold Spring Harbor Laboratory. ―Targe ted Resequencing of Twen t y -four Loci Im plicated in Colorectal Cancer ‖*.

Advances in Genome Biolo gy and Technology, February 2009 , Marco Island, Florida. ―Optimization of Direct Selection on Cancer Genomic Regions Using Multiple Next -generation Sequencing Platforms‖ a n d ―Quantitation of AB SOLiD Libraries Using Quantitative PCR‖.

The Biology of Genomes, May 2007, Cold Spring Harbor Laboratory. ―Large -Scale Detection of Sequence Variants Associated with Disease: Resequencing at Baylor College of medicine Human Genome Sequencing Center‖*.

Th e Biology of Genomes, May 2007, Cold Spring Harbor Laboratory. ―Genetic Dissection of Idiopathic Generalized Epilepsy Through SNP Discovery in Genes Encoding Ion Channels in Case Control Populations‖.

The Biology of Genomes, May 2006, Cold Spring Harbor La boratory. ―Medical Resequencing: High -Throughput Detection of Sequence Variants Associated with Disease‖.*

18

228 John D. McPherson, Ph.D.

Advances in Genome Biology and Technology, February 2006, Marco Island, Florida. ―Mutation Detection in Hepatocellular Car cin o m a Specimens using t he 454 GS Pyrosequencing Platform‖.

Advances in Genome Biology and Technology, February 2006, Marco Island, Florida. ―Med ica l Resequencing at the Baylor College of medicine Human Genome Sequencing Center‖.*

Advances in Genome Biology and Technology, Feb ruary 2006, Marco Island, Florida. ―High -Throughput Gene Rescue by RT-PCR for the Mammalian Gene Collection‖.*

Advances in Genome Biolo gy and Technology, February 2004 , Marco Island, Florida. ―A Ma p -Assisted Whole Genome Shotgun Strategy for Sequencing the Histoplasma Capsulatum Gen o m e‖.

The Biology of Genomes, May 2005, Cold Spring Harbor Laboratory. ―High -Throughput Cloning of Fu ll-Length Open Reading Frames Representing Human and Mouse Genes‖.

The Biology of Genomes, May 2004, Cold Spring Harbor La boratory. ―Large -Sca le RT-PCR Pipeline to Discover Novel Mammalian Genes, Recover Full-Length cDNA Clones and Characterize Genome Complexity‖.

Genome Mapping and Sequencing, May 2002, Cold Spring Harbor Laboratory. ―A Physical Map of the Mouse Genome‖.

Genome Mapping and Sequencing, May 2001, Cold Spring Harbor Laboratory. ―Large -Sca le Sequencing of the Mouse Genome‖.*

Genome Mapping and Sequencing, May 2001, Cold Spring Harbor Laboratory. ―A Fingerprinted BAC Clone Physical Map of the Mouse Genome‖.

Genome Mapping and Sequencing, May 2000, Cold Spring Harbor Laboratory. ―A BAC Physical Map of the Human Genome‖.*

Genome Mapping and Sequencing, May 2000, Cold Spring Harbor Laboratory. ―Fingerprinted BAC Clones for Sequencing the Mouse Genome‖.

Gen ome Mapping and Sequencing, May 2000, Cold Spring Harbor Laboratory. ―SNP Detection at the Genome sequencing Center‖.

Genome Mapping and Sequencing, May 1999, Cold Spring Harbor Laboratory. ―Large -Sca le Human Genomic Mapping and Sequencing at the Washin gton University Genome Sequencing Cen t er ‖.*

Genome Mapping and Sequencing, May 1999, Cold Spring Harbor Laboratory. ―En Route to a Human Chromosome Sequence: Progress on Chromosome 7‖.

Genome Mapping and Sequencing, May 1998, Cold Spring Harbor Laborato ry. ―Large -Sca le Human Genomic Mapping and Sequencing at the Washington University Genome Sequencing Cen t er ‖.* 19

229 John D. McPherson, Ph.D.

Genome Mapping and Sequencing, May 1998, Cold Spring Harbor Laboratory. ―Closing Gaps in the Chromosome 7 Sequence -Ready Map‖.

Genome Mapping and Sequencing, May 1997, Cold Spring Harbor Laboratory. ―Construction of BAC/ PAC COntig Maps Suitable for Large -Scale Sequencing: Early Experience with Human Chromosome 7‖.*

Genome Mapping and Sequencing, May 1995, Cold Spring Harbor Laboratory. ―Huma n Ch r o m o so m e -Specific cDNA Libraries: New Tools for Gene Identification and Genome Annotation‖.

Genome Mapping and Sequencing, May 1993, Cold Spring Harbor Laboratory. ―The Generation of a Framework STS Map for Human Chromosome 5‖.*

TEACHING EXPERIENCE

Next Generation Sequencing, Cold Spring Harbor Laboratory Course Instructor, 2006 - Present. This two-week course introduced the concepts behind the recent disruptive sequencing technologies. Lectures covered the new chemistries, hardware and analysis of the most advanced of these new technologies, primarily the Solexa and 454 Life Sciences platforms, and which sequencing projects each is best applied. Four 454 GS20 sequencers were used to sequence PCR amplicons, microRNA, two bacterial genomes and matched tumor and normal samples. This course continues annually and is updated in title and content to keep up with dramatic advancer in sequence technology.

Acquiring and Analyzing Genomic Sequence Data, Cold Spring Harbor Laboratory Course. Instructor, 1998 to 2004. This two-week all day course consists of four modules, which feature: 1) production sequencing and sequence finishing, 2) sequence variation analysis, 3) cross-species sequence comparison and 4) gene prediction and annotation.

Ad hoc Genetics, Genomics and Bioinformatics Courses: Department of Human and Molecular Genetics, Baylor College of Medicine and Department of Genetics, Washington University School of Medicine. Over the past 13 years, I have given one to two lectures during each of the Spring and Fall course periods as requested by Departmental course masters. These have been to undergraduate, graduate and medical students and have largely focused on the human genome, general genomics and its application to human disease analysis.

Introduction to Genomics: Department of Genetics, Washington University School of Medicine, Spring 2003 (3 hours of lectures and 2 hours of computer lab per week). This is a new course where lectures covered: genome structure and analysis, genomics, sequence analysis, proteomics, polymorphisms, linkage disequilibrium, microarray analysis and epigenomics.

Advanced Genetics: An Introduction to Genomic Analysis: Department of Genetics, Washington University School of Medicine, Fall 1998 (3 hours of lectures per week). Lectures covered genomic analysis and its role in genetic research.

Medical student Molecular Genetics course: Department of Biological Chemistry, University of California, Irvine, Fall, 1995 (3 hours of lectures per week). Lectures covered the structure of DNA and its relationship to gene expression.

Graduate Student Supervision:

Primary: Shirley Tam (2009- ): M.Sc. University of Toronto. ―Prognostic miRNA Markers in Non-Small Cell Lung Cancer‖.

Joseph Bedell (1995-1999): Ph.D. (1999) U.C., Irvine, Mentor (work completed at Washington University 1995-1999 due to my relocation) ―Molecular Analysis of the Human 1p36 Deletion Syndrome and Phylogenetic Analysis of a Novel Cyclin Gene Which is Frequently Deleted.‖ After a one year post-doctoral position in bioinformatics with Dr. Warren Gish, Joey worked in the Bioinformatics Group at Incyte Pharmaceuticals, as Director of Bioinformatics at Orion Genomics, LLC and is now with Sigma Aldrich, St. Louis, MO. as Marketing Manager, eCommerce.

20

230 John D. McPherson, Ph.D.

Co m m it tee Member: Jarret Glasscock: Ph.D. (2004) Washington University, Mentor: Warren Gish ―XomeBase : computational analysis of human ESTs translates to an informative representation of the transcript data.‖

Zhengyan (George) Kan: Ph.D. (2001) Washington University, Mentor: David States ―UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences.‖ Ph.D. 2001 - Rossetta Pharmaceuticals

Other Training: Throughout the years prior to joining the OICR, the large -scale genome research efforts aimed at generating publicly accessible data sets for the research community were very consuming of my time. As such, I chose not to formally take on graduate students, as I believed that the ―factory‖ nature of the work did not afford appropriate opportunities for individual research. This was especially true in an atmosphere where publications from large -scale efforts were not properly recognized. This did not preclude me from training countless individuals over the years as our teams were made up of people with u ndergraduate, Master’s and PhD degrees – many of whom have gone back to graduate school, to industry positions or on to academic careers.

21

231 Jay A. Shendure, M.D., Ph.D.

Current Position

Assistant Professor of Genome Sciences University of Washington School of Medicine Seattle, WA 98195

Education and Training

Harvard Medical School (Boston, Massachusetts)  M.D. (2007)

Harvard University (Cambridge, Massachusetts)  Ph.D. in Genetics (2005)  Research Advisor: George M. Church

Princeton University (Princeton, New Jersey)  AB, summa cum laude, in Molecular Biology (1996)  Research advisor: Lee M. Silver

Professional Experience

Assistant Professor (Dept. of Genome Sciences, University of Washington): Sep 2007 – Present

Graduate Student (Department of Genetics, Harvard Medical School): Jul 2000 – Aug 2005  Research Advisor: George M. Church

Research Scientist (Vaccine Division, Merck Research Laboratories): Aug 1997 – May 1998  Research Advisor: Xiaoping Liang

Fulbright Scholar to India (Dept. of Pediatrics, Sassoon General Hospital): Sep 1996 – Jun 1997  Research Advisor: Mrudula Phadke

Professional Activities

 2009 – Editorial Board, Genome Research  2009 – Associate Editor, American Journal of Human Genetics  2010 – Editorial Advisory Board, Genome Biology  2011 – Editorial Board, Biotechniques  2010 – Affiliate Appointment, Division of Human Biology, Fred Hutchinson Cancer Research Center  2009 – Member, Fred Hutchinson / University of Washington Cancer Consortium  2010 Grant reviewer, UK Medical Research Council, Molecular and Cellular Medicine Board  2009 Grant reviewer, National Science Foundation  2009 Grant reviewer, NIH ARRA Challenge Grants (Genes, Genomes and Genetics IRG)  2009 Grant reviewer, Ontario Research Fund (GL2 Competition)  2008 Grant reviewer, Genome BritishColumbia  2009 Program Committee, American Association for Cancer Research, 101st Annual Meeting  2009 – International Barcode of Life (iBOL) Technology Development Advisory Group

232 Jay A. Shendure, M.D., Ph.D.

Commercial Advisory Roles

 2010 – Scientific Advisory Board, OLink Genomics  2010 – Scientific Advisory Board, Tandem Technologies  2010 – Scientific Advisory Board, Adaptive TCR Technologies  2009 – Scientific Advisory Board, Good Start Genetics  2009 – Scientific Advisory Board, Stratos Genomics  2008 – 2009 Consultant, Complete Genomics  2006 Consultant, Highland Capital Partners  2004 – 2005 Consultant, Agencourt Biosciences

Honors and Awards

 2010 Prostate Cancer Foundation, Lowell Milken Young Investigator (2010-2013)  2008 Science in Medicine New Investigator Lecture, University of Washington  2007 James Tolbert Shipley Prize, Harvard Medical School  2006 TR35 Young Innovator Award, Technology Review, Massachusetts Institute of Technology  1998 Medical Science Training Program Fellowship, National Institutes of Health  1996 Fulbright Scholarship, U.S. State Department  1996 summa cum laude, Princeton University  1996 Honorary Major in Anthropology, Princeton University  1996 Sigma Chi Book Award for Molecular Biology Senior Thesis, Princeton University  1996 Senior Prize for Best Thesis in Anthropology, Princeton University  1996 Phi Beta Kappa, Princeton University  1992 National Merit Scholar

Active Patents & Pending Patent Applications

7,425,431 Polony fluorescent in situ sequencing beads (issued) 20100069263 Sequence tag directed subassembly of short sequencing reads into long sequencing reads 20090018024 Nanogrid rolling circle DNA sequencing 20080269068 Multiplex decoding of sequence tags in barcodes 20070207482 Wobble sequencing 20030228611 Nucleic acid memory device

Peer-Reviewed Research Articles (* denotes equal contributors; # denotes corresponding authors)

1. Melo JA, Shendure J, Pociask K, Silver LM#. Identification of sex-specific quantitative trait loci controlling alcohol preference in C57BL/ 6 mice. Nature Genetics 1996 Jun;13(2):147-53. 2. Shendure J*, Melo JA*, Pociask K, Derr R, Silver LM#. Sex-restricted non-Mendelian inheritance of mouse chromosome 11 in the offspring of crosses between C57BL/6J and (C57BL/6J x DBA/2J)F1 mice. Mammalian Genome 1998 Oct;9(10):812-5. 3. Peirce JL*, Derr R*, Shendure J, Kolata T, Silver LM#. A major influence of sex-specific loci on alcohol preference in C57Bl/6 and DBA/2 inbred mice. Mammalian Genome 1998 Dec;9(12):942-8. 4. Liang X#, Munshi S, Shendure J, Mark G 3rd, Davies ME, Freed DC, Montefiori DC, Shiver JW. Epitope insertion into variable loops of HIV-1 gp120 as a potential means to improve immunogenicity of viral envelope protein. Vaccine 1999 Jul 16;17(22):2862-72.

233 Jay A. Shendure, M.D., Ph.D.

5. Aach J*, Bulyk ML, Church GM#, Comander J, Derti A, Shendure J*. Computational comparison of two draft sequences of the human genome. Nature 2001 Feb 15;409(6822):856-9. 6. Badarinarayana V, Estep PW 3rd, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM#. Selection analyses of insertional mutants using subgenic-resolution arrays. Nature Biotechnology 2001 Nov;19(11):1060-5. 7. Weber G*, Shendure J*, Tanenbaum DM, Church GM, Meyerson M#. Identification of foreign gene sequences by transcript filtering against the human genome. Nature Genetics 2002 Feb;30(2):141-2. 8. Shendure J, Church GM#. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biology 2002 Aug 22;3(9):RESEARCH0044. 9. Mitra RD, Butty VL, Shendure J, Williams BR, Housman DE, Church GM#. Digital genotyping and haplotyping with polymerase colonies. Proceedings of the National Academy of Sciences 2003 May 13;100(10):5926-31. 10. Zhu J*, Shendure J*, Mitra RD, Church GM#. Single molecule profiling of alternative pre-mRNA splicing. Science 2003 Aug 8;301(5634):836-8. 11. Mitra RD, Shendure J, Olejnik J, Edyta-Krzymanska-Olejnik, Church GM#. Fluorescent in situ sequencing on polymerase colonies. Analytical Biochemistry 2003 Sep 1;320(1):55-65. 12. Zhu Z#, Shendure J, Church GM#. Discovering functional transcription-factor combinations in the human cell cycle. Genome Research 2005 Jun;15(6):848-55. 13. Shendure J*#, Porreca GJ*#, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 2005 Sep 9;309(5741):1728-32. Epub 2005 Aug 4. 14. Zhang K#, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM#. Polony haplotyping of individual human chromosome molecules. Nature Genetics 2006 Mar;38(3):382-7. Epub 2006 Feb 19. 15. Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C, Hurles ME#. Assaying chromosomal inversions by single-molecule haplotyping. Nature Methods 2006 Jun;3(6):439-45. 16. Moskowitz I, Kim JB, Moore M, Wolf C, Peterson MA, Shendure J, Norbrega M, Yokota Y, Berul C, Izumo S, Seidman JG*, Seidman CE*#. A Genetic Pathway Including Id2, Tbx5, and Nkx2-5 Required for Cardiac Conduction System Development. Cell 2007 Jun 29;129(7):1365-76. 17. Porreca GJ*, Zhang K*, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM*#, Shendure J*#. Multiplex Amplification of Large Sets of Human Exons. Nature Methods 2007 Nov;4(11):931-6. 18. Higgins AW, Alkuraya FS, Bosco AF, Brown KK, Bruns GA, Donovan DJ, Eisenman R, Fan Y, Farra CG, Ferguson HL, Gusella JF, Harris DJ, Herrick SR, Kelly C, Kim HG, Kishikawa S, Korf BR, Kulkarni S, Lally E, Leach NT, Lemyre E, Lewis J, Ligon AH, Lu W, Maas RL, MacDonald ME, Moore SD, Peters RE, Quade BJ, Quintero-Rivera F, Saadi I, Shen Y, Shendure J, Williamson RE, Morton CC#. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project. American Journal of Human Genetics 2008 Mar;82(3):712-22. 19. Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J#. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods. 2009 Apr 6:1-2. [Epub ahead of print] 20. Brkanac Z#, Spencer D, Shendure J, Robertson PD, Matsushita M, Vu T, TD, Olson MV, Raskind WH. IFRD1 is a candidate gene for SMNA on chromosome 7q22-q23. American Journal of Human Genetics 2009 May;84(5):692-7. Epub 2009 Apr 30. PubMed PMID: 19409521; PubMed Central PMCID: PMC2680994.

234 Jay A. Shendure, M.D., Ph.D.

21. Ng SB#, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J#. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009 Aug 16. [Epub ahead of print] 22. Vasta V, Ng SB, Turner EH, Shendure J#, Hahn SH#. Next generation sequence analysis for mitochondrial disorders. Genome Medicine 2009 Oct 23;1(10):100. PubMed PMID: 19852779; PubMed Central PMCID: PMC2784303. 23. Ng SB*, Buckingham KJ*, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J#, Bamshad MJ#. Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics 2009 Nov 13. [Epub ahead of print] PubMed PMID: 19915526. 24. Patwardhan RP#, Lee C, Litvin O, Young DL, Pe'er D, Shendure J#. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nature Biotechnology 2009 Nov 15. [Epub ahead of print] PubMed PMID: 19915551. 26. Hiatt JB*#, Patwardhan RP*, Turner EH, Lee C, Shendure J#. Parallel, tag-directed assembly of locally derived short sequence reads. Nature Methods. 2010 Feb;7(2):119-22. Epub 2010 Jan 17. PubMed PMID: 20081835. 27. Thomas JH#, Emerson RO, Shendure J. Extraordinary molecular evolution in the PRDM9 fertility gene. PLoS One. 2009 Dec 30;4(12):e8505. PubMed PMID: 20041164; PubMed Central PMCID: PMC2794550. 28. Roach JC*, Glusman G*, Smit AF*, Huff CD*, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB#, Hood L#, Galas DJ. Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science. 2010 Mar 10. [Epub ahead of print] PubMed PMID: 20220176. 29. Cooper GM#, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nature Methods. 2010 Apr;7(4):250-1. PubMed PMID: 20354513. 30. Yang F, Babak T, Shendure J, Disteche CM#. Global survey of escape from X inactivation by RNA- sequencing in mouse. Genome Research. 2010 Apr 2. [Epub ahead of print] PubMed PMID: 20363980. 31. Duan Z*, Andronescu M*, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA#, Noble WS#. A three-dimensional model of the yeast genome. Nature. 2010 May 20;465(7296):363-7. Epub 2010 May 2. PubMed PMID: 20436457. 32. Ng SB*, Bigham AW*, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura KI, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ#, Shendure J#. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genetics 2010 Aug 15. [Epub ahead of print] PubMed PMID: 20711175. 33. Rios J, Stein E, Shendure J, Hobbs HH#, Cohen JC#. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet. 2010 Sep 2. [Epub ahead of print] PubMed PMID: 20719861. 34. Sudmant PH*, Kitzman JO*, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE#. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6. PubMed PMID: 21030649. 35. Adey A* Morrison HG*, Asan*, Xun X*, Kitzman JO, Turner EH, Stackhouse B, Mackenzie AP, Caruccio NC, Zhang X#, Shendure J#. Rapid, low-input, low-bias construction of shotgun fragment libraries by high- density in vitro transposition. Genome Biology 2010 Dec 8;11(12):R119. [Epub ahead of print] PubMed PMID: 21143862.

235 Jay A. Shendure, M.D., Ph.D.

36. Kitzman JO#, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, Shendure J#. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotechnology 2010 Dec 19. [Epub ahead of print] PubMed PMID: 21170042.

Reviews, Perspectives and Book Chapters

1. Shendure J, Mitra RD, Varma C, Church GM#. Advanced sequencing technologies: methods and goals. Nature Reviews Genetics 2004 May;5(5):335-44. 2. Porreca GJ, Shendure J, Church GM. Polony DNA Sequencing. Current Protocols in Molecular Biology 2006. 7.8.1-7.8.22. 3. Shendure J, Porreca GJ, Church GM. Polony Sequencing, in Kim S, Tang H, Mardis ER, eds. Genome Sequencing Technology and Algorithms, 2008. 4. Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Current Protocols in Molecular Biology 2008 Jan; Chapter 7:Unit 7.1. 5. Shendure J. The beginning of the end for microarrays? Nature Methods. 2008 Jul;5(7):585-7. 6. Shendure J, Ji H. Next generation DNA sequencing. Nature Biotechnology 2008 Oct;26(10):1135-45. 7. Turner EH, Ng SB, Nickerson DA, Shendure J. Methods for genomic partitioning. Annual Reviews in Genomics and Human Genetics. 2009;10:263-84. PubMed PMID: 19630561. 8. Shendure J, Stewart CJ. Cancer genomes on a shoestring budget. New England Journal of Medicine 2009 Jun 25;360(26):2781-3. Epub 2009 Jun 10. PubMed PMID: 19516026. 9. Shendure J. Journal club. A geneticist discusses a way to assess the effects of disease-causing gene mutations. Nature. 2010 Jan 28;463(7280):405. PubMed PMID: 20110948. 10. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J#, Turner DJ#. Target-enrichment strategies for next-generation sequencing. Nature Methods 2010 Feb;7(2):111-8. PubMed PMID: 20111037. 11. Igartua C, Turner EH, Ng SB, Hodges E, Hannon GJ, Bhattacharjee A, Rieder MJ, Nickerson DA, Shendure J#. Targeted enrichment of specific regions in the human genome by array hybridization. Curr Protoc Hum Genet. 2010 Jul;Chapter 18:Unit 18.3. PubMed PMID: 20582915. 12. Ng SB#, Nickerson DA, Bamshad MJ, Shendure J. Massively parallel sequencing and rare disease. Hum Mol Genet. 2010 Oct 15;19(R2):R119-24. Epub 2010 Sep 15. PubMed PMID: 20846941; PubMed Central PMCID: PMC2953741.

Active Research Support

1R01HL094976-01 9/30/08-6/30/11 0.12 calendar NIH/NHLBI $1,227,569 SeattleSeq (MPI: Eichler, Green, Nickerson, Shendure) The major goal of this project is to develop a high-throughput pipeline for the comprehensive capture and high- throughput sequencing of all protein-coding sequences in individual human genomes. Role: PI (MPI award)

5P01CA078902-11 2/1/09-1/31/14 0.92 calendar NIH/NCI $140,870 (sub to UW)

236 Jay A. Shendure, M.D., Ph.D.

Identification of Canine Minor Histocompatability Antigens (Storb) The major goal of this subproject is to develop a novel genomics-driven approach for identifying minor histocompatability antigens in a canine transplantation model. Role: PI of Project 1

2P50HG003233-06 5/1/09-4/30/14 0.90 calendar NIH/NHGRI $481,057 (sub to UW) Center for the Epigenetics of Common Human Disease (Feinberg) The major goal of the UW component of this program is to develop and apply technology for large-scale targeted profiling of DNA methylation in epidemiological samples. Role: Co-investigator

3U54AI057141-06S1880509 8/1/09-7/30/11 0.90 calendar NIH/NIAID $344,950 Massively parallel genome sequencing of antibiotic-resistant emerging pathogens (Shendure) The goal of this proposal is to sequence the genomes of over 1,000 antibiotic-resistant bacterial strains representing emerging pathogens. Role: PI

1RC2HL102926-0110 9/30/09-9/29/11 1.20 calendar NIH/NHLBI $7,904,188 Northwest Genomics Center (MPI: Green, Nickerson, Rieder, Shendure) The goal of the Northwest Genomics Center is to apply next-generation exome sequencing to medically relevant DNA sample cohorts selected by the NHLBI. Role: PI (MPI award)

1RC2HG005608-0110 9/30/09-9/29/11 0.90 calendar NIH/NHGRI $1,249,939 Next Generation Mendelian Genetics (MPI: Bamshad, Nickerson, Raskind, Shendure) The goal of this proposal is to sequence and identify the candidate genes responsible for more than 20 Mendelian diseases/disorders. Role: PI (MPI award)

1RC1AG035681-0110 9/30/09-9/29/11 0.60 calendar NIH/NIA $316,045 Mutational Cloning in Familial Dementia and Alzheimer’s Disease (Raskind) The goal of this proposal is to apply whole exome sequencing in well-characterized pedigrees to identify functional mutations leading to familial dementia and/or Alzheimer’s disease. Role: Co-investigator

1RC2CA148317-0110 9/30/09-9/29/11 0.48 calendar NIH/NCI $125,756 (sub to UW) An infrastructure for cancer virus discovery from next-generation sequencing data (Meyerson) The aim of this grant is to develop automated pipelines for identifying virus-derived sequences in next- generation sequencing data from all public sources by computational subtraction. Role: Co-investigator

1RC2CA148232-0110 9/30/09-9/29/11 0.45 calendar NIH/NCI $666,500 Application of RiboTag-seq to Exploration of Tumor Microenvironments (Morris)

237 Jay A. Shendure, M.D., Ph.D.

The aim of this grant is to develop and apply methods for tagging of ribosome-associated RNAs to study cell- type specific gene expression in complex tissues. Role: Co-investigator

1I01BX000531 10/01/09-9/30/13 0.18 calendar Department of Veterans Affairs $199,398 Genetic Risk Factors for Parkinson's Disease (Zabetian) The major goal of this project is to validate findings from an ongoing genome-wide association study on PD using next generation sequencing and brain/CSF proteomic analyses. Role: Consultant

1R01HD065285-01 10/1/09-9/30/11 0.90 calendar NIH/NICHD $730,292 Genomic Identification of Autism Loci (Eichler) The aim of this grant is to explore the hypothesis that autism is caused by highly-penetrant, rare mutations using emerging technologies that screen regions for autism-specific copy-number variation (CNV) mutations and exonic point mutations. Role: Co-investigator 4/01/10-3/31/13 0.12 calendar Prostate Cancer Foundation $75,000 Methods & Tools for Next-Generation Analysis of Prostate Cancer Genomes (Shendure) The aim of this grant is to develop and deploy methods that enable the efficient characterization of primary and metastatic prostate cancer genomes in large numbers of samples. Role: PI

NIH/NHGRI 3/1/10-9/30/11 0.60 calendar A Genome-wide Mutation Resource for C. elegans (Waterston) $740, 082 The aim of this grant is to construct a community resource of several thousand chemically mutagenized C. elegans strains that have been whole genome sequenced. Role: Co-investigator

Completed Research Support

1R21HG004749-01 7/23/08-6/30/10 NIH/NHGRI $150,000 Molecular Tools for Genome Partitioning (Shendure) The major goal of this project is to develop and optimize methods for selective capture of gene families or long contiguous genomic regions. Role: PI

Invited Talks or Workshops

Dec 8, 2010 UCSF Biomedical Sciences Seminar Series (San Francisco, CA) Dec 2, 2010 Amgen, Molecular and Computational Toxicology seminar series (Seattle, WA) Nov 13, 2010 American Heart Association, Scientific Sessions 2010, “Whole Genome Sequencing and Integrative Genomics” session (Chicago, IL) Nov 14, 2010 American Heart Association, Scientific Sessions 2010, “Whole Exome Resequencing: Methods and Early Findings” session (Chicago, IL) Nov 6, 2010 American Society of Human Genetics annual meeting; invited session moderator & speaker (Washington DC) Oct 21, 2010 Pathobiology seminar series, Department of Global Health, University of Washington (Seattle,

238 Jay A. Shendure, M.D., Ph.D.

WA) Oct 12, 2010 Beyond the Genome: The true gene count, human evolution and disease genomics (Boston, MA) Sep 15, 2010 Prostate Cancer Foundation, 17th Annual Scientific Retreat (Washington DC) Jul 30, 2010 Illumina PNW User Group Meeting (Seattle, WA) Jul 29, 2010 BioC 2010 (Seattle, WA) Jun 17, 2010 PNW Prostate Cancer SPORE Seminar (Seattle, WA) Jul 6-8, 2010 Planning the Future of Genomics: Foundational Research and Applications in Genomic Medicine, NHGRI (Warrenton, VA) Jul 14, 2010 13th International MGED Meeting, Plenary Lecture (Boston, MA) Jul 14, 2010 Merck (Boston, MA) Jul 21, 2010 51st Annual Short Course on Medical and Experimental Mammalian Genetics, The Jackson Laboratory (Bar Harbor, ME) May 25, 2010 American Society for Microbiology 110th General Meeting, colloquium co-convener & speaker, “Ultra-Deep Sequencing in Infectious Diseases” (San Diego, CA) May 24, 2010 University of Washington Computational Molecular Biology Spring Symposium (Seattle, WA) May 21, 2010 University of Washington Dept. of Medical Genetics Seminar Series (Seattle, WA) May 12, 2010 CSHL - The Biology of Genomes; session co-chair for High Throughput Genomics & Genetics (Cold Spring Harbor, NY) May 7, 2010 NIH Director’s “Big Think” Meeting (Bethesda, MD) Apr 14, 2010 4th International Conference on Primate Genomics (Seattle, WA) Jan 14, 2010 Washington University in St. Louis, Department of Genetics (St. Louis, MO) Jan 6, 2010 University of Chicago, Department of Human Genetics (Chicago, IL) Dec 16, 2009 Simons Foundation, invited workshop on genome/exome DNA sequencing in autism (New York City, NY) Dec 14, 2009 Cardiovascular Center Breakfast Club, University of Washington (Seattle, WA) Oct 22, 2009 American Society of Human Genetics annual meeting; plenary session (Honolulu, HI) Sep 30, 2009 Grand Rounds in Laboratory Medicine, University of Washington (Seattle, WA) Sep 16, 2009 CSHL Personal Genomes meeting (Cold Spring Harbor, NY) Aug 3, 2009 eMERGE Network Steering Committee meeting (Seattle, WA) Aug 18, 2009 McDermott Center, Excellence in Human Genetics Lecture Series, UT Southwestern (Dallas, TX) Jun 9, 2009 Genomic Tools and Technologies Summit, Cambridge Healthtech Institute (San Francisco, CA) May 21, 2009 Northwest Institute of Genetic Medicine, 2009 Retreat (Seattle, WA) Mar 31, 2009 University of Michigan, Center for Translational Pathology (Ann Arbor, MI) Mar 18, 2009 Next-Generation Sequencing meeting, Cambridge Healthtech Institute (San Diego, CA) Feb 6, 2009 Advances in Genome Biology and Technology (AGBT) (Marco Island, FL) Feb 4, 2009 Advances in Genome Biology and Technology (AGBT), pre-meeting workshop (Marco Island, FL) Dec 2, 2008 Puget Sound Blood Center Research Seminar (Seattle, WA) Oct 21, 2008 Discovery2Diagnostics (San Diego, CA) Sep 25, 2008 New Investigator Science in Medicine Lecture, University of Washington (Seattle, WA) Sep 14, 2008 Institute for Systems Biology Annual Retreat; keynote address (Seabeck, WA) Sept 7, 2008 Nature Genetics Genomics of Common Disease (Cambridge, MA) Aug 14, 2008 Genome Sciences Centre, BC Cancer Agency (Vancouver, BC) Mar 10, 2008 Computational Biology Working Group seminar series, Fred Hutchinson Cancer Research Center (Seattle, WA) Mar 21, 2008 University of Washington Dept. of Medical Genetics Seminar Series (Seattle, WA) Mar 28, 2008 Joint Genome Institute (JGI) User 3rd Annual Meeting (Walnut Creek, CA) Feb 10, 2008 Association of Biomolecular Resource Facilities (ABRF) (Salt Lake City, UT) Feb 8, 2008 Advances in Genome Biology and Technology (AGBT); plenary session (Marco Island, FL)

239 Jay A. Shendure, M.D., Ph.D.

Nov 7, 2007 Frontiers in Biology Seminar Series, Stanford University (Palo Alto, CA) Nov 6, 2007 1st Annual Parallel Sequencing Genomics Meeting, Stanford Genome Technology Center, Stanford University (Palo Alto, CA) Sep 20, 2007 Program in Prostate Cancer Research Seminar Series, Fred Hutchinson Cancer Research Center (Seattle, WA) May 3, 2007 Stanford Genome Technology Center, Stanford University (Palo Alto, CA) Mar 30, 2007 Institute for Molecular Pediatric Sciences, University of Chicago (Chicago, IL) Mar 21, 2007 Next Generation Sequencing: Applications and Case Studies, Cambridge Healthtech Institute (San Diego, CA) Feb 27, 2007 Department of Genetics, University of Pennsylvania (Philadelphia, PA) Feb 15, 2007 Department of Bioengineering, University of California, Berkeley (Berkeley, CA) Feb 12, 2007 Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School (Boston, MA) Feb 9, 2007 Department of Pathology, Massachusetts General Hospital, Harvard Medical School (Boston, MA) Feb 5, 2007 Department of Genome Sciences, University of Washington (Seattle, WA) Feb 1, 2007 Broad Institute of M.I.T. and Harvard (Cambridge, MA) Jan 22, 2007 Department of Molecular & Cell Biology, University of California, Berkeley (Berkeley, CA) Jan 10, 2007 National Human Genome Research Institute, National Institutes of Health (Bethesda, MD) Jan 8, 2007 Workshop on Systems Biology and Information Medicine in a Global Society, Princeton University (Princeton, NJ) Jan 3, 2007 Institute for Systems Biology (Seattle, WA) Mar 27, 2006 Biological Physics & Biophysical Chemistry Seminar, State University of New York, Stony Brook (Stony Brook, NY)

Professional Service

 Ad hoc peer-reviewer for 22 journals (American Journal of Human Genetics, Analytical Chemistry, Bioinformatics, Biotechniques, BMC Genomics, Cell Stem Cell, Cellular & Molecular Biology Letters, Genome Biology, Genome Research, Genomics, Mammalian Genome, Nature, Nature Biotechnology, Nature Genetics, Nature Methods, Nucleic Acids Research, PLoS Computational Biology, PLoS Genetics, PNAS, Science, Science Translational Medicine, Trends in Genetics)

Faculty Administrative Responsibilities

 Symposium & Panel Discussion Co-Organizer, UW Dept. of Genome Sciences (2010)  Retreat Organizer, UW Dept. of Genome Sciences (2009)  UW "Two Years to Two Decades” (2y2d) initiative, Discovery focus group (2009)  Seminar Series Committee, UW Dept. of Genome Sciences (2008-2009)  Faculty Search Committee, UW Dept. of Genome Sciences (2008-2009)  Faculty Search Committee, UW Dept. of Medical Genetics (2008-2009)  Faculty Search Committee, UW Dept. of Medical Genetics (2009-2010)  Faculty Search Committee, UW Dept. of Genome Sciences (2010-2011)

Postdoctoral Fellows Trained

 Emily Turner (2007 – 2009) - present job: Lead Scientist, Northwest Genomic Center  Jerrod Schwartz (2009 – current)  Brian O’Roak (2009 – current) – joint trainee with Evan Eichler

Graduate Students Trained

240 Jay A. Shendure, M.D., Ph.D.

 Akash Kumar, MSTP / Genome Sciences (2010 – current)  Andrew Adey, Molecular & Cellular Biology (2010 – current)  Rupali Patwardhan, Genome Sciences (2007 – current)  Sarah Ng, Genome Sciences (2007 – current)  Joseph Hiatt, MSTP / Genome Sciences (2009 – current)  Jacob Kitzman, Genome Sciences (2009 – current)

Rotation Students Supervised

 Sarah Ng, Genome Sciences (Fall 2007)  Rupali Patwardhan, Genome Sciences (Winter 2008)  Sayer Herrin, Genome Sciences (Winter 2008)  Joseph Hiatt, MSTP (Summer 2008)  Matthew Maurano, Genome Sciences (Fall 2008)  Jarrett Egerston, Genome Sciences (Winter 2008)  Keisha Carlson, Genome Sciences (Winter 2009)  Jacob Kitzman, Genome Sciences (Spring 2009)  Akash Kumar, MSTP (Summer 2009)  David Young, MSTP (Summer 2009)  Andrew Adey, MCB (Fall 2009)

Graduate Student Committees (in addition to trainees)

 Alan Rubin (UW Genome Sciences, advisor: Phil Green, 2008 - present)  Steven Z. Josefowicz (UW Immunology, advisor: Sasha Rudensky, 2008 - 2010)  Kevin J. Schutz (UW Genome Sciences, advisor: Stan Fields, 2008 - 2010)  Marcia Noreen Paddock (UW Immunology, advisor: Andy Scharenberg, 2008 - 2010)  Joshua D. Bishop (UW Electrical Engineering, 2009 - present)  Cailyn Spurrell (UW Genome Sciences, advisor: Mary-Claire King, 2009 - present)  Kyle Minch (UW Molecular & Cellular Biology, advisor: David Sherman, 2009 - present)  Leslie Emery (UW Genome Sciences, advisor: Josh Akey, 2010 - present)  Peter Sudmant (UW Genome Sciences, advisor: Evan Eichler, 2010 - present)  Benjamin Whiddon (UW Genome Sciences, advisor: Richard Palmiter, 2010 - present)  Carlos Araya (UW Genome Sciences, advisor: Stanley Fields, 2010 - present)  Russell Berg (UW Molecular & Cellular Biology, advisor: Lalita Ramakrishnan, 2010 – present)  Thomas White (UW Molecular & Cellular Biology, advisor: Peter Nelson, 2010 – present)

Courses Taught

 Genome 550 (Fall 2008; with Bob Waterston) – Methods and Logic in Genetics  Genome 550 (Fall 2009; with Bob Waterston) – Methods and Logic in Genetics  Genome 373 (Spring 2010; with Jim Thomas) – Genome Informatics  Genome 550 (Fall 2010; with Bob Waterston) – Methods and Logic in Genetics

Other Teaching or Outreach Activities

 Lecturer for “Introduction to Human & Medical Genetics” course, UW Medical Genetics (October 15, 2010)

241 Jay A. Shendure, M.D., Ph.D.

 Moderator for UW Genome Sciences 2010 Panel Discussion on “"New Discoveries in Medicine: Implications for the Cost and Quality of American Healthcare" (April 6, 2010)  Panelist for Lasker Foundation / UW Dept. of Genome Sciences Round Table: “Personal Genomes: Promise or Hype?” (November 16, 2009)  Panelist for "The Two Body Question and Faculty with children" at HHMI Future Faculty Workshop (September 2, 2009)  Guest session leader for Genome 580 “Ethics in Biomedical Research and Teaching” (April 28, 2009)  Guest speaker, MSTP Dinner/Recruitment meeting (April 16, 2009)  Guest session leader for EPI590 "Introduction to Laboratory Methods in Population Research" (April 6, 2009)  Guest speaker, Rainier Scholars program (February 20, 2009)  Talk at StarNet 2008 Summer Workshop, UW Genome Sciences Education Outreach (July 14, 2008)  Talk at “Wednesdays at the Genome” UW Genome Sciences Public Lecture Series (July 30, 2008)  Chalk Talk Workshop, Women in Genome Sciences (WiGS) (October 16, 2008)  Guest session leader for Genome 580 “Ethics in Biomedical Research and Teaching” (May 27, 2008)  Teaching Assistant, Principles of Pharmacology, Harvard Medical School (2001 – 2003)

242

BARTON E. SLATKO, Ph.D

PRESENT EMPLOYMENT: Senior Research Scientist Head, DNA Sequencing Group 7/84- Present Molecular Parasitology Division New England Biolabs, Inc. 240 County Road, Ipswich MA 01938 USA ph: 978-337-2311; FAX: 978-921-1350 email: [email protected]

RELATED EXPERIENCE:

2007-2009 Director, Applications and Product Development New England Biolabs, Inc.

7/79 - 7/84 Assistant Professor of Biology Dept. Biology, Williams College Williamstown, MA 01267

7/86 - Present Reviewing Editor, BioTechniques

1995, 1998 National Science Foundation Review Panels (1998, chair), Directorate of Biological Sciences COV/BIR/DBI

1985 - Present Co-Instructor, New England Biolabs Summer Molecular Biology Workshops (70)

2004 - Present ITSI Scientific Board Member

2000 - Present Eaton Publishing Advisory Board

2000-Present Steering Committee, Wolbachia Consortium (NSF)

2009-Present SIP Nematode Division Committee Elected Member

1982 - 1988 Grant Review Panels National Toxicology Program Nat. Inst. Env. Health Sciences Research Triangle Park, NC 27709

6/80 - 8/80 Visiting Research Fellow 6/81 - 8/81 Laboratory Molecular Genetics, NIEHS Research Triangle Park, NC 27709

SOCIETY MEMBERSHIPS AAAS, ABRF, UCS, ASTMH, SIP, ISS

243 EDUCATION:

1/78 - 8/79 Postdoctoral Research Geneticist V (NIH Training Grant) Dept. Genetics, UC, Davis Davis, CA 95616

1977 Ph.D., Zoology (Genetics) Dept. Zoology, UT, Austin Austin, TX 78712

1971 B.A. Zoology Dept. Zoology, UT, Austin Austin, TX 78712

RECENT PUBLICATIONS: (not including scientific meeting abstracts, presentations or manuscripts in preparation)

Williams, S.A., Lizote-Waniewski, M., Foster, J., Guiliano, D., Daub, J., Scott, A., Slatko, B. and Blaxter, M. (2000). The Filarial Genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi. Int. J. Parasitology 30: 411-419. Sun, L., Foster, J., Tzertzinis, G., Ono, M., Bandi, C., Slatko, B. and O’Neill, S. (2001). Determination of Wolbachia genome size by pulsed-field gel electrophoresis. J Bact. 183: 2219- 2225. Foster, J., Kamal, I., Daub, J., Swan, M., J. Ingram, J., Ganatra, M., Ware, J., Guiliano, D., Aboobaker, A., Moran, L., Blaxter., M. and Slatko. B. (2001). DNA hybridization on high density filter arrays of a Brugia malayi BAC library using biotinylated oligonucleotides and PCR products (BioTechniques 30:1 216-1222. Albright LM, Slatko BE. 2001. Denaturing polyacrylamide gel electrophoresis. Curr Protoc Nucleic Acid Chem. 2001 May; Appendix 3B. In, Current Protocols in Molecular Biology, (ed. by Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K). Ch. 7, pp 7.0.1-7.6.13. New York: John Wiley & Sons. Albright LM, Slatko BE. 2001. Denaturing polyacrylamide gel electrophoresis. Curr Protoc Hum Genet. 2001 May; Appendix 3F. In, Current Protocols in Molecular Biology, (ed. by Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K). Ch. 7, pp 7.0.1-7.6.13. New York: John Wiley & Sons Slatko BE, Albright LM. 2001. Denaturing gel electrophoresis for sequencing. Curr Protoc Mol Biol. 2001 May;Chapter 7:Unit7.6. In, Current Protocols in Molecular Biology, (ed. by Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K). Ch. 7, pp 7.0.1-7.6.13. New York: John Wiley & Sons. Slatko BE, Albright LM, Tabor S, Ju J. 2001. DNA sequencing by the dideoxy method. Curr Protoc Mol Biol. 2001 May;Chapter 7:Unit7.4A. In, Current Protocols in Molecular Biology, (ed. by Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K). Ch. 7, pp 7.0.1-7.6.13. New York: John Wiley & Sons Slatko BE, Heinrich P, Nixon BT, Eckert RL. 2001. Preparation of templates for DNA sequencing. Curr Protoc Mol Biol. 2001 May;Chapter 7:Unit7.3. In, Current Protocols in Molecular Biology, (ed. by Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K). Ch. 7, pp 7.0.1-7.6.13. New York: John Wiley & Sons. Slatko B, Heinrich P, Nixon BT, Voytas D. 2001. Constructing nested deletions for use in DNA sequencing. Curr Protoc Mol Biol. 2001 May;Chapter 7:Unit7.2. In, Current Protocols in Molecular Biology, (ed. by Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K). Ch. 7, pp 7.0.1-7.6.13. New York: John Wiley & Sons.

244 Blaxter, M., Daub, J., Guiliano, D., Parkinson, J., Whitton, C. and The Filarial Genome Project. (2002). The Brugia malayi genome project; expressed sequence tags and gene discovery. Trans. Roy. Soc. Hygiene and Tropical Medicine 96: 7-17. Parkinson, J., Whitton, C., Guilliano, D., Daub, J., Blaxter, M. and the Filarial Genome Project. (2001). Trends in Parasitology 117: 394-396. Ware, J., Moran, L., Foster, J., Guiliano, D., Posfai, J., Kumar, S., Stewart, F., Eisen, J., and Slatko, B. (2002) Sequencing and Analysis of a 63 kb Wolbachia BAC from the human filarial parasite Brugia malayi. Int. J. Parasitology 32: 159-166. Whitton, C., Daub, J., Quail, M., Hall, N., Foster, J., Ware, J., Ganatra, M., Slatko, B., Barrell, B. and Blaxter, M. (2004). A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics. Mol Biochem Parasitol. 137: 215-227. Foster J, Baldo, L., Blaxter, M., Henkle-Duhrse, K., Whitton C, Slatko, B. and Bandi, C. (2004). The bacterial catalase from filarial DNA preparations derives from common pseudomonad contaminants and not from Wolbachia endosymbionts. Parasitol Res. 94(2): 141-146. Foster J, Kumar, S., Ganatra, M., Kamal, I., Ware, J., Ingram, J., Pope-Chappell, J., Guiliano, D., Whitton, C., Daub, J., Blaxter, M.L. and Slatko, B. (2004). Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont. Int J Parasitol 34: 733-746. Ghedin E., Wang, S., Foster, J. and Slatko, B. (2004). First sequenced genome of a parasitic nematode. Trends Parasitol. 20: 151-153. Foster, J, Ganatra, M., Kamal, I., Ware, J., Makarova, K., Ivanova, N., Bhattacharya, A., Kapatral, V., Kumar, S., Posfai, J., Vincze, T., Ingram, J., Moran, L., Lapidus, A., Omelchenko, M., Kyrpides, N., Ghedin, E., Wang, S., Goltsman, E., Joukov, V., Ostrovskaya, O., Tsukerman, K., Mazur, M., Comb, D., Koonin, E. and Slatko, B. (2005) The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode PLoS Biology 3: 0599- 0614. Turner, J., J. Foster, M. Ganatra, B. Slatko, and M. Taylor, M. (2006). The role of Wolbachia in the biology and pathogenesis of filariasis. in, “Insect Symbiosis”, V2, (ed by K. Bourtzis and T.Miller). CRC Press. Boca Ratan, Ch 11, pp. 187-198. Brownlie JC, Adamski M, Slatko B, McGraw EA. (2007). Diversifying selection and host adaptation in two endosymbiont genomes. BMC Evol Biol. ;7:68. Ghedin, E., K. Daehnel, J. Foster, B. Slatko, S. Lustigman (2007). The symbiotic relationship between filarial parasitic nematodes and their Wolbachia endosymbionts – a resource for a new generation of control measures. Symbiosis (in press). Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH. (2007). Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes. Science 317: 1753-1756. Pfarr K, Foster J, Slatko B, Hoerauf A, Eisen JA. (2007). On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes? Int J Syst Evol Microbiol. Aug;57(Pt 8):1677-8. Pfarr, K., J. Foster and B Slatko. (2007). It Takes Two: Lessons From the First Nematode Wolbachia Genome Sequence. in, “Wolbachia, A Bug’s Life in Another Bug”, (ed by A. Hoerauf and R. Rao). Issues in Infectious Disease, Karger Press. Basil,pp 52-65. Williams, S., Slatko, B. and McCarey, J. (2007). Laboratory Investigations in Molecular Biology. Jones and Bartlett, Publishers, Sudbury MA. Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder

245 AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL. (2007). Draft genome of the filarial nematode parasite Brugia malayi. Science 317(5845):1756-1760. Weiner M, Slatko B. 2008. Kits and their unique role in molecular biology: a brief retrospective. Biotechniques. Apr;44(5):701-704. Merritt, R., L. Bierwort, B. Slatko, M. Weiner, E, Weiner, J. Ingram, K. Sciarra and E. Weiner (2008). Tasting Phenylthiocarbamide (PTC): A New Lab With An Old Flavor. Am. Biol. Teacher (May) www.nabt.org/sites/S1/File/pdf/070-05-0023.pdf. Weiner MP, Slatko B. (2009). Tasting PTC: A new lab with an old flavor. BioTechniques. 2009 Jun;46: 83. Weiner MP, Slatko B. (2009). Discover the microbes within! The HHMI Wolbachia Project. Biotechniques. 2009 Jun;46(7):497. Wu B, Novelli J, Foster J, Vaisvila R, Conway L, Ingram J, Ganatra M, Rao AU, Hamza I, Slatko B. (2009). The Heme Biosynthetic Pathway of the Obligate Wolbachia Endosymbiont of Brugia malayi as a Potential Anti-filarial Drug Target. PLoS Negl Trop Dis. 2009 Jul 14;3(7):e475. Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CA, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL. (2009). The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One. 2009 Jul 1;4(7):e6085. Turner JD, Langley RS, Johnston KL, Gentil K, Ford L, Wu B, Graham M, Sharpley F, Slatko B, Pearlman E, Taylor MJ. (2009). Wolbachia lipoprotein stimulates innate and adaptive immunity through toll-like receptors 2 and 6 (TLR2/6) to induce disease manifestations of filariasis. J Biol Chem. 2009 May 19. [Epub ahead of print] Slatko BE, Taylor MJ, Foster JM The Wolbachia endosymbiont as an anti-filarial nematode target. (2010). Symbiosis. 51(1):55-65. Landmann F, Foster JM, Slatko B, Sullivan W. (2010). Asymmetric Wolbachia segregation during early Brugia malayi embryogenesis determines its distribution in adult host tissues. PLoS Negl Trop Dis.4(7):e758.PMID: 20689574. McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. (2010). Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. PLoS One. 5(6):e11029.PMID: 20543958. Chimura, H., Flores, K. and Slatko, B. (2010). A Plant Barcode of Life Project, BioTechniques (in press) Foster, J.M., Hoerauf, A., Slatko, B. and Taylor, M. 2010. The molecular biology, immunology and chemotherapy of Wolbachia bacterial endosymbionts of filarial nematodes. In, Kennedy. M. and Harnett, W. (eds) Parasitic Nematology: Molecular Biology, Biochemistry, Immunology

246 BAOLI ZHU Ph.D.

( Curriculum Vitae)

Date of Birth: February 4，1961 Place of Birth: Beijing, China Nationality: Chinese Sex: Male Marital Status: Married Language: English, Spanish, Chinese E-mail Address: [email protected] Phone #: +86-10-6480-7362 Present Address: Joint Center for Microbial Genomics, the Institute of Microbiology, Chinese Academy of Sciences, Beijijng, Chaoyang District, 100101, China.

CURRENT EMPLOYER & RESEARCH INTERESTS

2006-present Working as principal investigator and Director of Microbial Genome Research Center in The Institute of Microbiology, full professor of the graduate school, Chinese Academy of Sciences. Research interests: bacterial genomics, metagenomics and Immunogenomics.

RESEARCH EXPERIENCE & EMPLOYMENT

2001 – 2006 Working as assistant scientist in BACPAC Resource Center (CHORI) on many projects: The NIH funded ENCODE project; the rat genome project; human genome project, the zebrafish genome project; the chimpanzee genome project; The planaria genome project; the NIH funded BAC network project; the NSF funded BAC construction project.

Cancer Genomic Research: Study of genome amplicons and deletions in cancer patients using CGH (comparative genomic hybridization), ESP (BAC-End sequence Profiling), and DNA fingerprinting analysis of BAC clones created from cancer patients.

Genome Sequencing Projects: Orangutan genome project; Gorilla genome project

1999-2000 Working as Postdoctoral Fellow II in BAC-PAC resources (CHORI) on construction of a new circular Yeast Artificial Chromosome (cYAC) vector, which carries a conditional galatose promoter upstream the yeast centromere allowing the cYAC copy number amplification. Construction of cYAC library for Dictyostelium Discoideum genome using new cYAC vector. Application of the cYAC vector in order to isolate DNA sequences or genes by Transformation Associated Recombination (TAR cloning, ref. 10).

1996-1998 As a postdoctoral research associate in The Babraham Institute, Cambridge, UK, working on the construction of Bacterial Artificial Chromosome (BAC) Library for Cattle Genome in order to study the Quantitative Trait Loci of milk production (ref 9). Positional cloning of Polled gene in cattle by applying BAC clone contiqing, PCR, exon trapping (cell culture, RT-PCR) and microsatellite marker screening from BAC clones.

247

1995-1996 As a visiting scholar in The Babraham Institute, Cambridge, working on the identification of a putative tumor suppressor gene for human hepatocellular carcinoma.

1993-1995 As a research scientist in Beijing Agricultural University (BAU), China, working on the construction of human genomic library (EMBL3) and the isolation of human erythropoietin gene and the insulin gene. The expression of both genes in CHO cells and other mammalian cell lines was achieved (ref. 24, 25).

Isolation of bovine beta-lactoglobulin (BLG) gene's regulatory element by PCR, the DNA sequencing determination. The test expression of human growth hormone gene under the control BLG regulatory element both in cultured mouse mammary gland cells and in transgenic mice was succeeded (ref. 26).

Co-supervisor of the Project "Isolation and DNA sequence determination of human erythropoietin gene and its expression in mammalian cells" supported by China’s National Foundation for Natural Sciences".

1988-1992 As Ph.D. candidate in BAU, working on the construction of secretive- expression vector for the high-level expression of porcine growth hormone (pGH) gene in E.coli in order to obtain biologically active form of pGH directly from periplasmic space of E.coli (ref. 28).

Co-worker involving in the project “Construction of a vaccinia virus expression vector to express the pGH cDNA gene both in human h143 cells and in infected mouse (ref. 27).

1985-1987 As assistant research scientist in BAU, working on the construction of porcine genomic library, the characterization and the DNA sequence determination of pGH gene (ref. 29).

Participating in the construction of variety prokaryotic expression vectors to express the pGH cDNA gene in E.coli as a part of the NATIONAL 7th FIVE- YEARS PLAN REASEARCH PROGRAMME.

As assistant research scientist working on the expression of the Klenow Fragment gene in E.coli and its large-scale preparation and purification.

248

EDUCATION:

1988.7-1992.7 Ph.D. degree in Molecular Biology and Biochemistry, Dept. of Animal Biochemistry, Beijing Agricultural University (BAU，北京农业大学). Thesis work: (1) Cloning of porcine growth hormone (pGH) cDNA gene into E.coli expression vector and M13mp19. (2) Site-directed mutagenesis to correct the reading frame between the signal peptide sequence ompA and pGH structure gene. (3) Expression of pGH gene under PR-PL tandem promoter in order to obtain biologically active form of pGH directly from E.coli periplasmic space (ref. 3).

1979.10-1985.5 B.Sc. degree in Molecular Biology, Facultad de Ciencias, Universidad Nacional Autonoma de Mexico (UNAM，墨西哥国立自治大学); Centro De Investigacion sobre Ingenieria Genetica y Biotecnologia (Currently Institute of Biotechnology) UNAM, Mexico, majoring Biology and Molecular Biology.

1979.2-1979.8. As an undergraduate student in Dept. of Western Languages, Peking University （北京大学）.

1978.10-1979.1 As an undergraduate student in Beijing Agricultural University （北 京农业大学）.

TEACHING EXPERIENCE:

2007-2008 “Microbial Genomics” for graduate student in Chinese Academy of Sciences Graduate School. 1991-1995 "Biochemistry of nucleic acid” and “advanced biochemistry" for graduate students in BAU. 1985-1990 "Current Biochemistry" for undergraduate students in BAU.

PUBLICATIONS:

1. Zhao W. et al (2010) "The genome of rifamycin-producing Amycolatopsis mediterranei reveals its phylogeny and metabolism characteristics," Cell Research. 2010 March (accepted). 2. Di Kim Nguyen et al (2010) "Clcn4 introns conserved on the X in Mus spretus and other mammals are deleted on Mus musculus autosome: AT motif enrichment on the X" PNAS 2010 Feb. (accepted). 3. Yin Y, Lei F, Zhu L, Li S, Wu Z, Zhang R, Gao GF, Zhu B, Wang X. Exposure of different bacterial inocula to newborn chicken affects gut microbiota development and ileum gene expression. ISME J. 2010 Mar;4(3):367-76. Epub 2009 Dec 3. 4. Hu Y, Fu C, Huang Y, Yin Y, Cheng G, Lei F, Lu N, Li J, Ashforth EJ, Zhang L, Zhu B. Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment. FEMS Microbiol Ecol. 2010 Feb 16. [Epub ahead of print].

249 5. Hu Y, Fu C, Huang Y, Yin Y, Cheng G, Lei F, Lu N, Li J, Ashforth EJ, Zhang L, Zhu B. Construction and preliminary analysis of a deep-sea sediment metagenomic fosmid library from Qiongdongnan Basin, South China Sea. Marine Biotechnology (9259) 2010 Jan. 6. Abi-Rached L, Kuhl H, Roos C, ten Hallers B, Zhu B, Carbone L, de Jong PJ, Mootnick AR, Knaust F, Reinhardt R, Parham P, Walter L. A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC- G in gibbons. J Immunol. 2010 Feb 1;184(3):1379-91. Epub 2009 Dec 21. 7. Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol. 2009 Dec;5(12):e1000593. Epub 2009 Dec 11. 8. Zhu X, Chang S, Fang K, Cui S, Liu J, Wu Z, Yu X, Gao GF, Yang H, Zhu B, Wang J. (2009). MyBASE: a database for genome polymorphism and gene function studies of Mycobacterium. BMC Microbiol. 2009 Feb 20; 9:40. 9. Liu J, Tran V, Leung AS, Alexander DC, Zhu B. (2009). BCG vaccines: their mechanisms of attenuation and impact on safety and protective efficacy. Hum Vaccin. 2009 Feb;5(2):70-8. Epub 2009 Feb 20. 10. Leung AS, Tran V, Wu Z, Yu X, Alexander DC, Gao GF, Zhu B, Liu J. (2008). Novel genome polymorphisms in BCG vaccine strains and impact on efficacy. BMC Genomics. 2008 Sep 15;9:413. 11. von Schalburg KR, Leong J, Cooper GA, Robb A, Beetz-Sargent MR, Lieph R, Holt RA, Moore R, Ewart KV, Driedzic WR, Ten Hallers BF, Zhu B, de Jong PJ, Davidson WS, Koop BF. Rainbow Smelt (Osmerus mordax) Genomic Library and EST Resources. Mar Biotechnol (NY). 2008 Apr 2. [Epub ahead of print] 12. Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S, Scott C, Cox A, Deutsch S, Ucla C, Cruts M, Dahoun S, She X, Bena F, Wang SY, Van Broeckhoven C, Eichler EE, Guigo R, Rogers J, de Jong PJ, Reymond A, Antonarakis SE. Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. Genome Res. 2007 Nov;17(11):1690-6. 13. Wang S, Xu P, Thorsen J, Zhu B, de Jong PJ, Waldbieser G, Kucuktas H, Liu Z. Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes. Mar Biotechnol (NY). 2007 Nov-Dec;9(6):701-11 14. ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. 15. Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J. Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 2007 Jan;35 (Database issue):D376-80. 16. Carbone L, Vessere GM, ten Hallers BF, Zhu B, Osoegawa K, Mootnick A, Kofler A, Wienberg J, Rogers J, Humphray S, Scott C, Harris RA, Milosavljevic A, de Jong PJ. A high-resolution map of synteny disruptions in gibbon and human genomes. PLoS Genet. 2006 Dec 29;2(12):e223. 2006 Nov 13.

250 17. Chourrout D, Delsuc F, Chourrout P, Edvardsen RB, Rentzsch F, Renfer E, Jensen MF, Zhu B, de Jong P, Steele RE, Technau U (2006). Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature. 442(7103):684-7. 18. Leeb T, Vogl C, Zhu B, de Jong PJ, Binns MM, Chowdhary BP, Scharfe M, Jarek M, Nordsiek G, Schrader F, Blocker H. A human-horse comparative map based on equine BAC end sequences. Genomics. 2006 Jun;87(6):772-6. 19. Perrocheau M, Boutreux V, Chadi S, Mata X, Decaunes P, Raudsepp T, Durkin K, Incarnato D, Iannuzzi L, Lear TL, Hirota K, Hasegawa T, Zhu B, de Jong P, Cribiu EP, Chowdhary BP, Guerin G. Construction of a medium-density horse gene map Anim Genet. 2006 Apr;37(2):145-55. 20. Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, Davidson WS, Hoyheim B. A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics. 2005 Apr 4;6(1):50. 21. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005 Oct;86(4):396-404. 22. Milosavljevic A, Harris RA, Sodergren EJ, Jackson AR, Kalafus KJ, Hodgson A, Cree A, Dai W, Csuros M, Zhu B, de Jong PJ, Weinstock GM, Gibbs RA. Pooled genomic indexing of rhesus macaque. Genome Res. 2005 Feb;15(2):292-301. 23. ENCODE Project Consortium, The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40. 24. Kingsley D, Baoli Zhu, Kazutoyo Osoegawa, Pieter de Jong, Jacqueline Schein, Marco Marra, Catherine Peichel, Chris Amemiya, Dolph Schluter, Sarita Balabhadra, Brian Friedlander, Yee Man Cha, Mark Dickson, Jane Grimwood, Jeremy Schmutz, Williams Talbot & Richard Myers. (2004) New Genomic Tools For Molecular Studies Of Evolutionary Changes In Threespine Sticklebacks. Behaviour 141, 1331-1344. 25. Robledo R, Bender P, Leonard J, Zhu B, Osoegawa K, de Jong P, Xu X, Yao Z, Roe B. The immunoglobulin lambda variable light-chain region in primates has been shaped by multiple, independent, small-scale and large-scale insertion/deletion events. Genomics. 2004 Oct;84(4):678-85. 26. Zhao S, Shetty J, Hou L, Delcher A, Zhu B, Osoegawa K, de Jong P, Nierman WC, Strausberg RL, Fraser CM. Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. Genome Res. 2004 Oct;14(10A):1851-60. Epub 2004 Sep 13. 27. Zhu B, Osoegawa K, Shu CL, Ren T, Cao Q, Vessere GM, Lutz MM, Jensen- Seaman MI, Zhao S, de Jong PJ. BAC resources for the rat genome project. Genome Res. 2004 Apr;14(4):780-5. 28. Krzywinski M, Wallis J, Gosele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu AL, Shin H, Tanzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong PJ, Warren W, Mardis E, McPherson JD, Wilson R, Hubner N, Jones S, Marra M, Schein J. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. Genome Res. 2004 Apr;14(4):766-79. 29. Rat Genome Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.

251 30. Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 2003 Aug 14;424(6950):788-93. 31. Gernot Glockner, …, Baoli Zhu et al (2002) Sequence and analysis of chromosome 2 of Dictyostelium Discoideum. Nature 418:79-85. 32. Changjing Zeng, Natalay Kouprina, Baoli Zhu, Al Cairo, Maarten Hoek, George Cross, Vladimir Larionov and Pieter de Jong (2001) Large-Insert BAC/YAC Libraries for Selective Re-isolation of Genomic Regions by Homologous Recombination in Yeast. Genomics 77(1-2):27-34. 33. Zhu B, Smith JA, Miller JR et al (1999) A 5x Genome Coverage Bovine BAC Library: Production, Characterization, and Distribution. Mammalian Genome 10(7):706-9. 34. Siming Shou, Baoli Zhu, Shunzhang Qi (1999). Cloning of Human Insulin Genomic Gene by Enrichment Library. Chinese Journal of Biochemistry and Molecular Biology. Vol.15 #2 pp20-25. 35. Cui Zhenzhong, Zhu Baoli, et al (1998). Cloning and Sequencing of Erythropoietin Genomic Gene. Chinese Journal of Biochemistry and Molecular Biology. Vol.14 N#6 pp684-690. 36. Yang guoqing, Dai Yanping, Zhu Baoli, Chen Yongfu, Qi Shunzhang (1996). Cloning of 5'- regulatory Element of Bovine Beta-lactoglobulin Gene and its Utilization in generation of mammary Bioreactor; SCIENCE IN CHINA serie C-Life Sciences, 1996, Vol.39, N#6 pp662-669. 37. Lu Danhong, Zhu Baoli, et al (1994). Expression of pGH cDNA gene in h143 cells using vaccinia virus expression vector. Chinese Biochemical Journal 11(5):504-509. 38. Zhu Baoli et al (1993). Construction of a Secretory expression system for the overexpression of porcine growth hormone cDNA gene in E.coli. Journal of Agricultural Biotechnology, 1(1):50-56. 39. Yang Qing, Zhu Baoli et al (1992). Cloning and partly sequencing of the porcine growth hormone gene from pituitary gland DNA. Chinese Journal of Biotechnology, 8(4):318-323

252 Brief CV Brochmann - update 2010 08 19, 4 pp Brief CV and recent publications, Christian Brochmann (born March 16, 1953)

Current position: Centre Leader (2002-) and Professor of Systematic Botany (1996-), National Centre for Biosystematics (NCB), Natural History Museum (NHM), University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway; phone +47 22851611; fax +47 22851835; email [email protected]; http://www.nhm.uio.no/english/research/ncb/

Honours, prizes: Awarded The Research Prize of the University of Oslo for 2009; Elected member of The Norwegian Academy of Science and Letters (Det Norske Videnskaps-Akademi) from 2004; ‘Best lecturer in basic biology 2000’, University of Oslo ('Den Gyldne Pekestokk').

Education: 1992, Dr. philos. (equiv. to PhD), Univ. Oslo: 'Polyploid evolution in arctic-alpine Draba (Brassicaceae)'; 1984, Cand. scient. (equiv. to MSc), Univ. Oslo.

Research stays abroad: 1993 (3 months) and 1989 (7 months) at Washington State University, USA (hosts DE & PS Soltis).

Research interests: Molecular systematics including biogeography and evolutionary processes at low taxonomic levels, in particular in arctic and alpine regions. Recent projects focus on speciation genetics, comparative phylogeographic and phylogenetic analyses, DNA barcoding, ancient DNA analysis, polyploid evolution, and long-distance dispersal.

Research group: Current: 4 visiting scientists (Elvinger, Luxembourg; Pimentel, Spain; Pineiro, Spain; Suter, Switzerland), 5 postdocs (Bellemain, Boessenkool, Epp, Gussarova, Popp), 7 PhD students (Gizaw, Gustafsson, Hou, Masao, Mugizi, Westergaard, Wondimu), 2 technical/adm. staff (Kvernstuen, Mirré). Previous: Visiting scientists for 2-24 months: Bandyopadhyay, India; Geml, USA; Gussarova, Russia; Jimenez, Spain; Listl, Germany; Mikhaylova, Russia; Obermayer, Austria; Parisod, Switzerland; Pineiro, Spain; Popp, Sweden; Sannier, France; Schönswetter, Austria; Tribsch, Austria; Vilatersana, Spain; Volkova, Russia; Vrancken, Belgium), 5 postdocs (Alsos, Brysting, Ehrich, Gabrielsen, Sønstebø), 12 completed PhDs (Alsos, Assefa, Carlsen, Eidesen, Fjellheim, Gabrielsen, Grundt, Kapralov, Kebede, Skrede, Solstad, Tollefsrud), 6 research assistants, 17 completed Masters.

Synopsis of other main activities: Initiating and leading research centre for biological systematics (NCB) at Univ. Oslo involving 40-60 people (2001-); Initiating and leading a Norwegian-Swedish Research School in Biosystematics (2009-); Member of the Council for IOPB (International Organization for Plant Biosystematists, 2008-2013); Chair (2004-2008) and member (2003-2004) of the Board for the Biodiversity Research Programme at the Research Council of Norway; Member of the expert evaluation panel for the EU BiodivERsA call (2008); Member of 3 expert evaluation panels for the Academy of Finland (2001, 2004) and one for the Swedish Research Council (2009); Member of the National Committee for Development of Biological Sciences in Norway (‘Biofagplanutvalget’, 2002-2003); Member of the National committee for evaluation of professor competence in biology (2009-2011); Leader of (1996-2000) and participant in (2001-2006) the project ’The Botanical Discovery Centre’ in the Botanical Garden, Univ. Oslo. Board member, Botanical Garden and Museum (1996-99). Opponent/reviewer at doctoral defenses in Vienna, Zürich (x2), Bratislava, Cluj, Copenhagen, Lund, Uppsala (x3), Trondheim. Evaluator for habilitation at Univ. Osnabrück (2005). Participated in one-year project at the Centre of Advanced Studies, Norwegian Academy of Science and Letters (1998-99). Organizer and co-organizer of several international and national conferences. Member of Editorial Boards of 5 international journals.

Invited talks accepted since 2004: 2010 Ås, Norway; 2008 Bonn, Germany; Göttingen, Germany; Vysoke, Slovakia; Neuchatel, Switzerland; Trondheim, Norway; 2007 St Andrews, UK; Lund, Sweden; Trondheim, Norway; Ås, Norway; 2006 Zürich, Switzerland; Trondheim, Norway; Basel, Switzerland; 2005 Vienna, Austria; Uppsala, Sweden; Oslo, Norway; 2004 Amsterdam, The Netherlands; Addis Ababa, Ethiopia; Ås, Norway; Zürich, Switzerland; Regensburg, Germany; Kiel, Germany.

253 Brief CV Brochmann - update 2010 08 19, page 2 of 4

Major external grants since 2002 (as PI) 2010-2011: 5.3 mill NOK (Res. Council Norway project 199713/V20 and Norwegian Biodiversity Information Centre): ‘ForBio – Norwegian-Swedish Research School in Biosystematics 2010-2020: Preproject 2010-2011’ 2009-2012: 9.5 mill NOK (Res. Council Norway, FRIBIO project 191627/V40): ‘BarFrost – Reconstruction of past ecosystems by barcoding DNA preserved in permafrost’ 2007-2011: 3.0 mill NOK (partner EC Integrated Project FRP6 no 036866-2, coordinated by P. Taberlet, Grenoble): ‘ECOCHANGE: Challenges in assessing and forecasting biodiversity and ecosystem changes in Europe’ 2007-2011: 6.0 mill NOK (NUFU Norway project 2007/10058): ‘AFROALP-II – Afro-alpine ‘sky islands’: genetic versus taxonomic biodiversity, climate change, and conservation’ 2006-2010: 4.8 mill NOK (Res. Council Norway, FRIBIOØKO project 170952/V40): ‘SURV-ICE – Did vascular plants and bryophytes survive the last ice age in Scandinavia?’ 2003-2007: 3.2 mill NOK (NUFU Norway project 1127): ‘AFROALP - Afroalpine islands as natural laboratories: dynamics and units of plant biodiversity’. 2002-2006: 36.2 mill NOK (13.1 mill from Res. Council Norway, Strategic University Program 146515/420, and 23.1 mill from host inst. (NHM): ’National Centre for Biosystematics’. 2002-2006: 6.2 mill NOK (Res. Council Norway, Norklima program 150322/720): ’Effects of climate change on ecosystems in Svalbard: past and future immigration of thermophilous key species’.

Publications: H-index ~28. ~100 peer-reviewed papers in international journals (including Science, PNAS, Systematic Biology, Nucleic Acids Research, Evolution, Molecular Ecology etc.) and one monograph, ~120 abstracted contributions at international conferences, and ~20 popular papers and reports.

Five most-cited papers Bonin A, Bellemain E, Eidesen PB, Pompanon F, Brochmann C, Taberlet P 2004. How to track and assess genotyping errors in population genetics studies. Molecular Ecology 13: 3261-3273 (365 citations) Abbott RJ, Brochmann C 2003. History and evolution of the arctic flora: in the footsteps of Eric Hultén. Molecular Ecology 12: 299-313 (163 citations) Gabrielsen TM, Bachmann K, Jakobsen KS, Brochmann C 1997. Glacial survival does not matter: RAPD phylogeography of Nordic Saxifraga oppositifolia. Molecular Ecology 6: 831-842 (138 citations) Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen A-C, Elven R 2004. Polyploidy in arctic plants. Biological Journal of the Linnean Society 82: 521-536 (119 citations) Brochmann C, Gabrielsen TM, Nordal I, Landvik JY, Elven R 2003. Glacial survival or tabula rasa? The history of North Atlantic biota revisited. Taxon 52: 417-450 (99 citations)

Peer-reviewed publications since 2007 Piñeiro R, Popp M, Hassel K, Listl D, Westergaard KB, Flatberg KI, Brochmann C. Cryptic species, trans-Atlantic dispersal and colonization of South America: the arctic moss genus Cinclidium (submitted). Vrancken J, Brochmann C, Wesselingh R. A European phylogeography of Rhinanthus minor compared to R. angustifolius: an unexpected split and signs of widespread introgression into R. angustifolius (in review). Geml J, Timling I, Lennon N, Nusbaum HC, Brochmann C, Noordeloos ME, Taylor DL. An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA (in review). Alsos IG, Ehrich D, Thuiller W, Eidesen PB, Tribsch A, Schönswetter P, Lagaye C, Taberlet P, Brochmann C. Genetic consequences of climate change for northern plants (in review). Yoccoz NG, Bråthen KA, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Brochmann C, Willerslev E, Taberlet P. DNA in soil mirrors plant functional and structural diversity (in review). Popp M, Mirré V, Brochmann C. A single mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries (Empetrum). PNAS (Proceedings of the National Academy of Sciences of the United States of America) (tentatively accepted). Popp M, Mirré V, Suda J, Stedje B, Elven R, Brochmann C. Widespread and ecologically important, but poorly understood in terms of history and taxonomy: the circumarctic and bipolar crowberries (the genus Empetrum, Ericaceae) (in review). Geml J, Kauff F, Brochmann C, Lutzoni F, Laursen GA, Taylor DL. Scale-dependent long-distance dispersal: northern circumpolar gene flow and bipolar speciation in the high-latitude symbiotic agaric, Lichenomphalia umbellifera (Hygrophoraceae, Basidiomycota). (in review). Gussarova GL, Alsos IG, Brochmann C. Annual plants colonizing the Arctic? Phylogeography and genetic variation in the Euphrasia minima complex (Orobanchaceae). Taxon (tentatively accepted). Westergaard KB, Alsos IG, Popp M, Engelskjøn T, Flatberg KI, Brochmann C. Glacial survival may matter after all: nunatak signatures in the rare European populations of two west-arctic species. Molecular Ecology (accepted). Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology 10: 189 doi:10.1186/1471-2180-10-189 (9 p).

254 Brief CV Brochmann - update 2010 08 19, page 3 of 4

Sønstebø JH, Gielly L, Brysting AK, Elven R, Edwards M, Haile J, Willerslev E, Coissac E, Rioux D, Sannier J, Taberlet P, Brochmann C 2010. Using next-generation sequencing for molecular reconstruction of past arctic vegetation and climate. Molecular Ecology Resources 10: 1009-1018. Carlsen T, Elven R, Brochmann C 2010. The evolutionary history of Beringian Smelowskia (Brassicaceae) inferred from combined microsatellite and DNA sequence data. Taxon 59: 427-438. Volkova PA, Trávníček P, Brochmann C 2010. Evolutionary dynamics across discontinuous freshwater systems: rapid expansions and repeated allopolyploid origins in the Palearctic white water-lilies (Nymphaea). Taxon 59: 483-494. Geml J, Kauff F, Brochmann C, Taylor DL 2010. Surviving climate changes: high genetic diversity and transoceanic gene flow in two arctic-alpine lichens, Flavocetraria cucullata and F. nivalis (Parmeliaceae, Ascomycota). Journal of Biogeography 37: 1529-1542. Westergaard KB, Jørgensen MH, Gabrielsen TM, Alsos IG, Brochmann C 2010. The extreme Beringian/Atlantic disjunction in Saxifraga rivularis (Saxifragaceae) has formed at least twice. Journal of Biogeography 37: 1262- 1276. Parisod C, Holderegger R, Brochmann C 2010. Evolutionary consequences of autopolyploidy. New Phytologist 186: 5-17. Ehrich D, Eidesen PB, Alsos IG, Brochmann C 2009. An AFLP clock for absolute dating of shallow-time evolutionary history – too good to be true? Molecular Ecology 18: 4526-4532. Vrancken J, Brochmann C, Wesselingh RA 2009. How did an annual plant react to Pleistocene glaciations? Postglacial history of Rhinanthus angustifolius in Europe. Biological Journal of the Linnean Society 98: 1-13. Soininen EM, Valentini A, Coissac E, Miquel C, Gielly L, Brochmann C, Brysting A, Sønstebø JH, Ims RA, Yoccos NG, Taberlet P 2009. Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high- throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology 6: 16 (doi: 10.1186/1742-9994-6-16). Tollefsrud MM, Sønstebø JH, Brochmann C, Johnsen Ø, Skrøppa T, Vendramin GG 2009. Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies. Heredity 102: 549-562. Carlsen T, Bleeker W, Hurka H, Elven R, Brochmann C 2009. Biogeography and phylogeny of Cardamine (Brassicaceae). Annals of the Missouri Botanical Garden 96: 215–236.. Skrede I, Carlsen TA, Rieseberg LH, Brochmann C 2009. Microsatellites for three distantly related genera in the Brassicaceae. Conservation Genetics 10: 643-648. Alsos IG, Alm T, Normand S, Brochmann C 2009. Past and future range shifts and loss of diversity in dwarf willow (Salix herbacea L.) inferred from genetics, fossils, and modelling. Global Ecology and Biogeography 18: 223- 239. Skrede I, Borgen L, Brochmann C 2009. Genetic structuring in three closely related circumpolar plant species: AFLP versus microsatellite markers and high-arctic versus arctic-alpine distributions. Heredity 102: 293-302. Lihová J, Carlsen T, Brochmann C, Marhold K 2009. Contrasting phylogeographies inferred for the two alpine sister species Cardamine resedifolia and C. alpina (Brassicaceae). Journal of Biogeography 36: 104-120. Brochmann C, Brysting AK 2008. The Arctic – an evolutionary freezer? Plant Ecology & Diversity 1: 181-195. Tollefsrud MM, Kissling R, Gugerli F, Johnsen Ø, Skrøppa T, Cheddadi R, van der Knaap WO, Latalowa M, Terhürne-Berson R, Litt T, Geburek T, Brochmann C, Sperisen C 2008. Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen. Molecular Ecology 17: 4134-4150. Westergaard KB, Alsos IG, Ehrich D, Eidesen PB, Hollingsworth PM, Brochmann C 2008. Genetic diversity and distinctiveness in Scottish alpine plants. Plant Ecology & Diversity 1: 329-338. Gussarova GL, Popp M, Vitek E, Brochmann C 2008. Molecular phylogeny and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations in an old genus. Molecular Phylogenetics and Evolution 48: 444- 460. Schönswetter P, Elven R, Brochmann C 2008. Trans-Atlantic dispersal and large-scale lack of genetic structure in the circumpolar, arctic-alpine sedge Carex bigelowii s. l. (Cyperaceae). American Journal of Botany 95: 1006- 1014. Ehrich D, Alsos IG, Brochmann C 2008. Where did the northern peatland species survive the dry glacials: cloudberry (Rubus chamaemorus) as an example. Journal of Biogeography 35: 801-814. Volkova PA, Shipunov AB, Elven R, Brochmann C 2008. The seashore sedges of the Russian Kola Peninsula: how many species? Flora 203: 523-533. Skrede I, Brochmann C, Borgen L, Rieseberg LH 2008. Genetics of intrinsic postzygotic isolation in a circumpolar plant species, Draba nivalis (Brassicaceae). Evolution 62: 1840-1851. Popp M, Gizaw A, Nemomissa S, Suda J, Brochmann C 2008. Colonization and diversification in the African ‘sky islands’ by Eurasian Lychnis L. (Caryophyllaceae). Journal of Biogeography 35: 1016-1029. Alsos IG, Eidesen PB, Ehrich D, Skrede I, Westergaard K, Jacobsen GH, Landvik JY, Taberlet P, Brochmann C 2007. Frequent long-distance plant colonization in the changing Arctic. Science 316: 1606-1609. Brysting AK, Oxelman B, Huber KT, Moulton V, Brochmann C 2007. Untangling complex histories of genome mergings in high polyploids. Systematic Biology 56: 467-476. Vilatersana R, Brysting AK, Brochmann C 2007. Molecular evidence for hybrid origins of the invasive polyploids Carthamus creticus and C. turkestanicus (Cardueae, Asteraceae). Molecular Phylogenetics and Evolution 44: 610-621. 255 Brief CV Brochmann - update 2010 08 19, page 4 of 4

Assefa A, Ehrich D, Taberlet P, Nemomissa S, Brochmann C 2007. Pleistocene colonization of afro-alpine ‘sky islands’ by the arctic-alpine Arabis alpina. Heredity 99: 133-142. Eidesen PB, Alsos IG, Popp M, Stensrud Ø, Suda J, Brochmann C 2007. Nuclear versus plastid data: complex Pleistocene history of a circumpolar key species. Molecular Ecology 16: 3902-3925. Eidesen PB, Carlsen T, Molau U, Brochmann C 2007. Repeatedly out of Beringia: Cassiope tetragona embraces the Arctic. Journal of Biogeography 34: 1559-1574. Ehrich D, Gaudeul M, Assefa A, Koch MA, Mummenhoff K, Nemomissa S, IntraBioDiv Consortium, Brochmann C 2007. Genetic consequences of Pleistocene range shifts: contrast between the Arctic, the Alps and the East African mountains. Molecular Ecology 16: 2542-2559. Kebede M, Ehrich D, Taberlet P, Nemomissa S, Brochmann C 2007. Phylogeography and conservation genetics of a giant lobelia (Lobelia giberroa) in Ethiopian and Tropical East African mountains. Molecular Ecology 16: 1233- 1243. Vilatersana R, Susanna A, Brochmann C 2007. Genetic variation in Femeniasia (Compositae, Cardueae), an endemic and endangered monotypic genus from the Balearic Islands (Spain). Botanical Journal of the Linnean Society 153: 97-107. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E 2007. Power and limitations of the chloroplast trnL(UAA) intron for plant DNA barcoding. Nucleic Acids Research 35, e14: 1-8.

Monograph Brochmann C, Rustan ØH, Lobin W, Kilian N 1997. The endemic vascular plants of the Cape Verde Islands, W Africa. Sommerfeltia 24: 1-356.

Selected earlier publications Grundt HH, Kjølner S, Borgen L, Rieseberg LH, Brochmann C 2006. High biological species diversity in the arctic flora. PNAS (Proceedings of the National Academy of Sciences of the United States of America) 103: 972-975. Gabrielsen TM, Brochmann C, Rueness J. 2002. The Baltic Sea as a model system for studying postglacial colonisation and ecological differentiation, exemplified by the red alga Ceramium tenuicorne. Molecular Ecology 11: 2083-2095. Brochmann C, Borgen L, Stabbetorp OE 2000. Multiple diploid hybrid speciation of the Canary Island endemic Argyranthemum sundingii (Asteraceae). Plant Systematics and Evolution 220: 77-92. Gabrielsen TM, Brochmann C 1998. Sex after all: high levels of diversity detected in the arctic clonal plant Saxifraga cernua using RAPD markers. Molecular Ecology 7: 1701-1708. Brochmann C, Nilsson T, Gabrielsen TM 1996. A classic example of postglacial allopolyploid speciation re- examined using RAPD markers and nucleotide sequences: Saxifraga osloensis (Saxifragaceae). Symbolae Botanicae Upsalensis 31(3): 75-89. Brochmann C, Elven R 1992. Ecological and genetic consequences of polyploidy in arctic Draba (Brassicaceae). Evolutionary Trends in Plants 6: 111-124. Brochmann C, Soltis PS, Soltis DE 1992. Recurrent formation and polyphyly of Nordic polyploids in Draba (Brassicaceae). American Journal of Botany 79: 673-688. Brochmann C, Stedje B, Borgen L 1992. Gene flow across ploidal levels in Draba (Brassicaceae). Evolutionary Trends in Plants 6: 125-134.

256

Family name: Singer Given names: Gregory Arthur Coleman

Title of address:

Job title: Project Manager, International Barcode of Life Project

Mailing Organization: University of Guelph address:

Number and Street: 570 Gordon Street

City: Guelph

Province: ON

Country: Canada

Postal Code: N1G 2W1

Telephone number (with country and area codes): 1-519-824-4120 Ext 58229

Email address: [email protected] Facsimile number: 519-824-4120 LANGUAGE SKILLS: Indicate competence in all languages used by the research team. E = excellent; G = good; F = fair.

Language Read Write Speak Understand

English x x x x

French x

Other (specify)

A. Work experience: List in chronological order starting with your current position. 1. 2009-present, Project Manager, International Barcode of Life Project 2. 2007-2009, Research Associate, The Ohio State Medical Center 3. 2004-2007, Postdoctoral Fellow, The Ohio State Medical Center 4. 2002-2004, Postdoctoral Fellow, Trinity College, Dublin

257 B. Academic qualifications: List your degrees, diplomas, or certificates in chronological order starting with the most recent. 1. MBA (business analytics), Fisher College of Business, The Ohio State University, 2008 2. PhD (biology), University of Ottawa, 2002 3. Certificate in Bioinformatics, University of British Columbia, 2000

C. Credentials : List up to five awards, distinctions, or professional designations you feel are pertinent to this application.

D. Funded research: List up to 10 grants or contracts that you have received or have played a significant role in. List them in chronological order starting with the most recent. Indicate your role in each. 1. 2007-2009, Co-Applicant, Integrative Cancer Biology Program, National Cancer Institute, USA - $5M 2. 2004-2007, Co-Applicant, Modeling the epigenetic changes in alternative promoters of cancer genes , American Cancer Society, $500K

258 E. Publications:

1. Hajibabaei, M. and Singer, G. A. C. (2009) Googling DNA sequences on the World Wide Web. BMC Bioinformatics. Suppl 14:S4. 2. Singer G. A. C. and Hajibabaei, M. (2009) iBarcode.org: web-based molecular biodiversity analysis. BMC Bioinformatics. Suppl 6:S14. 3. Singer, G. A. C., Wu, J., Yan, P., Plass, C., Huang, T-H, and Davuluri, R. V. (2008) Genome- wide analysis of alternative promoters of human genes using a custom promoter tiling array. BMC Genomics. 9:349 4. Meusnier, I., Singer, G. A. C., Landry, J. F., Hickey, D. A., and Hebert, P. D., Hajibabaei M. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics. 9:214. 5. Hajibabaei, M., Singer, G. A. C., Clare, E. L., and Hebert, P. D. (2007) Design and applicability of DNA arrays and DNA in biodiversity monitoring. BMC Biol, 5, 24 Note: MH and GACS are co-first-authors of this manuscript. 6. Hajibabaei, M., Singer, G. A. C., Hebert, P. D., and Hickey, D. A. (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet, 23(4), 167–172. 7. Hajibabaei, M., Singer, G. A. C., and Hickey, D. A. (2006) Benchmarking DNA barcodes: An assessment using available primate sequences.. Genome, 49(7), 851–854. 8. Jin, V. X., Singer, G. A. C., Agosto-Perez, F. J., Liyanarachchi, S., and Davuluri, R. V. (2006) Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. BMC Bioinformatics, 7, 114 Note: VXJ and GACS are co-first-authors of this manuscript. 9. Singer, G. A. C., Lloyd, A. T., Huminiecki, L., and Wolfe, K. H. (2005) Clusters of co- expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol, 22(3), 767–775. 10. Singer, G. A. C. and Hickey, D. A. (2004) Genomic and proteomic adaptations to growth at high temperature. Genome Biol, 5(10), 117. 11. Wang, H. C., Singer, G. A. C., and Hickey, D. A. (2004) Mutational bias a ffects protein evolution in flowering plants. Mol Biol Evol, 21(1), 90–96. 12. Singer, G. A. C. and Hickey, D. A. (2003) Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene, 317(1-2), 39– 47. 13. Lynn, D. J., Singer, G. A. C., and Hickey, D. A. (2002) Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res, 30(19), 4272–4277. 14. Singer, G. A. C. and Hickey, D. A. (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol, 17(11), 1581–1588. F. Other information:

259

INTERNATIONAL BARCODE OF LIFE CONSORTIUM (IBOL) REVISED GE3LS RESEARCH PLAN ETHICAL, ENVIRONMENTAL, ECONOMIC, LEGAL AND/OR SOCIAL ASPECTS OF GENOMICS RESEARCH

Mobilising iBOL Knowledge Through Integrated GE3LS Research

Appendix I: Curricula Vitae for Key Personnel

260 PROTECTED WHEN COMPLETED

GenomeCanada CV Module

Family Name Given Name Middle Initial(s) Phillips Peter WB

Salutation: Correspondence preferred in

X Dr X Mr Mrs Ms Prof English French

Primary AffiliationAddress

University of Saskatchewan Political Studies Department 280 Arts Building 9 Campus Drive Saskatoon, Saskatchewan CANADA (S7N 5A5)

Contact numbers Electronic Addresses Phone Fax E-Mail Primary 01 (306 966-4021 Primary 01(306)966-5250 peter.phillips@;usask.ca

Secondary Temporary Web Address agbio-management.org Temporary

Expertise

List up to ten (10) key words that best describe your expertise in research, instruments and techniques.

Governance/Regulation Innovation clusters crop biotech Emerging Technologies

Intellectual Property Int’l political economy Risk Management Riotechnology/genomics Technology transfer trade policy

28/08/08 Date

CV Module, Page 1 (08/2003) Disponible en Français 261

CV

Degree

Also

degree

Academic

France)

Indicate

PeterWB

Module,

Bachelor’s.

Honours

Doctorate

Master’s

(PhD)

Type

indicate

I

Training

from

Page

enter

all

PHILLIPS

I

university

Training

more

2a

research

each

(08/2003)

Economics

Double

Economics;

Monetary

M.Sc.Econ.

(International

International

Doctorate

than

institution

degrees

Degree

Background

training,

one

High

Theory

institution

and

Name

Trade

separately.

obtained

Honours

Relations

such

Political

Political and

-

and

as

One

(e.g.

Specialty

and

postdoctoral

Intl

Economy

Science

Do

additional

under

those

not

enter

the

in

or

progress

Soutien

page

CANADA

University

UNITED

London

UNITED

London

honorary

fellowship

may

aux

(where

School

School

KINGDOM

degrees

KINGDOM be

of

training.

cotutelles

added

Saskatchewan

applicable)

of

of

Economics

here,

Economics

Organization

de

they

these

starting

should

and

and

de

and

doctorat

with

Political

Political

Country

be

the

listed

agreement

most

Science

Science

in

the

recent.

Distinctions

between

If

you

hold

Quebec

section.

Date

(MMIYYYY)

04/1980

06/1981

12/1989

a

received

co— and 262

CV

Senior

Director

Minister,

Assistant

Vliet

Professor

Professor

SSIIRC

Director

Acting

Department

Appointment)

Tenured

Tenured

Position

the

Start Work

PeterWB

Module.

Research

beginning

Economist

with

Director

Chair

Experience

Policy

Deputy

(term),

(term), Professor

Professor

Page

the

Ilead

PHILLIPS

in

Chair

3

most

MOTC

Van

of

NSERC

(0812003)

(Joint

your

recent,

university

CANAI)A

Saskatchean

CANADA

Trade

Sask

CANADA

Development

Saskatchewan

CANADA

University

CANADA

University

CANADA

University

CANADA

University

CANADA

University

CANADA

University

CANADA

University

Organization

indicate

Economic

studies.

of

of

of

of

of your

of

of

Exeeutie

Saskatchewan

Saskatchewan

Economic

Saskatchewan

Sa%katchewan

Saskatchewan

Saskatchewan

L)i

Saskatchewan

and

current

For

ersification

Country

your

Council

position,

current

and

where

positions

Policy

Policy

Policy

Agricultiaral

Agricultural

Virtual

Johncon-Shoyama

Policy

Political

Johnson

Policy

Political

Department

applicable,

Secretariat

and

leave

College

Studies

Shoyama

Research

Studies

Economics

the

Economics

and

of

end

Biotechnology

School

other

School

Branch

date

academic

of

blank.

of

Public

Public

No

and

additional

non-academic

07

03

03/1

01/1997

(MM/YYYY)

07/1999

07/2002

Start

07/2007

07/2007

0712008

07/2004

1983

1990

pages

992

Date

may

position(s)

091987

be

03

06/I

12/1996

(MMIYYYY)

06/2004

06/2005

06/2008

06/2012 End

06/2013

added.

1992

999

Date since 263

CV

Research

Fellow

Distinction

International

Nominated

Supervisors

Distinction

Credential

Associate

Research

Visiting

Professor-at-large

Research

Research

Honorary

Distinction

Researcher Nominated

Credential

Professor

Credential

Associate

Work

Module.

qualifications,

Starting

Distinctions

Peter

award

Experience.

Research

WB

Name

award

member

award

award

Page

Research

for

with

Award

Member

Chris

Award

for

PHILLIPS

the

and

4a

Distinguished

the

I

professional

Graduate

Award

Fellow

Credentials

(08/2003)

Type

Fellow

most

One

recent,

additional

designation

CANADA

([FIEC’IS)

The

UNITED

Columbus

Festival

CANADA

University

CANADA

University

ITALY

European

AUSTRALIA

University

AUSTRALIA

University

CANADA

University

CANADA

Public

Johnson

indicate

CANADA

University

Centre

page

Organization

Policy

STATES

International

Shoyama

University

for of

any

of

of

or

of

of

may

of

Saskatchewan

Saskatchewan

Innovation

Western

Western

credentials.

Saskatchewan

recognitions

Saskatchewan

be

Graduate

institute added.

and

Australia

Film

Australia

Studies

Country

and

Do

received,

School

Video

not

include

of

including

Effective

06

Academic

07/2004

01/2006 (MM1YYYY)

04/2006

2004

04/2006

2004

01/2008

07/2008

07/2008

2003

awards,

Date

Appointments

fellowships,

06/2010

03/2006 (MMIYYVY)

06/2008

06/2006

End

06/2012

06/2011

Date

here,

scholarships,

Studies

Innovation

Educational

and

Policy,

Bioresource

Social

Political

Department

Advanced

Institute

Resource

Economics

Agriculture

School

Research

Public

Department

Economics

as

Economics

they

Specialty

Sciences

Business

of

Policy

and

of

are

Study

Video

licenses.

of

and

of

detailed

Total

under

Amount

$30,000

$5,000

$5,000

SO

$1)

SO

SO

$0 $0 264

CV

Research

551

Award

Research

Overseas

Van

Research

Credential

Associate

Research Technological

Chair

Distinction

for

Saskatchewan

Work

qualifications,

Starting

Distinctions

Peter

Module,

IRC

Scholarly

Vliet

in

Experience.

Doctoral

WB

Name

award

award

Managing

Student

award

Page

award

Chair

with

Member

PHILLIPS

Writing

and

Change

4b

Books

the

I

Professorship

professional

Fellowship

Research

Credentials

(08/2003)

Type

most

One

Award

recent,

additional

designation

CANADA

SSI1RC

UNITED

UK

CANADA

University

CANADA

University

CANADA

NSERC/SSHRC

indicate

CANADA

Saskatchewan

Government

page

Organization

KINGDOM

any

or

of

of

may

credentials.

Saskatchewan

Saskatchewan

recognitions

Writers

be

added.

and

Association

Country

Do

received,

not

include

including

Effective

Academic

(MMIYYYY)

04/1988

06/1988

01

07’!

07/1999

I

22001

/

1997

awards,

999

Date

Appointments

fellowships,

(MMIYYYY)

01/1

12/1989

01/1999

End

06/2005

07/2004

990

Date

here,

scholarships,

Political

International

Political

International

Economics

Agricultural

Department

Marketing

Management

Department

Agricultural

Economics

Department

Scholarly

as

they

Specialty

Economy

Economy

are

Wnting

licenses,

of

of

of

and

detailed

Total

under

$1,100,000

$300,000

Amount

S30.000

$12,000

$3,000 $0 265

CV

specified

Give

Accepted

Already

Presentations

Publications

There

patents Patents

Peter

Total

Module,

the

WB

individual

are

Published

0

number

in

/

or

and

Page

copyrights

the

two

Publications PHILLIPS

in

as

the Copyrights

AND

“Contributions

5

components

guest

of

(08/2003)

Press

publications

presentations

Total

in

speaker

OBTAINED

the

collective

following

0 to

-

entry:

details”

and

presentations

table.

total

section.

Refereed

Papers

numbers

37

Sub-total

0

Details

0

in

regarding

of

the

patents

Monographs course

Books

Total

the

0

8

I

copyrights;

of

and

individual

entries

0

your

APPUCATIONS

career.

may

and

Contributions

Book

collective

be

Total

Detailed

detailed

attached

Chapters

35

0

collective

UNDER

0

work

content.

information

to

within

I

a

PROCESS

the

Record

Abstracts

should

Contributions

Sub-total

0

0

the

be

I

Notes

total

attached

numbers

Section.

COPYRIGHTS

PATENTS

TOTALS

as

TOTAL

67

124

124

0

0

of I 266

CV

Total

Principal

Funding

Title

Total

Principal

Funding

Title

Total

Principal

Funding

Title

Total

Principal

Funding

Title

role

proposal,

Funds List

PeterWB

Module,

Castle.

Genomc

Value

of

Amount

of

Amount

of

Amount

all

in

of

Amount

$6,000,000

Proposal

Proposal

Source

Applicant!

Proposal

the

Source

Proposal

sources

Applicant!

Source

REQUESTED

Applicant

Page

Source

Applicant

Generation

David’Phillips,

funding

Awarded

funding

PHILLIPS

Canada

Awarded

Awarded

Awarded

Ga

of

(08/2003)

Project

I

source,

Project

support

I

(principal

Project

Project

Through

Leader

Peter

Leader

program

Leader

applied

Leader

applicant/project

Genomics

for

name,

as

in an

From Support

From Support total

From

Support

the

From Support

applicant

leader

04/2009

(MMIYYYY)

ABC

amount

(MMIYYYY)

(MM/YYYY)

(MM)YYYY)

Period

Period

Period

Period

or

Competition

or

co-applicant).

awarded

as

a

co-applicant

(in

Your

Program

Your

Program

Canadian

Your

Program

Your

Program

Principal

ABC

Role

Role

Role

Role

Include

Name

Name

(If

Competition

Name

(If

Name

dollars)

(If

(If

you

you

you

Applicant

you

the

are

are

are

are

and

To

not

principal

To

not

To

not

To

not

(MMIYYYY)

the

(MMIYYYY) the

03/2013

the

(MMIYYYY)

(MMIYYYY)

the

the

principal

period

principal

principal

applicant’s

principal

of

applicant)

the

applicant)

applicant)

applicant)

name,

support.

title

Indicate

of

the your 267

CV

Total

Principal

Funding

Title

Total

Principal

Funding

Title

Total

Principal

Funding

Title

Total

Principal

Funding

Title

role

proposal,

List

Funds Peter

Fulton,

Social

Adapting

Keller,

Genome

Module,

Designing

Caufield,

Genome

Translating

Wolfe,

Social

Major

of

Amount $17,000,000

of

Amount

of

all

Amount

$2,500,000

S3000.000 in

of

Amount

$2,600,000

Proposal

Proposal

WB

Source Proposal

the

Applicant!

sources

Proposal

Source

Sciences

CURRENTLY

Applicant!

Source

Murray

Applicant!

Source

Wilf

Applicant

Page

Collaborative

Sciences

David

funding

Canada

to

PHILLIPS

funding

Canada

Tim

Awarded

Awarded

Oilseeds

Awarded

Awarded

New

Knowledge

7a

of

and

(08/2003)

Project

source,

support

and

I

1/nvironmcnts: Project

(principal

Project

Project

Humanities

for

HELD

Humanities

Research

Tomorrow’s

Leader

Leader in

program

currently

Leader

Leader

applicant/project

Health

Initiative

Research

Agriculture

Research

name,

held

Systems

Markets

as

From

Support

total

Support

From

on

Council

Support

From

an

From Support

01

Council

04/2006

04/2006

leader

03/2006

Innovation

and

applicant

‘2006

amount

(MMIYYYY)

(MMIYYYY>

(MMIYYYY)

(MMIVVYY)

Period

Rural

Period

Period

of

Period

or

of

Canada

co-applicant)

awarded

Canada

or

Economies

Systems

as

a

(

co-applicant.

(

(in

Research

Your

Program

Your

Canadian

Program

Your

Program

in

Your

Program

Co-Applicant

Knowledge

Co-Applicant

Comp

Co-Applicant

Comp

Co-Applicant

the

MCRI

Role

Role

Role

Role

21st

Name

Network

Name

lii

(If

Name

Ill

Name

(If

dollars)

lndude

(If

(If

Century

you

you

you

you

Impact

are

are

are

are

II.

the

and

not

not

To

not

To not

in

To

principal

To

the

01/2009

the

03/2010

(MMIYYYY)

the

03/20

Society

(MM!YYYY)

the

03/2011

(MM/YYYY)

the

(MMIYYYY)

pencxl

principal

principal

principal

principal

10

applicant’s

Grant

of

applicant>

the

applicant>

applicant)

applicant>

support.

name,

Indicate

title

of

the your 268

CV

one

Descriptions

the

research

interruption/delay

Identify

Interruption(s)!

Use

Research

The

Preparation Peter

- Module, - - - -

-

boards, post-doctoral -

-

influence technology

other

your

following:

Each

Number

Six

page.

Minimum

8.5”

Margins

with

up

following

WB

any lines

most

to

actvities

X

page

Page

environment.

page

three

or

11”

PHILLIPS

administrative

and

pages

of

might

per

policy-making significant

Contributions

font

academia, transfers,

8

9.).

format

3/4k

header

(21.5

(08/2003,

fellows,

pages

impact

inch,

and

that

might

size

(2

include

consecutively

Delays X

cm).

show

should

single-spaced,

formatting

must

12

to

28.0

be

on

contributions

other

consulting,

career,

describe:

point.

the

responsibilities,

a

the

the

bodies.

cm)

contain

bereavement

be

forms

start

target

impact

adhered

white

scientific

after

and

contributions

of

your

of

community

with

to

single-sided

of

CV

research

end

research

attachments:

to

your

name,

no

research,

(If,

family

period

for

dates,

condensed

for

work,

these

the

output).

and;

example,

or

to

following (articles,

the

paper.

Attachment

health

professional

application

other

such

attachments.

impact

type

For

as

research,

reasons,

the

mongraphs,

the

your

each

or

areas,

print-out

death

submission

spacing.

practice

track

contribution,

Instructions

or

dissemination

and

of

any

record books,

of

a

or

the

loved

the

other

date,

public

reason(s)

CV

in

patents,

one,

describe

factors

the

and

ends

policy

of

training

maternity/parental

results,

the

on

copyrights,

or

that

and

the

section

a

page

brief

might of

significance

training,

membership

graduate

8,

explanation

header.

the

have

products,

etc.

attachment

leave,

delayed

students

in

on

Common

terms

services,

of

committees,

or

the

relocation or

and

of

would

absence.

interrupted

examples

begin

of

your

Attach

of

any

an of 269

9

Phillips,

Smyth.

Haggui,

Smyth,

Phillips,

Phillips,

Phillips,

Book

Phillips,

Phillips,

Smyth,

Phillips,

Phillips,

Phillips,

Books:

1. political

change

chapters

examined

and

I PHILLIPS,

CONTRIBUTIONS

am

academia.

chapters, an

pp.

NBAC

for

V

Wallingford:

Challenges

security.

Economics

S.. in

agriculture,

(eds)

A.,

Press.

S.,

IPRs.

Invention,

Press/Queens

Biotechnology.

P.

F.,

Edward

World Revolution.

S.

REFEREED

P. in

P.

P.W.B.

P.

P

applied

P.,

P.

R.E. P.

Santamello

and

and

G.

GM

141-154.

2003.

P.

P.

Mahoney,

PETER

Canada

and

P.

and

the

2007.

and

2007.

and

S.

The

Phillips

G.

Phillips,

Chapter

Phillips

Report

social

given

Just,

Products,

of

interface

Smyth

R.

C.

Chapter

G.G.

Since

Khachatourians

Elgar,

C.

including:

Traceability

Forthcoming

Handbook

international

Biotechnology.

Farmers’

W.B.

Innovation

Governing

Wolfe

Facing

Ryan.

and

and

Onwuekwe

MIHR,

J.M.

CABI

Kluwer/Springer,

more

aspects

Khachatourians

and

R.

(eds)

15

School

in

and

1981.

W.

and

CONTRIBUTIONS:

Policy,

pp.

around

Wallingford,

between

Nelsen,

E.

15

Aiston,

2007.

CABI

(eds).

W.

the

Biotechnology Kerr

than

R.

Publishing, W.

privilege

306.

281-294.

Einsiedel

in

of

of

International

I

Gray.

Kerr, of

and

Commercialization

transformative

and

have

R.

Kerr

2008.

political

Springer

best

new

the

60

and

The

(eds).

2001.

Publishing,

Policy

and

L,

and

Nova

Evenson

the

trade

Investment

invited

world.

published

practices

“Managing

G.

Thomson,

(eds).

2006.

role

technology.

and

Technology,

P.

UK: state

D.

(ed),

2007.

(eds).

Governing

pp.

Khachatourians.

pp

Science

Studies,

economist

of

W.

Publishers,

Zilberman,

of

patented

presentations

Opposition

CABI

224.

GM 133-146.

and

2006.

and

Key

Trade

Foresight

Science

clusters

B.

pp.

Accessing

2001.

for

technological

8

in

Phillips.

J.,

market,

V.

food.

Liabilities

contributions

referred

Publishers,

175-190.

pp.

My

the

Publishing,

Governing

management

and

Food:

Satyanarayana,

of

Santaniello

ownership

seeds.

with

The

and

in

2006.

174.

eds.,

Canola

Plant-made

work

A.

on

Polic

to

driving

and

Biotechnology

with

Society 2006.

extensive

2004.

(in

Eaglesham.

Science,

books,

Emerging

genetically

Chapter

Regulating

Arising

focuses

ic’s

Sharing

more

pp.

innovation:

a

Sector.

Risk

pp.

and

related

Governing

for

specific

Regulating

(eds),

innovation.

of

at

112.

37

Pharmaceuticals.

210.

Sqfety

than

intellectual

K.,

in

5

governance:

experience

a

Genetically

from

on

referred

Technologies.

in

(ros.sioad(NABC

the

the

CABI,

modified

international

S.

Agricultural

to

Bennett,

various

Phillips

Revolution

15

emphasis

Ristow

Benefits

2J’ Genome

Agricultural and

io

Innovative

countries),

the

Chapter

journal

pp.

Century:

Trade.

property

‘s

in

Liabilities

aspects

wheat

Modified

A,

and

an

and

in

360.

RESEARCH

industry,

on

of

Canada

and

alternative

charge?

University

in

Biotechnology:

In

Trade

Onwuekwe,

3.1.1

the

R.

articles,

the

McGill

Global

and

Science:

Biotechnology,”

F.

All

Lessons

Fernandez,

of

Hardy

in

Genomics

economic,

Evenson

Products

Ithaca

ofAgricultural

technological

in

and

global

include:

health

of

government

CONTRIBUTIONS

Krattinger,

Oxford:

University

35

Agriculture.’ my

view

(eds)

2008-08-21

of

Policies

from

book

eds.

NY)

work

Calgary

food

and

and

C.

of

the has 270

•

10 2.

Smyth,

Phillips,

Smyth,

Smyth

Ryan,

Phillips,

Malla,

Smyth,

Beicher,

Coenen,

Gray,

Phillips,

Das,

Refereed

PHILLIPS,

Phillips,

Phillips,

Phillips,

Improving

19

NON

Technical

V.,

C.

Nature

R.,

S.

September,

Segregation

S.,

21(9),

Government examination

S.

Chain

S.,

277-297.

Flow

Rights

Spatial

an

innovation.

S.,

C’hain

framework.

Canada:

P.

CAB

R.E. perspective.

Calgary Family

Saskatoon

P.

Kalaitzanondakes

and

K.,

and

L.,

P. P.

and

G.

S.

R.

P.

Agro-food

2002.

articles, P.

G.

P.

PETER

and

REFEREED

and

Phillips

J.

3.

Malia

in

Khachatourians

P.

and

Gray,

Evenson

2002

P.

the

Sept.,

in

P.

G.

International,

Biotechnology,

2003.

Management.:

and

Moodysson,

Nolan

Patterns

S.

Plant-made

Phillips.

Business

Phillips.

Canada. S.

Phillips.

reports

Press,

Biotechnology

Khachatourians

Regulation

A

H.

W.B.

Smyth.

pp.

Research

Smyth.

Regional

and

and

Biotechnology

and

Industry

including

distant

3

and

Bulletin

of

and

The

McNeill.

89-393.

Kluwer,

and

Bioregion:

376-381.

and

international

pp.

P.

Traceability.

P.

of

Policy,

G.

2004.

Supply economic

2003.

relevant

and

2003.

CONTRIBUTIONS:

2004.

P.

Phillips.

Phillips.

Contamination.

2007.

D.

(ed)

dream?

31-58.

Khachatourians.

Pharmaceuticals.

C.

pp.

and

Subsidies. Phillips. of

Systems

of

and

An

20(6,),

Economic

Zilberman

pp.

2002.

Ryan,

Science,

Labeling

Genetically Knowledge

245-261. The

Product

22(2):

Managing

in

Chain

Innovation

Grounding

International

On

and

P.

119-140.

to

Cluster.

the

2006.

2004.

impact

2008.

economic

agricultural

Phillips.

Labeling

537-541.

AgBioForum

the

B.

academic

2005.

P.

of

global

Management,

217

Review

Asheim

Differentiation

Technology

W.

Innovation

Development:

importance

to

(eds.),

Product

Gains

Health

of

the

Ecological In Manage

—

management Genetically

Modified B.

the

13(4), 2008.

Biotechnology

2002.

agri-food herbicide

232.

J.

for

and

Value

Journal

Phillips.

ofAgricultural

Market

field,

to

management

biotechnology

Chrisman

and

Law

GM

innovation

Research

5(2),

environmental

Commercialization

393-414.

Liabilities

as

Marketing

and

of

P.

of

9(4),

Foods

including:

Foods:

Review

a

Economics

A

knowledge

tolerant

Phillips.

system.

Development

11(1),

2004.

Alternatives:

pp. New-Trait

Modified

Modem

Society

in

Western

et

pp.

30-42.

advanced

in

and

and

al.

in

of

Theory

The

65

and

16(4),

313-322.

Economics,

the

of

clusters.

the

canola

Trends

(eds.).

liabilities

2006.

27:4,274-286.

Other

Genetic R&D

—

CBAC

impacts

GM

Crops

Canadian

53,

Liability

Economics Presence

bases

Varieties

74.

Canadian

25-29.

Identity for

and

pp.

technology

Foods?

Comparing

of

Innovation,

in

Entrepot:

Novel

in

and

(acted Environment

for

Genetically

Engineering

plant-derived

Canada.

Practice.

Biotechnology,

387-401.

ofagbioiech:

in

26(1)

from

of

socio-spatial

the Perspective.

in

Agricultural

canola

Preservation,

Foods

of

Trends

RESEARCH

Intellectual

the

as

risk

The

Transgenic

Regulating 63-81,

industries:

co-chair).

In

a

Canola Entrepreneurship,

.

Pharmaceutical

In

in

sector.

analysis

N.

Modified

Case

in

Reviews,

and

V.

Canada:

vaccines

A

Feb.

Biotechnology

CON

20(9),

patterns

Landscapes:

University

global

Santaniello,

Planning

Property

Supply

of

Supply

2008-08-2

2002.

Crops. An

Gene

TRIBLITIONS

the

Foods.

21:

A

in

of

and

C:

of 1 271 PHILLIPS. PETER W.B. RESEARCH CONTRIBUTIONS

Report to the Government of Canada Biotechnology Ministerial Coordinating Committee (Final report). • More than 60 nvited lectures and key-note conference presentations, including: talks or lectures in Canada US, Mexico Chile Uruguay Australia New lealand UK France ERG Itah India, Sweden, France and the Netherlands.

3. CONTRIBUTIONS TO TRAINING

in the past ii years at the University of Saskatchewan I have been increasingly engaged in graduate

and undergraduate training. I currently supervise 6 M.Sc. students, 1 PhD students, 1 post docs and am on the committees of 2 PhD students and 3 other Masters. Students. I have either supervised or been a contributing committee member in 8 MSc. and 8 PhDs that have completed, and have been external examiner on 8 Masters and 4 PhDs. I have also developed, acquired funding and hired five post doctoral fellows. I have developed four new course related to managing technological change: POE ST 362.3: The International Political Economy of Biotechnology; ID 898.3: The International Political Economy of Biotechnology; AG EC 292.3: The Economics of Biotechnology; and AG EC 898.3: The Economics of Biotechnology. So far 500 undergraduates and 30 graduate students have taken the courses.

4. POLICY AND OUTREACH CONTRIBUTIONS

I have been an active policy participant with industry and government advisory groups, including: - Senior research associate of the Estey Centre for Law and Economics in International Trade, Saskatoon, 2001-; member of the board of directors (2008-); - Advisor/expert witness in two civil litigations related to biotechnology innovations, 2001-2006. - Member, Canadian Biotechnology Advisory Committee (1999-2007); Co-chair of the subcommittee investigating the Regulation of GM Foods (2000-2003); member of executive committee (2003-2007). - Member, NAFTA CEC Chapter 13 Expert Panel on Transgenic Maize in Mexico (2002-4). - Founding Member, Board of Directors, Canadian Agri-food Policy Institute (CAP1) (2004-5). - Member, Saskatchewan Innovation Council (2003-5) - Fellow, The Centre for Innovation Studies (THECIS), Calgary (2003-) - Member, Board of Directors, Pharmalytics Inc., Saskatoon (2003-6); spun out company to private interests. - Participant in the OECD Food Safety Conference, Edinburgh, UK, March 2000. - Founding member of and active participant in the International Consortia on Agricultural Biotechnology Research based in Rome, Italy (1998-). - Associate editor, AgBioForum, (2007-)

Over the past decade I have also been invited to do more than 60 formal presentations to industry and others involving approximately 5000 people, more than half from the biotechnology sector and have satisfied more than 75 formal requests by the media to provide expert opinions on IPRs and trade related to biotechnology. I have also consulted with and advised the European Union, the Government of the Australian State of Victoria, the International Food Policy Research Institute, the OECD, the LAO the US National Academy of Sciences the Third World Academy of Sciences the governments of Saskatchewan and Canada and a number of industry associations and private sector firms.

11 2008-08-2i

272 PROTECTED WHEN COMPLETED

GenomeCanada CV Module

Family Name GivenName Middle Initial(s) Castle David GA

Salutation: Correspondence preferred in

English X Dr Mr Mrs Ms Prof x French

Primary Affiliation Address

University of Ottawa Department of Philosophy Simard 229-C 70 Laurier Avenue East, Room 234 Ottawa, Ontario CANADA (KiN 6N5)

Contact numbers Electronic Addresses Phone Fax E Mail Primary (613 562 5800 #2795 Primary (613 562 5215 dcastle@uottawa ca Office Secondary Temporary Web Address

Temporary

Expertise

List up to ten (10>key words that best describe your expertise in research, instruments and techniques.

Philosophy of Science Intellectual Property Bioethics Agbiotech Biotechnology GMO Philosophy of Biology Ethics Agricultural Biotechnolog Genetics

08/07/08 Date

CVModule,Page 1 (08/2003) Disponible en Français

273 Degree

Academic Also degree David France) Indicate

CV

Bachelor’s,

Bachelor’s

Doctorate

Module, Master’s Honours

(PhD) Type

indicate

GA

/

from

Training

enter

all

CASTLE

I

Page

university

Training

more

research

each

2a

Doctor

Philosophy Biology Philosophy Master’s Bachelor’s Bachelor’s

than

(08/2003)

institution

degrees

Background

Degree

training,

one

of

of

institution

Philosophy

of of

Name separately.

Arts

obtained

such

Arts

Science

and -

as

One

(e.g.

and

Specialty

postdoctoral

additional Do

under

those

not

enter

the

in

progress

or

Soutien page

honorary

CANADA University CANADA fellowship CANADA McMaster University CANADA University

may

aux

(where

be

degrees

training. cotutelles

University

of

of of

added

Guelph

Alberta Alberta applicable)

here,

Organization

de

they these

starting

should

de

and

doctorat

with

Country

be

the

listed

agreement

most

in

the

recent.

Distinctions

between

If

you

hold

Quebec

section.

Date

(MM!YYYY)

a

04/1998

04/1993

04/1989 04/1991

co

received

and 274 David GA CASTLE

Work Experience

Start with the most recent, indicate your current position, where applicable, and other academic and non-academic position(s) since the beginning of your university studies. For your current positions leave the end date blank. No additional pages may be added.

Position Organization and Country Department Start Date End Date (MM!YYYY) (MM!YYYY) Associate Professor Umersity of Otta\4a Philosophy 07/2006 CAN DA

Associate Professor University of Guelph 07/2004 07/2006 CANADA

Assistant Professor University of Guelph Philosophy 08/2000 07/2004 CANADA

Adjunct Professor University of Guelph Graduate Studies 09/1998 08/2000 CANADA

Program Development University of Guelph 0712000 Coordinator Office of Open Learmn 06/1999 CANADA

Lecturer University of Guelph Philosophy 01/1998 07/2000 CANADA

Program Manager Umversity of Guelph Office of Open Learning 01/1998 05/1999 CANADA

CV Module,Page 3 (08/2003)

275 David GA CASTLE

Distinctions I Credentials

Starting with the most recent, indicate any recognitions received, including awards, fellowships, scholarships, licenses, qualifications, professional designation or credentials. Do not include Academic Appointments here, as they are detailed under Work Experience. One additional page may be added.

Effective Date End Data Specialty Total Amount Name and Type Organization and Country (MMIYYYY) (MMIYYYY)

Canada Research Chair in Canada Research Chairs I0’2006 10’2011 Science and $500,000 Science and Society CANADA Society Research award

Ontario Graduate Scholarship Ontario Graduate Student Scholarship 1997 Philosophy of $11,859 Research award Program Science CANADA

Doctoral Fellowship Social Sciences and Humanities 1996 Philosophy of $14,400 Research award Research Council of Canada Science CANADA

Visiting Scholar Stipend Wageningen Agricultural University 1996 Philosophy of $4,000 Research award NETHERLANDS Science

CVModule, Page 4a (08/2003>

276 David GA CASTLE

Patents and Copyrights

There are two components to entry: total numbers of patents / copyrights; and detailed content. Record the total numbers of patents I copyrights in the following table. Details regarding the entries may be attached within the Contributions Section.

OBTAINED APPLICATIONS UNDER PROCESS TOTAL PATENTS I COPYRIGHTS Total individual Total collective Sub-total Total Individual Total collective Sub-total

0 0 0 0 0 0 0

Publications AND presentations

Give the number of publications and presentations in the course of your career. Detailed information should be attached as specified in the ‘Contributions - 0details section.

Publications Refereed Books and Book Chapters / Abstracts I Notes TOTALS Papers Monographs Contributions to a collective work

Already Published 20 2 15 0 37

Accepted or in the Press 1 4 2 0 7

44

Presentations as guest speaker 28

CV Module, Page 5 (08/2003)

277 List Title Funds David proposal, role Funding

Principal Total Title

Total Funding

Principal Title

Total Principal Funding Title

Total Principal Funding

CV

Canadian CIHR Wilson,

all Module,

in

of

of

of

of

Amount

Sl,500,000 Amount

Amount

Amount

GA

the

sources

Proposal

Proposal REQUESTED

Proposal

Proposal

Source

Source

Source

Source Emerging

Applicant!

Applicant!

Applicant! Applicant

funding

CASTLE

funding

Brenda

Page

Institutes

Awarded

Awarded

Awarded

Awarded

of

6a

source,

support

(principal

I

Team

(08/2003)

Project

Project

Project

Project

of

Health

in

program

applied

Leader

Leader

Leader

Leader

applicant/project

Genomics

Research

for

name,

as

in

an

total Screening

(CIHR)

applicant

Support

From

Support From

Support From

From Support

leader

amount 12/2008

(MM!YYYY)

(MM!YYYY)

(MMIYYYY)

(MMIYYYY)

or

Period

Period

Period

Period or

co-applicant). awarded

as

a

co-applicant.

(in

Canadian

Your Program

Your Program

Your Program

Your Program

Applied Co-Applicant

Role

Role

Role

Role

Include

dollars)

Name

Name

Name

Name

(If

(If

(If

(If

Health

you

you

you

you

the

are and

are

are

are

principal

Services

not

To

not

not

To

To not

To the

09/2013

(MMIYYYY)

(MM!YYYY)

the

(MM!YYYY)

(MM!YYYY)

the

the

the

period

applicant’s

and

principal

principal

principal

principal

of Policy

the

applicant)

applicant)

applicant)

applicant)

name,

support

Research

title

Indicate

of

the

your 278 David GA CASTLE

Funds CURRENTLY HELD

List all sources of support currently held as an applicant or as a co-applicant. Include the principal applicant’s name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal Strengthening the Role of Genomics and Global Health

Funding Source Program Name Genome Canada Knowledge Management and Global Food Security Principal Applicant I Project Leader Your Role (Ifyou are not the principalapplicant) Singer, Peter Co-Applicant Support Period Total Amount Awarded From (MM!YYYY) To (MMIYYYY) $10,245,584 04/2006 03/2010

Title of Proposal Advanced Food Materials Network

Funding Source Program Name Networks of Centres of Excellence (NCE) Principal Applicant I Project Leader Your Role (If you are not the principal applicant) Yada, Rickey Co-Applicant Support Period Total Amount Awarded From (MMIYYYY) To (MMIYYYY) $22,700,000 04/2003 03/2010

Title of Proposal Social Issues in Nutrigenomics

Funding Source Program Name Networks of Centres of Excellence (NCE) Advanced Food and Materials Network (AFMNet) Principal Applicant! Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM!YYYY) To (MM!YYYY) $1,132,650 04/2006 03/2009

Title of Proposal

Funding Source Program Name

Principal Applicant! Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM!YYYY) To (MMIYYYY)

CVModule, Page 7a (0812003)

279 David GA CASTLE

Attachment Instructions

Preparation and formatting of attachments:

The following format should be adhered to for these attachments. - 8.5” X 11(21.5 X 28.0 cm) white single-sided paper. - Margins of %“ (2 cm). - Minimum font size 12 point. - Six lines per inch, single-spaced, with no condensed type or spacing. - Number pages consecutively after CV (If,for example, the print-out of the CV ends on page 8. the attachment would begin with page 9.). - Each page header must contain your name, the application submission date, and the section header.

Research Contributions Use up to three pages to describe: - your most significant contributions to research (articles, mongraphs, books, patents, copyrights, products, services, technology transfers, other forms of research output). For each contribution, describe the significance in terms of influence and impact on the target community and; - other actvities that show the impact of your work, such as your track record in the training of graduate students and post-doctoral fellows, consulting, contributions to professional practice or public policy and membership on committees, boards, or policy-making bodies.

Interruption(s)! Delays Identify any administrative responsibilities, family or health reasons, or any other factors that might have delayed or interrupted any of the following: academia, career, scientific research, other research, dissemination of results, training, etc. Common examples of an interruption/delay might be a bereavement period followingthe death of a loved one, maternity/parental leave, or relocation of your research environment.

Descriptions might include the start and end dates, the impact areas, and the reason(s) or a brief explanation of the absence. Attach one page.

CV Module, Page 8 (0812003>

280 David

Most As reports. including technology international agricultural has the editorial Theme

and Models Committee been McGill position in environment, As example:

the highly I

have

• • my my •

• • •

Council

a included

a

course

Challenges Genome Foundation Technologies Dynamic 2008 New Toronto, derived Meeting, Technology Ethical Social result Canadian on Significant

member

Castle

being

list

Leader

also The

qualified University.

of

the board

papers

books,

of

approaches

Biotechnology

innovation,

of biotechnology for of of

innovation, Research topics trained

asked

literature publications considerable considerations,

vaccines.

Canada economics,

my

January their of Canadian November systems for of

the

Institutes

for

in

edited

for

the

researchers Career the Transfer

accomplishments

the

on to Social for health

Genome For

graduate more

Innovation.

Research

Journal

twice Genorne

Management which Networks Workshop,

to

on a

16, Institute modelling and

books,

the

the

second

Academies

getting

of

Research than the

Sciences indicates. 20, and law Intellectual research

and 2008.

Annual

major science chair

public

Health

Canada. I pitfalls

and

who of intersection

2007

publish what and

20 Canada peer-reviewed ethics, Management

life. for Agricultural

of technology Inventing

the post-doctoral

graduate Rome, research

of

either

society),

good

Meeting,

management Centres and Research, the for

genomics Committee.

I Contributions as

and Celebration expert

technology Genome

have

science Property

include

CV a

development.

History

Humanities

and researcher, work opportunities

April

of

published the projects

Attachment students,

panel of

and

out

June science Committee. the

and

papers

Ottawa, and can Canada the Excellence

on

Future:

7, studies. Protection: and

I

the My

invention-innovation

diffusion experience,

of

have Environmental

on paid 2008.

philosophy

offer. 12, society,

I Philosophy Canada

Research door:

I leadership

and

and nanotechnology.

have and

These consistently

9 have

2007.

March GE3LS

Ideas contracts been of

Italian

society

I I chapters,

CIHR

Open for

had currently in have intellectual

been A

Research significant

a

for

which developing

Transdisciplinary

Advance Council of 19, principal

Symposium funded

National in

of

source the also partnerships

or an have science,

Ethics.

2007.

the and

Science

as

have

invited

has 21st

maintain

been

well field Chairs

led My by widely gap. of property

Foods

for research

investigator created

joined

Tn Century. Research

countries:

Canada particularly

Genome

to

on extensive

as biotechnology. and of

speaker Federal (Genomics, 2008

my

and with the commissioned

a science in

and

Technology.

staff my

opportunities and Approach

being

contributions a

Research 1

the funded

Gatineau, number

the Materials was

Council Canada,

research

Partners The to

science

and research

of

Canadian

biology,

and

Private many

invited

also

more

ethics,

case

co-PT

project

society

based

of ACCT

Management

(CNR)

I

asked

and

events, team in University March (AFMNet),

research

have

of than formats,

portfolio

to

Sector. to

to

on 080708

plant-

be

join

Legal at

the

funding resulted

during Annual

a to

also

-

a

26,

dozen

for

join

the

of 281 David Edited Books Castle Articles and Publications Communication. Castle, Castle Forthcoming Castle Castle Journal Journal Castle regulating Castle and Castle biotechnology. Castle Castle 70. Castle Book Castle Integrated contract, Castle. Biology. Ethics.

Sons.

Molecular

Castle

Chapters

D.

D. D. D. D. D. Books D. D. D. D.

D. D.

Law. D. of of

Edited 2009. et The

and 2008. 2008.

and and Forthcoming 2006. 2007.

2008. and and

the Law, service Assessment 2008.

al.

under

List Regulation

K.

R. N.M. Role

American K. N.M.

Plant

Mechanisms

Techne

Nutrigenomics

Genomic

The The Science The

by

Culver. DeBusk. Forthcoming

Agricultural

Culver.

delivery

of contract,

M.

Ries.

Ries.

Derived balance ethics

personal

Genome

Intellectual

Ruse. Journal

under

9:1

and

Dietetic

and Aquaculture,

2006.

2007.

nutritional

Nutrition

2008.

-13.

and

of

of

Technology. 2009.

between

Communication. Vaccines:

Oxford

contract.

personalized

and and

under

Canada

Mutagenesis

6:137-52. building

and

Public

Ethical,

The

Association.

Property

agricultural

the

Patents.

and

contract, profiling:

electronic

University

public expertise

Innovation

engagement,

CV 2008.

Innovations

Genomics:

health legal

Attachment Rights nutrition.

Health

622:138-143.

in

and

2009.

biotechnology.

Edited

innovation professional

nutrigenomics.

health

and

Press.

social and

in

Law Issues

authority public 10

and

Biotechnology

Teknoscienze:

by

record, Social

525-44.

Regulatory

issues Review

D.

of

and

consultation,

Castle capacity.

Ethics,

Transformation.

in

In genetic

regulation

In

in

citizen

Oxford

16:58-64.

Nutrition nutrigenomics:

and

Burdens.

Agro Innovation.

Law,

Mutation

information

N.M.

engagement

Companion innovation

in

Food

Regulation

and

nutrigenomics.

Ries.

New

Dordrecht:

Research

Genornics: Industry

Edward

the

and

Jersey:

Forthcoming

and

about

to

challenges

and

patient

Philosophy

the

Hi-tech. Elgar

-Fundamental

Springer.

new

John

Issues

Minnesota

market,

privacy.

080708

Press.

Wiley

of

under

18:

of

of

2008.

The

68- 282

Report

Castle

Canada.

Hoye

Commercialization

Hoye,

Technology

Research

Castle

new

Hoye

Management

diffusion:

Refereed Castle

Kaput

nutritional

Castle

Ordovas

Castle

C.

transaction.

Castle

by

presuncôes.

Gold

David

Onwuekwe.

biotechnology

K.

E.B.

D.

K.,

for

K.

D.

D.,

and

E.R.,

and D.,

D.

2006.

D.

and

Castle

Health

2008.

E.R.

Reports

Rodrigues

and

Conference

the

K.

2006.

Cline

R.L. and

Policy genomics.

D.

D.

Castle

Accessing

of

Kumagai,

case In

Gold R.

Open

Castle.

Decision

E.R.

Castle.

Engineering

Canada.

Rodriguez.

Propriedade Dordrecht:

Carmena.

Science

C.,

and

and

of

of

firms.

and

D.

Source

and

Gold.

Daar

Publicly-Funded

plant-derived

2008. Nutritional

Proceedings

Commissioned Regulation.

and

2008.

D.

L.M.

and

Genome

F.P.

Making

quality

Proceedings

A.S.,

2006.

Castle.

M. Madrid:

and

New

Springer.

Understanding

Sharing

and

Intelectual

Polido.

Access Cloutier

Cloutier,

Tsamis,

Patent

in

Traditional

Technology.

Frameworks:

Jersey:

Canada

Genomics:

2008.

A

vaccines. nutrigenomics,

MonographIas

the

Editora

to

Report

In

Publications

of

Research.

and

Pooling

venture

2007,

C.

-

press.

Benefits

Bridging

John

the

CV

Novos

E.R.

and

Technology

for

R&D knowledge

Elsevier-Campus.

Proceedings Discovering

Attachment

Wiley

Agrobiotechnologia

Ethical

in

P.A.

Gold.

capital:

Health

11

Paradigmas

of

Canadian

the

Management

Humanitas.

Nutrigenetics

the

Singer.

&

Invention-Innovation

A

Issues

Sons.

Canada.

Genomics

Comparing

Transfer

model

and

of

the

Science

2006.

benefit

the

Intemacionais,

and

Path

of

In

Conference Portland

and

in

Implications

regulatory

press.

Nutrients

Revolution.

nos

to

university

Canada.

sharing:

and

Nutrigenomics.

Personalized

tribunas:

Biotechnology

International

Gap

2008.

and

Conflitos A

burden

from

spin-offs

for

Edited

Report

patentes,

in

norms:

Science compensation

Nutrition.

the

in

Edited

by

e for

technology

Center

against Policy:

Desafios,

Ethical

P.

privilégios

Industry

and

Phillips

by

Edited

for

A

other

J.M.

issues

080708

to

the

edited

and

by

e

in J. 283 PROTECTED WHEN COMPLETED

CV Module

Family Name Given Name Middle Initial(s) Gold Edward Richard Salutation: Correspondence preferred in

X Dr. X Mr. Mrs. Ms. Prof. English French

Primary Affiliation Address

Faculté de droit Université McGill 3664 rue Peel Montreal, Québec CANADA (H3A 1W9)

Contact numbers Electronic Addresses Phone Fax E-Mail Primary (514) 398-6636 Primary [email protected] Montreal Secondary (514) 967-5258 Temporary Web Address

www.theinnovationpartnership.org Temporary

Expertise

List up to ten (10) key words that best describe your expertise in research, instruments and techniques.

intellectual property governance innovation development biotechnology globalisation patents globalisation property law

14/04/10 Date

CV Module, Page 1 (08/2003) Disponible en Français 284 Edward Richard GOLD

Academic / Training Background - One additional page may be added Indicate all university degrees obtained and those in progress (where applicable) starting with the most recent. If you hold a co- degree from more than one institution (e.g. under the Soutien aux cotutelles de these de doctorat agreement between Quebec and France) enter each institution separately. Do not enter honorary degrees here, they should be listed in the Distinctions section.

Also indicate research training, such as postdoctoral or fellowship training.

Date received Degree / Training Degree Name and Specialty Organization and Country Type (MM/YYYY) Doctorate S.J.D. University of Michigan Law School 06/1995 Equivalent Property and Intellectual Property UNITED STATES (PhD)

Master's LL.M. University of Michigan Law School 06/1992 Law UNITED STATES

Bachelor's, LL.B. (Honours) University of Toronto 06/1988 Honours Law CANADA

Bachelor's B.Sc. McGill University 06/1984 Computer Science and CANADA Mathematics

CV Module, Page 2a (08/2003)

285 Edward Richard GOLD

Work Experience

Start with the most recent, indicate your current position, where applicable, and other academic and non-academic position(s) since the beginning of your university studies. For your current positions leave the end date blank. No additional pages may be added.

Start Date End Date Position Organization and Country Department (MM/YYYY) (MM/YYYY) Associate McGill University Human Genetics 04/2010 CANADA

President The Innovation Partnership 06/2008 CANADA

Expert Organisation for Economic 06/2008 Cooperation and Development FRANCE

Associate Professor McGill University Law 07/2001 CANADA

Expert UNITAID 04/2008 09/2009 SWITZERLAND

Director McGill University Centre for Intellectual Property Policy 03/2003 08/2008 CANADA

Consultant UNITAID 06/2007 08/2007 SWITZERLAND

Consultant Organisation for Economic Biotechnology Unit 07/2003 11/2005 Cooperation and Development FRANCE

Lecturer Université René Descartes (Paris V) Faculte de droit 03/2005 04/2005 FRANCE

Lecturer Université René Descartes (Paris V) Faculte de droit 04/2004 05/2004 FRANCE

CV Module, Page 3 (08/2003)

286 Edward Richard GOLD

Distinctions / Credentials

Starting with the most recent, indicate any recognitions received, including awards, fellowships, scholarships, licenses, qualifications, professional designation or credentials. Do not include Academic Appointments here, as they are detailed under Work Experience. One additional page may be added.

Effective Date End Date Specialty Total Amount Name and Type Organization and Country (MM/YYYY) (MM/YYYY)

Jean Monnet Fellow European University Institute 01/2003 06/2003 Law $11,000 Research award ITALY

Associate Fellow Centre for Interuniversity Research and 08/2002 Intellectual $0 Credential Analysis property and CANADA property

Bell Chair in e-Governance McGill University 07/2001 06/2006 intellectual $0 Distinction CANADA property

Senior Fellow Einstein Institute for Science Health 2000 2003 Biological $3,000 Credential and the Courts Property UNITED STATES

Research Associate Health Law Institute, University of 2000 Intellectual $0 Credential Alberta Property CANADA

Fellow Einstein Institute for Science Health 1999 09/2000 Biological $10,000 Credential and the Courts property UNITED STATES

CV Module, Page 4a (08/2003)

287 Edward Richard GOLD

Patents and Copyrights

There are two components to entry: total numbers of patents / copyrights; and detailed content. Record the total numbers of patents / copyrights in the following table. Details regarding the entries may be attached within the Contributions Section.

OBTAINED APPLICATIONS UNDER PROCESS TOTAL PATENTS / COPYRIGHTS Total individual Total collective Sub-total Total individual Total collective Sub-total

0 0 0 0 0 0 0

Publications AND presentations

Give the number of publications and presentations in the course of your career. Detailed information should be attached as specified in the "Contributions - details" section.

Publications Refereed Books and Book Chapters / Abstracts / Notes TOTALS Papers Monographs Contributions to a collective work

Already Published 33 3 34 2 72

Accepted or in the Press 1 0 1 0 2

74

Presentations as guest speaker 100

CV Module, Page 5 (08/2003)

288 Edward Richard GOLD

Funds REQUESTED

List all sources of support applied for as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

CV Module, Page 6a (08/2003)

289 Edward Richard GOLD

Funds CURRENTLY HELD

List all sources of support currently held as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal Value Addition to Genomics and GE3LS

Funding Source Program Name Genome Canada ABC Competition Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Castle, David/Phillips, Peter Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $5,413,000 07/2009 06/2013

Title of Proposal RMEthNet

Funding Source Program Name Canadian Institutes of Health Research (CIHR) Team Grant Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Daar, Abdallah Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $301,000 12/2004 11/2011

Title of Proposal Performance, Modelisation, Coordination et Transformation des Entreprises de Biotechnologie

Funding Source Program Name Fonds Québécois de la Recherche sur la Société et la Culture (F Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Cloutier, Marin Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $482,880 11/2006 10/2010

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

CV Module, Page 7a (08/2003)

290 Edward Richard GOLD

Attachment Instructions

Preparation and formatting of attachments:

The following format should be adhered to for these attachments. - 8.5" X 11" (21.5 X 28.0 cm) white single-sided paper. - Margins of ¾" (2 cm). - Minimum font size 12 point. - Six lines per inch, single-spaced, with no condensed type or spacing. - Number pages consecutively after CV (If, for example, the print-out of the CV ends on page 8, the attachment would begin with page 9.). - Each page header must contain your name, the application submission date, and the section header.

Research Contributions Use up to three pages to describe: - your most significant contributions to research (articles, mongraphs, books, patents, copyrights, products, services, technology transfers, other forms of research output). For each contribution, describe the significance in terms of influence and impact on the target community and; - other actvities that show the impact of your work, such as your track record in the training of graduate students and post-doctoral fellows, consulting, contributions to professional practice or public policy and membership on committees, boards, or policy-making bodies.

Interruption(s) / Delays Identify any administrative responsibilities, family or health reasons, or any other factors that might have delayed or interrupted any of the following: academia, career, scientific research, other research, dissemination of results, training, etc. Common examples of an interruption/delay might be a bereavement period following the death of a loved one, maternity/parental leave, or relocation of your research environment.

Descriptions might include the start and end dates, the impact areas, and the reason(s) or a brief explanation of the absence. Attach one page.

CV Module, Page 8 (08/2003)

291 Most Significant Research Contributions E. Richard Gold 1. Most Significant Research Contributions 1) I was Principal Investigator of the Expert Group on Biotechnology, Innovation and Intellectual Property, an international and transdisciplinary team of researchers from law, management, science, philosophy, ethics, economics and political science. In 2008, the Expert Group released its final report that details the interrelation between intellectual property and innovation in the biotechnology sector. Some of the recommendations included a greater focus on the management and strategic use of intellectual property rights, a greater investment by granting agencies and universities on developing metrics to assess the real social, academic and economic impact of research investments (and abandoning measures such as number of patents held), greater investments in the collection of patent and licensing data and the establishment of technology assessment organisations to assist developing country universities and enterprises demonstrate the quality of their innovation. Funded since 2002 by grants by the Social Sciences and Humanities Research Council and by the Canadian Institutes for Health Research, the Expert Group developed a unique methodology combining the tools and analysis drawn from various fields. In addition to its final report, the Expert Group released four case studies that focus on various aspects of biotechnology innovation and intellectual property including a detailed examination of the crisis surrounding Myriad Genetics’s patents over two breast-cancer genes, an analysis of how to introduce a new plant-based vaccine. The Expert Group has published two books with another in production, and articles in a variety of journals including Public Affairs Quarterly, the European Journal of International Relations, Nature Genetics and Genetics in Medicine. 2) I have been active in developing robust and sustainable methods of translating social science research into industrial strategy and government policy. Through innovative workshop structures, we brought policy-makers into the very design of our research project and have included them in our internal peer-review process. As a result of the findings of the Expert Group, I have, together with several colleagues, created a non-profit organisation, The Innovation Partnership (www.theinnovationpartnership.org) whose purpose is to translate the findings of social science into tangible industrial strategy and government policy. Through this process of knowledge translation, I have not only been able to ensure uptake of government funded research, but have developed a better appreciation for the issues, risks and perspectives of actors within the innovation system that in turn better focuses my research efforts. Thus, my work on knowledge translation has led me to write and publish articles in high impact journals such as, recently, PLoS Medicine and The Lancet. 3) My book, Body Parts: Property Rights and the Ownership of Human Biological Materials, published by Georgetown University Press in 1996, set out a foundation for work on the intersection of intellectual property and social policy. This was further developed in my book chapter, "Making Room: Reintegrating Basic Research, Health Policy, and Ethics into Patent Law" in 1999 and in my article "Biomedical Patents and Ethics: A Canadian Solution" published in the McGill Law Journal in 2000, I investigated available policy options to address ethical concerns regarding biotechnology patents. All three publications were favourably cited by the Supreme Court of Canada in the Harvard onco-mouse case. 4) I have trained and am continuing to train a new generation of researchers across several disciplines in a transdisciplinary understanding of intellectual property and its role in innovation. Two of my doctoral students have obtained teaching positions at the Université de Sherbrooke, a former post- doctoral fellow is teaching in the Political Science Department at the Université Libre de Bruxelles and another post-doctoral fellow will commence teaching at Carleton this summer. I have organised my supervision of students and post-doctoral fellows in such a way as to actively bring them into the research process, from design, to implementation to drafting and presenting.

8 8 April 2010

292 Selected Publications and Works since 2005 Gold, E. Richard

Selected Publications and Works since 2005 Peer-reviewed articles: 1. Gold, E. Richard,& Carbone, Julia, “Myriad Genetics: In the Eye of the Policy Storm” (2010) 12:4 Genetic in Medicine, doi: 10.1097/GIM.0b013e3181d72661 (SSHRC and NIH) 2. Gold, E. Richard, Kaplan W, Orbinski J, Harland-Logan S, N-Marandi S, “Are Patents Impeding Medical Care and Innovation?” (2010) PLoS Med 7(1): e1000208. doi:10.1371/journal.pmed.1000208 (Genome Canada) 3. Gold, E. Richard, “Avoiding the Mistakes of Biotech: How Intellectual Property can be Better Managed to Advance Nanotechnology Research” (2010) 3 Studies in Ethics, Law, and Technology, Article 4, doi: 10.2202/1941-6008.1114 (SSHRC) 4. Gold, Richard (2009) "Avoiding the Mistakes of Biotech: How Intellectual Property Can Be Better Managed to Advance Nanotechnology Research," Studies in Ethics, Law, and Technology: Vol. 3 : Iss. 3, Article 4. DOI: 10.2202/1941-6008.1114 (SSHRC) 5. Gold, E. Richard and Morin, Jean-Frederic, “The missing ingredient in medicine patent pools” (2009) 374 The Lancet 1329-30 (SSHRC and CIHR) 6. Heaney, Christopher, Carbone, Julia, Gold, Richard, Bubela, Tania, Holman, Christopher M., Colaianni, Alessandra, Lewis, Tracy & Cook-Deegan, Robert, “The Perils of Taking Property Too Far” (2009) Stanford Journal of Law, Science and Policy, online: http://www.stanford.edu/group/sjlsp/cgi- bin/users_images/pdfs/61_Heaney%20et%20al%20SJLSP%20perils%20of%20taking%20property %20too%20far.pdf (SSHRC and NIH) 7. Gold, E. Richard, Bubela, Tania, Miller, Fiona, Nicol, Dianne & Piper, Tina, “Gene patents – more evidence needed, but policymakers must act” (2007) 25 Nature Biotechnology 388-389 (SSHRC) 8. Gold, E. Richard, “Intellectual architecture as place brand” (2006) 2 Place Branding 220-228 9. Gold, E. Richard & Durell, Karen L., “Innovating the Skilled Reader: Tailoring Patent Law to New Technologies” (2005) 19 Intellectual Property Journal 189 (SSHRC) In press peer-reviewed articles: 10. Morin, Jean-Frederic and Gold, E. Richard, “Consensus-Seeking, Distrust, and Rhetorical Entrapment: The WTO Decision on Access to Medicines” (forthcoming 2009) European Journal of International Relations (CIHR) Published books: 11. Gold, E. Richard and Knoppers, Bartha Maria, eds, Biotechnology IP & Ethics, (Toronto: LexisNexis, 2009) (SSHRC and CIHR) Book chapters: 12. Gold, E. Richard and Durell, Karen L., “Looking Beyond the Firm: Intellectual Asset Management and Biotechnology” in The Role of Intellectual Property Rights in Biotechnology Innovation, David Castle, ed. (New York: Edward Elgar, 2009) (SSHRC) 13. Gold, E. Richard and Morin, Jean-Frederic, “From Agenda to Implementation: Working Outside the WIPO Box” in Implementing the World Intellectual Property Development Agenda, Jeremy de Beer, ed. (Ottawa: International Development Research Centre, 2009) at 57 (SSHRC and NCE) 14. Gold, E. Richard, “Commentary: Mending the Gap – Intellectual Property, Competition Law, and Compulsory Licensing” in Competition Policy and Intellectual Property, Marcel Boyer, Michael Trebilcock and David Vaver, eds (Toronto: Irwin Law, 2009) at 396

9 8 April 2010

293 Selected Publications and Works since 2005 Gold, E. Richard 15. Gold, E. Richard, “The Ethics of Biotechnological Intellectual Property” in Biotechnology IP & Ethics, E. Richard Gold and Bartha Maria Knoppers, eds (Toronto: LexisNexis, 2009) at 15 (SSHRC) 16. Gold, E. Richard, “Legal Foundations of the U.S. Dollar, 1933-1934 and 1971” in Orderly Change: International Monetary Relations since Bretton Woods, David Andrews, ed. (Ithaca: Cornell University Press, 2008) at 177 (SSHRC) 17. Gold, E. Richard, “Biotechnology and Boundary Busting: Legal Challenges in the Biotech Era” in Life, Technology and Law, Carlo Casanato, ed. (Verona: CEDAM, 2007) (SSHRC) 18. Gold, E. Richard and Castle, David, “Traditional knowledge and benefit sharing: from compensation to transaction” in Accessing and Sharing the Benefits of the Genomics Revolution, P. Phillips and C. Onwuekwe, eds. (Dordrecht: Springer, 2007) (SSHRC and Genome Canada) 19. Gold, E. Richard and Durell, L. Karen, “Comparative Intellectual Property Issues in Biotechnology” in Food, Health and Biotechnology: Consumer and Social Issues in Canada’s New Food and Health Product Industries, Nola M. Ries & Jacob J. Shelley, eds (Victoria: AFMNet, 2007) (NCE) 20. Gold, E. Richard and Bubela, Tania, “Drafting Effective Collaborative Research Agreements and Related Contracts” in Intellectual Property Management in Health and Agricultural Innovation: A Handbook of Best Practices, A Krattiger, RT Mahoney, L Nelson, et al., eds (Oxford: MIHR, 2007), available online at www.ipHandbook.org. 21. Gold, E. Richard, Castle, David and Cloutier, L. Martin, “Agrobiotecnologia nos Tribunais: Patentes, Privilegios e Presuncoes” in Propriedade Intelectual, Edson Rodrigues Jr., & Fabricio Polido, eds. (Rio de Janeiro: Elsevier, 2007) 275 (SSHRC) 22. Caulfield, Timothy, Sheremeta, Lorraine, Gold, E. Richard, Merz, Jon and Castle, David, “Informing Genomic Patent Policy” in Genetic Testing: Care, Consent and Liability, Neil F. Sharpe, Ronald F. Carter eds. (New York: John Wiley & Sons, 2006). 23. Cloutier, L. Martin and Gold, E. Richard, “A Legal Perspective on Intellectual Capital” in Perspectives on Intellectual Capital: Multidisciplinary insights into management, measurement, and reporting, B. Marr, ed. (Boston: Elsevier, 2005) (SSHRC) 24. Gold, E. Richard, “The Diversity of Intellectual Properties” in Human Diversity and the Law, Mauro Bussani & Michele Graziadei, eds. (Brussels: Bruylant Ltd., 2005) (SSHRC) In-press book chapter: 25. Gold, E. Richard and Srulovicz, Tal, “Beyond Economics: Cultural and Institutional Barriers to Commercializing Innovation in Perspectives on Commercializing Innovation, F. Scott Kieff and Troy A. Paredes, eds. (Cambridge: Cambridge University Press, forthcoming) (SSHRC) Government, international organisation and other reports: 26. Gold, E. Richard et al, Toward a New Era of Intellectual Property: from confrontation to negotiation (Montreal: The Innovation Partnership, 2008) online: http://www.theinnovationpartnership.org/data/ieg/documents/report/TIP_Report_E.pdf (SSHRC) 27. Gold, E. Richard, Piper, Tina Piper, Morin, Jean-Frédéric, Durell L. Karen, Carbone, Julia and Henry, Elisa, Preliminary Legal Review of Proposed Medicines Patent Pool, 2007 report for UNITAID. 28. Gold, E. Richard, Herder, Matthew, and Trommetter, Michel, The Role of Biotechnology Intellectual Property Rights in the Bioeconomy of 2030, 2007 report for the OECD. 29. Herder, Matthew and Gold, E. Richard, Intellectual Property Issues in Biotechnology: Health and Industry, 2007 report for the OECD. 30. Organisation for Economic Cooperation and Development, Guidelines on the Licensing of Genetic Inventions, 2006. 10 8 April 2010

294 PROTECTED WHEN COMPLETED

CV Module

Family Name Given Name Middle Initial(s) Secko David M Salutation: Correspondence preferred in

X Dr. X Mr. Mrs. Ms. Prof. English French

Primary Affiliation Address

Department of Journalism Concordia University 7141 Sherbrooke St. W. Montreal, Québec CANADA (H4B 1R6)

Contact numbers Electronic Addresses Phone Fax E-Mail Primary (514) 848-2424 #5175 Primary (514) 848-2473 [email protected]

Secondary Temporary Web Address http://www.csjp.ca/ Temporary

Expertise

List up to ten (10) key words that best describe your expertise in research, instruments and techniques.

Science Journalism GE3Ls Models of Communication Molecular Biology Journalism Ethics Science Education Democratic Studies Qualitative Methods

14/04/10 Date

CV Module, Page 1 (08/2003) Disponible en Français 295 David M SECKO

Academic / Training Background - One additional page may be added

Indicate all university degrees obtained and those in progress (where applicable) starting with the most recent. If you hold a co- degree from more than one institution (e.g. under the Soutien aux cotutelles de these de doctorat agreement between Quebec and France) enter each institution separately. Do not enter honorary degrees here, they should be listed in the Distinctions section.

Also indicate research training, such as postdoctoral or fellowship training.

Date received Degree / Training Degree Name and Specialty Organization and Country Type (MM/YYYY) Postdoctorate Postdoctoral Research Fellow University of British Columbia 04/2007 Applied Ethics CANADA

Master's Masters of Journalism University of British Columbia 05/2006 Science Journalism CANADA

Doctorate University of British Columbia 08/2004 (PhD) Microbiology and Immunology CANADA

Bachelor's, Bachelor of Science Queen's University at Kingston 05/1998 Honours Life Science CANADA

CV Module, Page 2a (08/2003)

296 David M SECKO

Work Experience

Start with the most recent, indicate your current position, where applicable, and other academic and non-academic position(s) since the beginning of your university studies. For your current positions leave the end date blank. No additional pages may be added.

Start Date End Date Position Organization and Country Department (MM/YYYY) (MM/YYYY) Assistant Professor Concordia University Journalism 06/2007 CANADA

Freelance Science Writer W.H. Freeman N/A 07/2009 09/2009 UNITED STATES

Science Reporter The Scientist Magazine N/A 06/2003 07/2008 UNITED STATES

Post-Doctoral Fellow University of British Columbia Applied Ethics 04/2006 05/2007 CANADA

Staff Writer Separations Now N/A 07/2003 05/2007 UNITED KINGDOM

Associate Editor The Science Creative Quarterly N/A 05/2005 01/2007 CANADA

Media Consultant Human Early Learning Partnership N/A 09/2005 04/2006 CANADA

Graduate Research University of British Columbia Applied Ethics 09/2005 04/2006 Assistant CANADA

Health Columnist Canadian Medical Association Journal N/A 01/2005 04/2006 CANADA

Science Reporter The Tyee N/A 04/2005 09/2005 CANADA

CV Module, Page 3 (08/2003)

297 David M SECKO

Distinctions / Credentials

Starting with the most recent, indicate any recognitions received, including awards, fellowships, scholarships, licenses, qualifications, professional designation or credentials. Do not include Academic Appointments here, as they are detailed under Work Experience. One additional page may be added.

Effective Date End Date Specialty Total Amount Name and Type Organization and Country (MM/YYYY) (MM/YYYY)

Teaching Fellowship School of Journalism, Indiana 2008 07/2008 Journalism $4,000 Research award University UNITED STATES

Post-doctoral fellow University of British Columbia 04/2006 05/2007 Applied Ethics $40,000 Research award CANADA

Hal Straight Gold Medal in School of Journalism, University of 2006 05/2006 $500 Journalism British Columbia Research award CANADA

Science Writing Fellow U.S. Public Library of Science (PLoS) 04/2005 05/2005 Science $1,200 Research award UNITED STATES Journalism

Travel Award Canadian Institutes of Health Research 2005 10/2005 $1,000 Research award CANADA

Grant Supplement Award Faculty of Arts, University of British 2005 12/2005 $4,000 Research award Columbia CANADA

Health Communication Award Canadian Institutes of Health Research 2004 05/2006 Science $42,000 Research award CANADA Journalism

Graduate Research Fellowship University of British Columbia 1998 08/2004 $78,400 Research award CANADA

CV Module, Page 4a (08/2003)

298 David M SECKO

Patents and Copyrights

There are two components to entry: total numbers of patents / copyrights; and detailed content. Record the total numbers of patents / copyrights in the following table. Details regarding the entries may be attached within the Contributions Section.

OBTAINED APPLICATIONS UNDER PROCESS TOTAL PATENTS / COPYRIGHTS Total individualTotal collective Sub-total Total individualTotal collective Sub-total

0000000

Publications AND presentations

Give the number of publications and presentations in the course of your career. Detailed information should be attached as specified in the "Contributions - details" section.

Publications Refereed Books and Book Chapters / Abstracts / Notes TOTALS Papers Monographs Contributions to a collective work

Already Published 80 0 19

Accepted or in the Press 00 0 00

9

Presentations as guest speaker 37

CV Module, Page 5 (08/2003)

299 David M SECKO

Funds REQUESTED

List all sources of support applied for as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

CV Module, Page 6a (08/2003)

300 David M SECKO

Funds CURRENTLY HELD

List all sources of support currently held as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal Genozymes for Bioproducts and Bioprocesses Development

Funding Source Program Name Genome Canada ABC competition Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Tsang, Adrian Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $17,422,953 10/2009 09/2013

Title of Proposal Nouveaux modèles en journalisme scientifique

Funding Source Program Name Fonds Québécois de la Recherche sur la Société et la Culture (F Établissement de nouveaux professeurs-chercheurs Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $40,500 07/2008 06/2011

Title of Proposal Media Saturated Publics: Understanding News Media Roles in Engaging the Public Effectively

Funding Source Program Name Canadian Institutes of Health Research (CIHR) Needs, Gaps and Opportunities Assessments in Health Service Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Abelson, Julia Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $98,500 11/2009 11/2010

Title of Proposal The Politics of Health Information - Adversaries or Advocates: The Government, The Media, and The Academy

Funding Source Program Name Concordia University VPRGS Aid to Research Related Events Grant Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $3,150 10/2009 09/2010

CV Module, Page 7a (08/2003)

301 David M SECKO

Funds CURRENTLY HELD

List all sources of support currently held as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal The Unfinished Science Story: Exploratory Analysis of Journalist-Audience Interactions Online

Funding Source Program Name Concordia University VPRGS Seed Funding Program Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $6,903 06/2009 05/2010

Title of Proposal Start Up Grant

Funding Source Program Name Concordia University FRDP Grant Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $15,000 06/2007 05/2010

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

CV Module, Page 7b (08/2003)

302 David M SECKO

Attachment Instructions

Preparation and formatting of attachments:

The following format should be adhered to for these attachments. - 8.5" X 11" (21.5 X 28.0 cm) white single-sided paper. - Margins of ¾" (2 cm). - Minimum font size 12 point. - Six lines per inch, single-spaced, with no condensed type or spacing. - Number pages consecutively after CV (If, for example, the print-out of the CV ends on page 8, the attachment would begin with page 9.). - Each page header must contain your name, the application submission date, and the section header.

Research Contributions Use up to three pages to describe: - your most significant contributions to research (articles, mongraphs, books, patents, copyrights, products, services, technology transfers, other forms of research output). For each contribution, describe the significance in terms of influence and impact on the target community and; - other actvities that show the impact of your work, such as your track record in the training of graduate students and post-doctoral fellows, consulting, contributions to professional practice or public policy and membership on committees, boards, or policy-making bodies.

Interruption(s) / Delays Identify any administrative responsibilities, family or health reasons, or any other factors that might have delayed or interrupted any of the following: academia, career, scientific research, other research, dissemination of results, training, etc. Common examples of an interruption/delay might be a bereavement period following the death of a loved one, maternity/parental leave, or relocation of your research environment.

Descriptions might include the start and end dates, the impact areas, and the reason(s) or a brief explanation of the absence. Attach one page.

CV Module, Page 8 (08/2003)

303 David M. Secko MOST SIGNIFICANT CONTRIBUTIONS

1. “Learning to swim with salmon: Pilot evaluation of journalism as a method to create information for public engagement,” Health Law Review, 15(3):32-35, 2007. This study piloted a methodology for bridging theory and practice in science journalism. It contrasted the science literacy and interactive science models of communication through the creation of test journalism, revealing the usefulness of the latter for creating information for public engagement. It involved building robust collaborations, in particular with the consortium for Genomic Research on All Salmonids Project (cGRASP).

2. “Biobanking in BC: Enhancing discussions of the future of personalized medicine through deliberative public engagement” (with Michael Burgess and Kieran O'Doherty) Personalized Medicine, 5(3): 285-296, 2008. This paper outlined the engagement method and overviewed the results of the “Biobanking in British Columbia” public consultation, which brought 21 people together over two weekends in April and May 2007 to deliberate over the values that should direct the creation of a B.C. biobank. The principal investigator of the project was Michael Burgess (Centre for Applied Ethics, UBC). I chaired the 12- member research group that organized and ran the event.

3. “Sequencing the Salmon Genome: A Deliberative Public Engagement” (with Dan Badalescu, Michael Burgess, Emma Cohen, Isaac Filate, Alice Hawkins, Holly Longstaff, Ania Mizgalewicz, Shauna Nep, Kieran O'Doherty, Alexis Paton, Liz Wilcox) http://salmongenetalk.com/ This event brought 25 people together over two weekends in November 2008 to deliberate over potential benefits and concerns related to sequencing the salmon genome. The project made use of deliberative democracy theory as a method to engage and support groups that are often unable to shape policy decisions on genomic topics such as genome sequencing.

4. “Canadian news media influence on biobank deliberations” (with Holly Longstaff) Submitted to Journal of Health & Mass Communication. This study tracked the influence of media reports on the deliberations of 21 citizens during a deliberative event on biobanking. While deliberative engagement is becoming increasingly popular in Canada, the effect of media on these events has remained unexplored. We find media reports are used as a source of new discussion topics, to rally and reinforce discussions, and as a source of comfort for deliberants, potentially at the expense of creating out-groups.

5. “Assessing Moral Perspectives on the Technical Application of a Fish's DNA: An Interview Study with Salmon Genomic Researchers” (with Michael Burgess) Submitted to the edited volume Iconic Species (eds. Keith Culver and Kieran O'Doherty).

April 12, 2010 9

304 David M. Secko This study involved 33 in-depth interviews with salmon genomic researchers to assess their perspectives on their moral responsibilities to towards the future applications of their work. Despite the controversies around genetics and genomics, few studies have sought to do this. We found that most interviewees report little direct responsibility for the subsequent application of their work.

6. “The identification of Dictyostelium phosphoproteins altered in response to the activation of RasG” (with Robert Insall, George Speigelman and Gerald Weeks) Proteomics, 4(9):2629-2639, September 2004. This paper adapted and applied the technique of proteomics to Dictyostelium. The intention of the study was to better our understanding how the protein RasG (an oncoprotein in humans) sent signals that allowed Dictyostelium move and grow. We opened up this avenue of research by indentifying 13 proteins that were altered by RasG. This past research informs my current research program by providing a rich foundation from which to understand the nature of scientific pursuits.

OTHER ACTIVITIES AND CONTRIBUTIONS

GE3LS RESEARCH MANAGEMENT ACTIVITY  Lead Researcher, GE3LS component of the Genozymes for Bioproducts and Bioprocesses Development Project, Concordia University, Montreal, QC, 2009-2013.  Lead Researcher, GE3LS component of the consortium for Genomics Research on All Salmonids Project (cGRASP), W. Maurice Young Centre for Applied Ethics, University of British Columbia, 2006-2007.  Group Manager, Face to face (F2F) and deliberative democracy (D2) in Biotechnology Research Group, W. Maurice Young Centre for Applied Ethics, University of British Columbia, 2006-2007.  Co-investigator, Norms Evolving in Response to Dilemmas (NERD) Research Group, W. Maurice Young Centre for Applied Ethics, University of British Columbia, 2006-2007.

EXPERIENCE IN SCIENCE JOURNALISM  Science journalist for organizations such as The Scientist magazine (reporter; 2003-2008), Separations Now (writer; 2003-2007), Canadian Medical Association Journal (columnist; 2005- 2006), The Tyee (reporter; 2005), The Science Creative Quarterly (Associate Editor; 2005-2007), Bioteach (Editor and Chief; 2002-2003)

SELECTED SCIENCE JOURNALISM AND COLUMNS  “Science journalism in a connected future,” J-Source.ca, December 4, 2009.  “Rare History, Common Disease,” The Scientist 22(7), 2008.  “A Mix between Education and Stand-up Comedy: Conversations with Science Journalists on their Role in Society,” Sciencejournalism.net, May 10, 2007.  “The Small Side of Cancer,” The Scientist 22(4): 73, 2008.  “Journalism, Science & Democracy: Education as a Window to Reflection,” Sciencejournalism.net, April 22, 2007. April 12, 2010 10

305 David M. Secko  “Opening Potassium Channels to Scrutiny,” The Scientist 21(11): 75, 2007.  “Selling the self-evident,” The Scientist 21(8): 18, 2007.  “Fifteen months in an icebox,” The Scientist Online, June 15, 2007.  “Pathogens fight back,” Canadian Medical Association Journal, 173(8):864, 2005.

SELECTED WORKSHOPS ORGANIZATION  Politics of Health Information: Reflections on a , 2nd Annual Health Journalism Workshop, Concordia University, Montreal, March 19, 2010.  Media, Public Engagement & Health Policy, Research Agenda Setting Workshop, Le Meridien, Salon Beaujolais, Montreal, November 19, 2009.  My genes are unique: Pharmacogenomics, a visual and scientific event for the general public, The Grande Place du Complexe Desjardins, Montreal, QC, January 2009.  Is Good Health Reporting an Oxymoron, Health Journalism Workshop, Concordia University, Montreal, QC, November 2008.  Young Journalist Workshop 2, Montreal, QC, January 26, 2008.  Deliberative Democracy and Biobanks Workshop, Vancouver, BC, November 11, 2006.

SELECTED PRESENTATIONS IN CONFERENCES/WORKSHOPS  “Health reporting: How it‟s done and how it should be done,” Invited presentation at Between the Lines, Canadian University Press Regional Conference, Montreal, QC, March 5-7.  “Embedding Journalism in Public Engagement Initiatives on Emerging Biotechnologies,” Paper presented at the Publics and Emerging Technologies: Culture, Context and Challenges Conference, Banff, Alberta, Canada, October 30-31.  “„A mix between education and stand-up comedy‟: Conversations on the production of science journalism in Canada from within different theoretical frames,” Territore/Places of Writing Studies in Higher Education: Canadian and International Perspectives Conference, Canadian Association for the Study of Discourse and Writing, Carleton University, Ottawa, ON, May 24-26.  “Unfinished Science Story: Exploring the Journalist-Audience Interactions in the Online Environment,” Canadian Communication Association Conference, Vancouver, BC, Canada, June 4- 6, 2008. “Movement in Positions on the Right to Withdraw Consent from Biobank Research as the Result of Public Deliberation,” Translating “ELSI”: Ethical, Legal and Social Implications of Genomics Conference, Cleveland, May 1-3, 2008.  “Consensus Formation in Deliberation: The Case of Informed Consent in Biobanking,” poster to be presented at Navigating the Changing Landscape, International GE3LS Symposium, Calgary, April 28-30, 2008.  “Innovative Designs in Public Engagement: The Case of the BC Biobank Deliberation” poster presented at the First Annual Canadian Human Genetics Conference, St. Sauveur, Quebec, April 9- 12, 2008.  “Informed Consent in Biobank Research: Fresh Evidence for the Debate,” Paper presented at the One Origin, One Race, One Earth Conference, Calgary, AB, Canada, November 15-17, 2007.

April 12, 2010 11

306 PROTECTED WHEN COMPLETED

CV Module

Family Name Given Name Middle Initial(s) Bubela Tania M Salutation: Correspondence preferred in

X Dr. X Mr. Mrs. Ms. Prof. English French

Primary Affiliation Address

School of Public Health 3030 Research Transition Facility University of Alberta Edmonton, Alberta CANADA (T6G 2V2)

Contact numbers Electronic Addresses Phone Fax E-Mail Primary 1 (780) 492-9335 Primary 1 (780) 248-1546 [email protected]

Secondary 1 (780) 932-5164 Temporary Web Address

http://www.phs.ualberta.ca/t_bubela.cf Temporary m

Expertise

List up to ten (10) key words that best describe your expertise in research, instruments and techniques.

intellectual property health policy traditional knowledge technology transfer law biotechnology law health law knowledge transfer commercialisation bioethics

15/04/10 Date

CV Module, Page 1 (08/2003) Disponible en Français 307 Tania M BUBELA

Academic / Training Background - One additional page may be added Indicate all university degrees obtained and those in progress (where applicable) starting with the most recent. If you hold a co- degree from more than one institution (e.g. under the Soutien aux cotutelles de these de doctorat agreement between Quebec and France) enter each institution separately. Do not enter honorary degrees here, they should be listed in the Distinctions section.

Also indicate research training, such as postdoctoral or fellowship training.

Date received Degree / Training Degree Name and Specialty Organization and Country Type (MM/YYYY) Bachelor's Bachelor of Law (LLB) University of Alberta 06/2003 Law CANADA

Doctorate Doctor of Philosophy University of Sydney 12/1995 (PhD) Biological Sciences AUSTRALIA

Bachelor's, Bachelor of Science (Honours) Australian National University 11/1988 Honours Biological Sciences AUSTRALIA

CV Module, Page 2a (08/2003)

308 Tania M BUBELA

Work Experience

Start with the most recent, indicate your current position, where applicable, and other academic and non-academic position(s) since the beginning of your university studies. For your current positions leave the end date blank. No additional pages may be added.

Start Date End Date Position Organization and Country Department (MM/YYYY) (MM/YYYY) Assistant Professor University of Alberta Public Health Sciences 07/2008 CANADA

Assistant Professor University of Alberta Marketing, Business Economics and 07/2004 06/2008 CANADA Law

Law Clerk to The Supreme Court of Canada 08/2003 07/2004 Honourable L. Arbour CANADA

Research Assistant University of Alberta Health Law Institute 07/2000 06/2004 CANADA

Sessional Lecturer University of Alberta Biological Sciences 01/2000 06/2000 CANADA

Tutor University of Toronto Erindale College 07/1997 06/1999 CANADA

Post-Doctoral Fellow University of Toronto Zoology 09/1995 07/1997 CANADA

Sessional Lecturer University of Toronto Scarborough College 07/1996 06/1997 CANADA

CV Module, Page 3 (08/2003)

309 Tania M BUBELA

Distinctions / Credentials

Starting with the most recent, indicate any recognitions received, including awards, fellowships, scholarships, licenses, qualifications, professional designation or credentials. Do not include Academic Appointments here, as they are detailed under Work Experience. One additional page may be added.

Effective Date End Date Specialty Total Amount Name and Type Organization and Country (MM/YYYY) (MM/YYYY)

Investigator Stem Cell Network 05/2007 GE3LS Credential CANADA

Member Law Society of Alberta 02/2005 Law Credential CANADA

S M Chumir Memorial Essay University of Alberta 2003 LAW: Best essay $3,500 Prize in Human Rights CANADA in human rights Distinction law

The Mr Justice W G Morrow University of Alberta 2003 Law: Highest $1,500 Memorial Prize CANADA standing in Distinction graduating class

The Master L D Hyndman University of Alberta 2003 LAW: Best essay $2,000 Memorial Prize CANADA in Professional Distinction Responsibility

The Horace Harvey (Gold) University of Alberta 2003 Law: Highest Medal in Law CANADA standing in Distinction graduating class

Jason Lang Scholarship Alberta Learning 09/2002 06/2003 Law $2,000 Distinction CANADA

Honourable Mr. Justice University of Alberta 2002 LAW: Academic $2,500 Arnold F Moir Scholarship CANADA achievement in Distinction second year

Blake Cassels and Graydon University of Alberta 06/2001 06/2003 Law: Blake's $10,000 Second Year Scholarship CANADA Scholar Distinction

The Chief Justice S Bruce University of Alberta 2001 Law: Highest $1,200 Smith Prize CANADA Standing in First Distinction Year Class

CV Module, Page 4a (08/2003)

310 Tania M BUBELA

Distinctions / Credentials

Starting with the most recent, indicate any recognitions received, including awards, fellowships, scholarships, licenses, qualifications, professional designation or credentials. Do not include Academic Appointments here, as they are detailed under Work Experience. One additional page may be added.

Effective Date End Date Specialty Total Amount Name and Type Organization and Country (MM/YYYY) (MM/YYYY)

Ph.D. Scholarship Vertebrate Biocontrol Centre 06/1992 12/1994 Biological $32,000 Research award AUSTRALIA Sciences

CV Module, Page 4b (08/2003)

311 Tania M BUBELA

Patents and Copyrights

There are two components to entry: total numbers of patents / copyrights; and detailed content. Record the total numbers of patents / copyrights in the following table. Details regarding the entries may be attached within the Contributions Section.

OBTAINED APPLICATIONS UNDER PROCESS TOTAL PATENTS / COPYRIGHTS Total individual Total collective Sub-total Total individual Total collective Sub-total

0 0 0 0 0 0 0

Publications AND presentations

Give the number of publications and presentations in the course of your career. Detailed information should be attached as specified in the "Contributions - details" section.

Publications Refereed Books and Book Chapters / Abstracts / Notes TOTALS Papers Monographs Contributions to a collective work

Already Published 30 0 21 2 53

Accepted or in the Press 2 0 0 0 2

55

Presentations as guest speaker 74

CV Module, Page 5 (08/2003)

312 Tania M BUBELA

Funds REQUESTED

List all sources of support applied for as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal Impacts of Private Sector Representations of Genomics on Media Coverage, Public Perceptions and Health Policy

Funding Source Program Name Canadian Institutes of Health Research (CIHR) RFA: Facing Our Future Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $75,000 02/2006 02/2007

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

CV Module, Page 6a (08/2003)

313 Tania M BUBELA

Funds CURRENTLY HELD

List all sources of support currently held as an applicant or as a co-applicant. Include the principal applicant's name, title of the proposal, funding source, program name, total amount awarded (in Canadian dollars) and the period of the support. Indicate your role in the funding (principal applicant/project leader or co-applicant).

Title of Proposal Biosystems for the Production of High-Value Plant Metabolites

Funding Source Program Name Genome Canada Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Facchini, Peter; Martin, Vincent Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $13,471,000 04/2009 04/2013

Title of Proposal Assessing health system barriers to the commercialization and utilization of stem cell therapies in Canada.

Funding Source Program Name Networks of Centres of Excellence (NCE) Strategic Core Grant, Public Policy & ELSI Research Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Principal Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $150,000 11/2010 11/2012

Title of Proposal H1N1 Knowledge Translation for Pregnant Women and Seniors

Funding Source Program Name Canadian Institutes of Health Research (CIHR) Operating Grant Principal Applicant / Project Leader Your Role (If you are not the principal applicant) Jardine, Cynthia Co-Applicant Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY) $99,989 04/2010 04/2011

Title of Proposal

Funding Source Program Name

Principal Applicant / Project Leader Your Role (If you are not the principal applicant)

Support Period Total Amount Awarded From (MM/YYYY) To (MM/YYYY)

CV Module, Page 7a (08/2003)

314 Tania M BUBELA

Attachment Instructions

Preparation and formatting of attachments:

The following format should be adhered to for these attachments. - 8.5" X 11" (21.5 X 28.0 cm) white single-sided paper. - Margins of ¾" (2 cm). - Minimum font size 12 point. - Six lines per inch, single-spaced, with no condensed type or spacing. - Number pages consecutively after CV (If, for example, the print-out of the CV ends on page 8, the attachment would begin with page 9.). - Each page header must contain your name, the application submission date, and the section header.

Research Contributions Use up to three pages to describe: - your most significant contributions to research (articles, mongraphs, books, patents, copyrights, products, services, technology transfers, other forms of research output). For each contribution, describe the significance in terms of influence and impact on the target community and; - other actvities that show the impact of your work, such as your track record in the training of graduate students and post-doctoral fellows, consulting, contributions to professional practice or public policy and membership on committees, boards, or policy-making bodies.

Interruption(s) / Delays Identify any administrative responsibilities, family or health reasons, or any other factors that might have delayed or interrupted any of the following: academia, career, scientific research, other research, dissemination of results, training, etc. Common examples of an interruption/delay might be a bereavement period following the death of a loved one, maternity/parental leave, or relocation of your research environment.

Descriptions might include the start and end dates, the impact areas, and the reason(s) or a brief explanation of the absence. Attach one page.

CV Module, Page 8 (08/2003)

315 Tania M. Bubela, April 2010 Page 1 of 3

Areas of Interest Intellectual property, biotechnology, technology transfer, innovation and knowledge management, health law, science/health communication and media studies.

Description of Current Research Program and Contributions My empirically grounded research program focuses in two main areas, both related to my training and experience in health and biotechnology law and policy. The three principal foci are:

1. Impacts of commercialisation/open science and intellectual property policies on scientific culture and knowledge and technology flows in biotechnology. We have developed a range of novel bibliometric and scientometric methods to address this question to be used in conjunction with more traditional methods such as survey instruments, key informant interviews and social network analysis.

• Castle D, Phillips PWB, Brown A, Culver K, Castrataro D, Bubela T, Harmon S, Dutfield G, Barclay P. (2010, in press) Floating the Knowledge Management Boat in a Sea of Intellectual Property Rights. Submitted October 2009 SCRIPTed - A Journal of Law, Technology & Society • Prado M. Cristina D, Bubela T (2010, in press) “The Challenges and Opportunities in Setting up a Technology Transfer Office in a Life Sciences Research Institute in Portugal” Submitted June 2009: Tomorrow's Technology Transfer: The Journal of the Association of University Technology Transfer Managers. • Schofield, PN, Bubela T, et al. (2009) Post-publication sharing of data and tools. 461 Nature 171-173. • Strotmann, A., Zhao, D., & Bubela, T. (2009). Author name disambiguation for collaboration network analysis and visualization. Proceedings of The American Society for Information Science and Technology 2009 Annual Meeting, November 6-11, 2009, Vancouver, British Columbia, Canada. • Strotmann, A., Zhao, D., & Bubela, T. (2009). A multi-database approach to field delineation. Proceedings of the International Society for Scientometrics and Informetrics 2009 Conference, July 14-17, 2009, Rio de Janeiro, Brazil. • Heaney, C, Carbone, J., Gold, R., Bubela, T., Holman, C.M., Cliaianni, A., Lewis, T., Cook-Deegan, R. (2009) The Perils of Taking Property Too Far. 1 Stanford Journal of Law, Science and Policy 46-64. • Knowles L, Bubela T (2008) Challenges for Intellectual Property Management of HIV Vaccine-Related Research and Development: Part 1, The Global Context. 16 Health Law Journal 55-96. • Patten S, Bubela T, Knowles L (2008) Challenges for Intellectual Property Management of HIV Vaccine-Related Research and Development: Part 2, The Canadian Context. 16 Health Law Journal 97-142.

316 Tania M. Bubela, April 2010 Page 2 of 3

2. Genetic Resources and Associate Traditional Knowledge. This research which is in progress examines the issue of indigenous knowledge and access to genetic resources from an indigenous rights perspective. A book proposal for a comparative case study has been accepted by Edward Elgar.

• Bubela T, Gold ER (eds) Respecting and Promoting Indigenous Rights and Traditional Knowledge: International Case Studies. (Book contract with Edward Elgar—for submission by Fall 2010). – Includes three chapters co-authored by Bubela • Bubela T, Beas Rodriguez E, Metcalf C, Nnadozie K, Rodriguez E, Carbone J (2008) Respecting, Promoting, and Protecting Traditional Knowledge: A Comparative Case Study of Brazil, Kenya and Northern Canada. (2008) A Report to The International Expert Group on Biotechnology, Innovation and Intellectual Property. (The Innovation Partnership, 2008). Summary available online: http://www.theinnovationpartnership.org/en/ieg/cases/ • Bubela T, Beas Rodriguez E, Metcalf C, Nnadozie K, Rodriguez E, Carbone J “Respecting, Promoting, and Protecting Traditional Knowledge: A Comparative Case Study of Brazil, Kenya and Northern Canada.” Propriété intellectuelle, biotechnologies, et enjeux sociaux à l’heure de la globilisation, Science Po, Paris, 13-14 November 2008. • Bubela T, Canadian Perspectives on Traditional Knowledge. Unpacking Access: Towards the Practical Implementation of Biotechnology European University Institute, Florence, Italy June 4-5, 2007 • C. Metcalf and T. Bubela. “Traditional Ecological Knowledge, Indigenous Rights and the Constitution” Law and Society Summer Institute, Oxford University, UK, June 2005.

3. Knowledge translation in biotechnology and new technologies in biomedicine. This area of research explores how biotechnology research is represented by the research community, industry, politicians and policy makers, and the popular media, including the internet and publics. The research compares the translational layers between these stakeholder groups.

Media Representations of Biomedical Research: Examination of accuracy of newspaper coverage of biomedical and biotechnology research in Canada, the United States, Great Britain, and Australia. We compared the contents, claims, and conclusions of scientific journal articles on genetics with those of the associated newspaper article and the headlines in 627 international newspaper articlesOur study showed that though newspaper articles generally uncritically reflect scientific research, exaggerated and inaccurate reporting does occur. This sensationalism may not always be a product of the media. There is some evidence that it may also be facilitated by scientists and public research institutions through exaggerated claims made in the scientific journal articles themselves, interviews, and press releases. Both the scientific journal and newspaper articles emphasized the benefits while rarely commenting on the risks. I am continuing this research with media representations of stem cell research and have recently published a synthesis article in Nature Biotechnology on current issues and trends in science

317 Tania M. Bubela, April 2010 Page 3 of 3

communication. Other research has been submitted on international media coverage of stem cell research.

1. Bubela T, Nisbet, M, et al. (2009) Science Communication Reconsidered: Challenges, Prospects, and Recommendations. 27 Nature Biotechnology 514- 518. 2. Bubela T, Caulfield T (2004) Does the Print Media Hype Genetic Research?: A Comparison of Newspaper Stories and Peer Reviewed Research Papers. 170(9) Canadian Medical Association Journal 1399-1407. 3. Caulfield T, Shelley J, Alfonso V, Bubela T (2008) Nutrigenomics and the Promise of Prevention: Representations and Realities Health Law Journal Special Edition 41-65. 4. Caulfield T, Bubela T, Murdoch C (2007) "Myriad and the Mass Media: The Covering of a Gene Patent Controversy." 9 Genetics in Medicine 850-855.

Media Representations of d Clinical Trials of Complementary and Alternative Medicine: Qualitative exploration of media representations of clinical trials of herbal remedies with those of pharmaceuticals for the treatment of the same medical condition.

• Bubela T, Boon H, Caulfield T (2008) Herbal Remedy Clinical Trials in the Media: a Comparison with the Coverage of Conventional Pharmaceuticals. 6 BMC Medicine 35 (14 pages).

Analysis of Political Debates: Qualitative discourse analysis of all the parliamentary debates in upper and lower houses in Canada and the United Kingdom on legislation related to the regulation of stem cell research reported in the respective Hansards. This was published in the American Journal of Bioethics. Similar research on the success and influence of a variety of stakeholders on the development of amendments to the Patent Act for Canada’s Access to Medicine Regime has been submitted and is under review at the Health Law Journal. That research uses a combination of semi-structured interviews and qualitiative and quantitative text analyses of stakeholder press releases, public statements, legislative debates and media reports.

• Caulfield T, Bubela T (2007) Why a Criminal Ban?: Analyzing the Arguments Against Somatic Cell Nuclear Transfer in the Canadian Parliamentary Debate. 7(2) American Journal of Bioethics 51-61.

318 ANDREW MITCHELL

CURRICULUM VITAE

Address: The Australian Museum 6 College Street Sydney NSW 2010 Australia Tel (work): + 61 2 9320 6346 Fax: + 61 2 9320 6011 E-mail: [email protected]

RESEARCH EXPERTISE AND INTERESTS • Systematics of , particularly Noctuoidea • DNA barcoding, species discovery, diagnostics and phylogeography • Molecular phylogenetics of • Application of these techniques in quarantine control, insect pest management and biological control of invasive species

EDUCATION PhD Entomology, University of Maryland, USA (1998) MSc Entomology (cum laude ), University of Natal, South Africa (1993) BSc Hons Entomology (cum laude ), University of Natal, South Africa (1991)

EMPLOYMENT The Australian Museum, Sydney (2010–present) Integrative Systematist, Entomology NSW Department of Primary Industries/Industry & Investment NSW (2004-2010) Research Leader Biotechnology, Wagga Wagga Agricultural Institute Senior Research Scientist, Orange Agricultural Institute University of KwaZulu-Natal, South Africa (2001–2004) Senior Lecturer, School of Molecular and Cellular Biosciences University of Alberta, Edmonton, Canada (1999–2000) Postdoctoral Fellow, Department of Biological Sciences Smithsonian Institution, Washington DC, USA (1998–1999) Postdoctoral Fellow, Laboratory of Molecular Systematics

TEACHING EXPERIENCE Senior Lecturer, University of KwaZulu-Natal, South Africa (2001-2004) • Genetics 306 - Genome Organisation & Evolution • Genetics 322 - Introduction to Bioinformatics • Genetics 328 – Molecular Phylogenetics • Genetics 213 - Introduction to Genetics Graduate Teaching Assistant, University of Maryland at College Park, USA (1995 –1996)

319

• Laboratory components of 1st year biology courses, a 2nd year course in general entomology and graduate courses in systematics. Lecturer (part-time), University of Natal, South Africa (1991-1992) • 2nd year entomology course on insect diversity

SCIENTIFIC RECOGNITION • NSW BioFirst Award, 2004 • South African National Research Foundation “Y1” rating, 2001 • Fulbright Scholar, 1992-1995 • Adjunct Associate Professor, School of Agriculture, Charles Sturt University (2006-2009) • Chair of the Steering Committee of the Australian Barcode of Life Network (ABOLN) • Australian Entomological Society, Membership Secretary (2004 – 2007) • Natal Evolutionary Biology Society, President (2003 – 2004) • IUCN/SSC Southern African Invertebrates Specialist Group, Member (2002 – 2004)

MANAGEMENT EXPERIENCE • Managed the Biotechnology Unit, comprising 15 research staff working in the fields of molecular plant breeding (marker discovery and marker-assisted selection in wheat and canola) and DNA diagnostics/molecular systematics of fungi and insects (2006-2010) • Ministerial correspondence, technical briefings, speech notes and cabinet minutes relating to gene technology (2006-2009) • Secretary of the NSW Agricultural Advisory Council on Gene Technology (2006-2007) • Secretary of the national GM Taskforce established under the Primary Industries Standing Committee to investigate issues related to GMO legislation (2006-2007) • Representing DPI at several high-level strategic meetings regarding industry GM issues and national and international collaborative joint ventures (2006-2007) • Chair of the DPI Institutional Biosafety Committee for Plant Research (2008 – 2009) • Research Management Committee, EH Graham Centre for Agricultural Innovation (2008-2009)

RESEARCH FUNDING Funding as Principal Investigator (last 5 years) 1. Novel DNA technologies for weed diagnostics (2009-2010) $34,000 (NSW DPI component of budget) - Australian Weeds Research Centre 2. Genetic diversity of alligator weed (2008-2010) $60,000 - CSIRO 3. A NSW centre for DNA barcoding (2007-2011) $800,000 - NSW Office for Science and Medical Research 4. Molecular systematics of Nimbya spp., biological control agents of alligator weed (2006-2007) $34,000 - CRC for Australian Weed Management 5. Training Scholarship in Diagnosing Exotic Plant Pests (2005-2006) $15,000 - Department of Agriculture, Fisheries and Forestry 6. Molecular Tools for the Discrimination and Diagnosis of Australian Agricultural Pests (2004- 2008) $400,000 - NSW Ministry for Science and Medical Research

2

320

Funding as Co-Investigator (last 5 years) 7. Integrated pest management for Finschafen disorder of oil palms in PNG (2007-2010) PI: Prof. Geoff Gurr (CSU) $36,000 (NSW DPI component of budget) - ACIAR 8. Clarifying the taxonomy of the light brown apple – A revision of Epiphyas (2006-2007) PI: Dr. Marianne Horak (CSIRO) $10,000 (NSW DPI component of budget) - CRC for National Plant Biosecurity

POSTGRADUATE STUDENTS SUPERVISED /CO -SUPERVISED 1. Catherine Car, PhD, Charles Sturt University, 2008-present Supervisor: Prof. Nick Klomp Taxonomy and diversity of millipede communities in South-East Australia. 2. Linda Semeraro, PhD, LaTrobe University, 2008-present Supervisor: Prof. Tim New Systematics of Australian Macropsinae (Hemiptera: Cicadellidae). 3. Bobbie Hitchcock, PhD, Australian National University, 2007-present Supervisor: Prof. Michael Crisp Revision and phylogeny of Epiphyas ( and related species). 4. Ross Gilbert, PhD, Charles Sturt University, 2005-present (part-time) Supervisor: Prof. Geoff Gurr Systematics of Nimbya plant pathogenic fungi, biological control agents of alligator weed. 5. Willy Heimoana, PhD, Charles Sturt University, 2008-present Supervisor: Prof. Geoff Gurr Biological control of Brassica pests. 6. Getachew Ali, MSc, Charles Sturt University, graduated 2008 Supervisor: Prof. Geoff Gurr Australian lucerne yellows disease: development of disease management strategies. 7. Gudrun Dittrich, MSc, University of KwaZulu-Natal, graduated 2008 Co-supervisor: Dr. Des Conlong, South African Sugarcane Research Institute. Diagnostics for identification of white grubs (Coleoptera: Scarabaeidae) in southern African sugarcane. 8. Yoseph Assefa, PhD, University of KwaZulu-Natal, graduated 2007 Co-supervisor: Dr. Des Conlong, South African Sugarcane Research Institute Sugarcane Stem Borers in Ethiopia: Ecology and Phylogeography. 9. Mariaan Ponsie, MSc, University of KwaZulu-Natal, graduated 2007 (cum laude ) Supervisor: Prof. Steven Johnson Taxonomic Revision and Molecular Phylogeny of Bonatea (Orchidaceae).

SELECTED PEER -REVIEWED PUBLICATIONS DNA BARCODING 1. deWaard, J.R., Mitchell, A., Keena, M.A., Gopurenko, D., Boykin, L.M., et al. 2010. Towards a global barcode library for Lymantria (Lepidoptera: Lymantriinae) tussock of biosecurity concern. PLoS ONE 5(12): e14280. doi:10.1371/journal.pone.0014280 2. Mitchell, A. & Maddox, C. 2010. Scolytid beetles of importance to the macadamia industry: an integrative taxonomic approach to species diagnostics. Australian Journal of Entomology 49: 104-113. 3. Hausmann, A., Hebert, P., Mitchell, A., Rougerie, R., Sommerer, M., Edwards, T., Young, C.J., 2009. Revision of the Australian Oenochroma vinaria Guenée 1858 species-complex 3

321

(Lepidoptera: Geometridae: Oenochrominae): DNA barcoding reveals cryptic diversity and assesses status of type specimen without dissection. Zootaxa 2239: 1-21. 4. Mitchell, A. 2008. DNA barcoding demystified. Australian Journal of Entomology 47: 169-173. [Invited mini-review] 5. Assefa, Y., Mitchell, A. , Conlong, D.E., Moyal, P. 2007. DNA identification of Busseola (Lepidoptera: Noctuidae) larvae in Ethiopian sugarcane. African Entomology 15: 375–379. 6. Mitchell, A . & Samways, M.J. 2005. DNA evidence that the morphological ‘forms’ of Palpopleura lucia (Drury) are separate species (Odonata: Libellulidae). Odonatologica 34: 173- 178.

TAXONOMY 7. Pogue, M.G., Matthews, M.J. & Mitchell, A. Chapter 1. Identification and Taxonomy. In: Heliothine Moth Pests: Biology, Ecology, and Management. Ed: Benedict, J.H. CABI publishing (in press). [Book Chapter] 8. Dittrich-Schröder, G., Conlong, D.E., Way, M., Harrison, J.duG. & Mitchell, A. 2009. Identification key to scarabaeid larvae attacking sugarcane in South Africa. Proceedings of the South African Sugarcane Technologists’ Association 82: 500-524. 9. Mitchell, A. 1997. The first endemic Hawaiian Heliothis (Lepidoptera: Noctuidae): H. melanoleuca , a new species from riparian forest. Records of the Hawaii Biological Survey 1996 Part 1: 78-81. 10. Mitchell, A. & Brothers, D.J. 2002. Phylogeny of the genera of Ticoplinae (Hymenoptera: Mutillidae). Journal of Hymenoptera Research 11: 312-325. 11. Mitchell, A. & Brothers, D.J. 1998. Revision and cladistic analysis of the Afrotropical genus Areotilla Bischoff (Hymenoptera: Mutillidae). African Entomology 6: 193-214.

MOLECULAR PHYLOGENETICS OF NOCTUIDAE 12. Cho, S., Mitchell, A. , Mitter, C., Regier, J., Matthews, M. & Robertson, R. 2008. Molecular phylogenetics of heliothine moths (Lepidoptera: Noctuidae: Heliothinae), with comments on the evolution of host range and pest status. Systematic Entomology 33: 581-594. 13. Mitchell, A ., Mitter, C. & Regier, J.C. 2006. Phylogeny of Noctuidae (Lepidoptera): Evidence from nuclear protein-coding genes. Systematic Entomology 31: 21-46. 14. Mitchell, A. , Mitter, C. & Regier, J.C. 2000. More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Systematic Biology 49: 202-224. 15. Fang, Q.Q., Mitchell, A ., Regier, J.C., Mitter, C., Friedlander, T.P. & Poole, R.W. 2000. Phylogenetic utility of the nuclear gene dopa decarboxylase in noctuoid moths (Insecta: Lepidoptera: Noctuoidea). Molecular Phylogenetics and Evolution 15: 473-486. 16. Mitchell, A. , Cho, S., Regier, J.C., Mitter, C., Poole, R.W. & Matthews, M. 1997. Phylogenetic utility of elongation factor-1α in Noctuoidea (Insecta: Lepidoptera): the limits of synonymous substitution. Molecular Biology and Evolution 14: 381-390. 17. Cho, S., Mitchell, A. , Regier, J.C., Mitter, C., Poole, R.W., Friedlander, T.P. & Zhao, S. 1995. A highly conserved nuclear gene for low-level phylogenetics: Elongation Factor-1α recovers morphology-based tree for heliothine moths. Molecular Biology and Evolution 12: 650-656.

SELECTED OTHER PUBLICATIONS 18. Gitau, C.W., Gurr, G.M., Dewhurst, C.F., Mitchell, A ., Fletcher, M.J., Liefting, L.W. & Cowling, A. 2011. Zophiuma lobulata (Hemiptera: Lophopidae) causes Finschhafen disorder of coconut and oil palms. Annals of Applied Biology 158: 139-148. 4

322

19. Assefa, Y., Conlong, D.E., van den Berg, J. & Mitchell, A . 2010. Distribution of sugarcane stem borers and their natural enemies in small-scale farmers' fields, adjacent margins and wetlands of Ethiopia. International Journal of Pest Management 56: 233-241. 20. Gitau, C.W., Gurr, G.M., Dewhurst, C.F., Fletcher, M.J. & Mitchell, A. 2009. Insect pests and insect-vectored diseases of palms – a review. Australian Journal of Entomology 48: 328-342. 21. Assefa, Y., van den Berg, J., Mitchell, A. , Le Rü, B. and Conlong, D.E. 2009. Record of Eldana saccharina in inland South Africa and its genetic relationship with the coastal population. Journal of Applied Entomology 133: 449-455. 22. Herbert, D.G. & Mitchell, A. 2008. Phylogenetic relationships of the enigmatic genus Prestonella (: ) – the missing African element in the Gondwanan family . Biological Journal of the Linnean Society 96: 203-221. 23. Assefa, Y., Mitchell, A ., Conlong, D.E. & Muirhead, K. 2008. The establishment of Cotesia flavipes (Hymenoptera: Braconidae) in sugarcane fields of Ethiopia and the origin of the founding population. Journal of Economic Entomology 101(3): 686-691. 24. Abdel Rahman Ahmad, E.H., Ducroz, J-F., Mitchell, A., Lamb, J., Contrafatto, G., Denys, C., &Taylor, P. 2008. Phylogeny and historical demography of economically-important rodents of the genus Arvicanthis (Mammalia: Muridae) from the Nile Valley: of mice and men. Biological Journal of the Linnean Society 93: 641-655. 25. Ponsie, M.E., Mitchell, A. , Edwards, T.J. and Johnson, S.D. 2007. Phylogeny of Bonatea (Orchidaceae: Habenariinae) based on molecular and morphological data. Plant Systematics and Evolution 263: 253–268. 26. Getachew, M.A., Mitchell , A. , Gurr, G.M., Fletcher, M.J., Pilkington, L.J., Nikandrow, A. & Elliott, E. 2007. First report of a “ Candidatus Phytoplasma australiense”-related strain in lucerne ( Medicago sativa ) in Australia. Plant Disease 91: 111. 27. Assefa, Y., Mitchell, A. & Conlong, D.E. 2006. Phylogeography of Eldana saccharina Walker (Lepidoptera: Pyralidae). Annales de la Société entomologique de France 42: 331-337. 28. Assefa, Y., Conlong, D.E. & Mitchell, A. 2006. Inter-population fertility in sugarcane stem borer Eldana saccharina Walker (Lepidoptera: Pyralidae). Proceedings of the South African Sugarcane Technologists’ Association 80: 218-225. 29. Assefa, Y., Conlong, D.E. & Mitchell, A . 2006. Status of Eldana saccharina Walker (Lepidoptera: Pyralidae), its host plants and natural enemies in Ethiopia. Bulletin of Entomological Research 96: 497-504. 30. Dittrich, G., Conlong, D.E. & A. Mitchell . 2006. Genetic diversity of Sturmiopsis parasitica Curran (Diptera: ). Annales de la Société entomologique de France 42: 325-329. 31. Mitchell, A. , McClay, A., Pohl, G.R. & Sperling, F.A.H. 2005. PCR-based methods for identification of two species of Eteobalea (Lepidoptera: ) used as biological control agents of weedy Linaria species. The Canadian Entomologist 137: 129-137. 32. Duncan, G.D., Edwards, T.J. & Mitchell, A . 2005. Character variation and a cladistic analysis of the genus Lachenalia Jacq.f. ex Murray (Hyacinthaceae). Acta Horticulturae 673: 113-120. 33. Masters, J.C., Anthony, N., , M.J. & Mitchell, A . 2005. Phylogenetic relationships of the Lorisidae using a combined molecular and morphological data set. American Journal of Physical Anthropology 127: 465-480. 34. Mitchell, A. , Sperling, F.A.H. & Hickey, D. 2002. Higher level phylogeny of mosquitoes (Diptera: Culicidae): mtDNA data support a derived placement for Toxorhynchites . Insect Systematics and Evolution 33: 163-174.

5

323 CURRICULUM VITAE – ANDREW LOWE

Contact and professional details

Mob: +61 (0)434 607 705 Phone: +618 8222 9326 Fax: +618 8222 9387 Email: [email protected]

Specialisation: Evolutionary, ecological and population genetics , mainly of plants Nationality: British (Australian Citizen) DoB: 15th December 1968

Current position

Professor of Plant Conservation Biology Director, Australian Centre for Evolutionary Biology & Biodiversity The Environment Institute and School of Earth and Environmental Science University of Adelaide, North Terrace SA5005, Australia and

Head of Science Science Resource Centre (including State Herbarium of South Australia and Bioknowledge SA) Client Services Directorate Department of Environment and Natural Resources Hackney Road, Adelaide SA 5005, Australia

Short Biography

Professor Andrew Lowe is Chair in Plant Conservation Biology at the University of Adelaide and Head of Science at the State Herbarium and Bioknowledge groups with the South Australian Department for Environment and Heritage. He is also Director of the Australian Centre for Evolutionary Biology and Biodiversity, within the Environment Institute, which integrates evolutionary biology and biodiversity science across the University, State Herbarium and South Australian Museum. Andrew‟s predominant research interest is „how do plants survive and adapt to anthropomorphized landscapes?‟ His group apply molecular markers, landscape analysis and genomic assessments of adaptive genes, to demonstrate gene flow and selection pressure changes across a range of landscapes; contemporary, historical, fragmented and exploited.

324 Education

1992–1996 Ph.D Plant Evolutionary Genetics: University of St Andrews, UK „The origin and maintenance of a new Senecio hybrid in England‟ 1987-1991 BSc (Hons) Applied Biology: University of Bath, UK Included placements at MAFF, IGER and Purdue University, USA

Career Details

2006- ongoing Joint position: Professor of Plant Conservation Biology and Director of Australian Centre for Evolutionary Biology and Biodiversity (ACEBB), University of Adelaide and Head of Science, State Herbarium and Bioknowledge, DEH (SA) My current responsibilities are to develop strategic direction and science capability within the State Herbarium and Bioknowledge, a group of over 75 staff and Honorary Research Associates. More broadly within the South Australian Department for Environment and Heritage, I also have a science leadership and coordination role. At the University, I lead a research team of postdocs and students on evolutionary and ecological genetics.

2003-2006 Lecturer, University of Queensland, Australia Researcher and lecturer in ecological and evolutionary genetics. Research focus on population and evolutionary genetic questions of Australian, SE Asian and pacific interest, and new research into ecological and evolutionary functional genomics.

1998-2003 Senior/Higher Scientific Officer, Centre for Ecology & Hydrology, UK Managed and supervised staff and resources of the Ecological Genetics Lab within the Biosystem Management section. Responsible for attracting section funding, covering salary costs of staff, fulfilling contracts, delivering reports and publications. Attracted more than 5 million Euros of funding for international projects.

1998 Postdoctoral Scientist, Long Ashton /John Innes Research Stations, UK Developed microsatellites and database management tools for genetic mapping

1997 Postdoctoral Scientist, CEH/ Scottish Crop Research Institute, UK

Assessed genetic conservation priorities for African multipurpose trees

1996 Consultant, International Livestock Research Institute, Kenya & Ethiopia Molecular characterisation of germplasm collection of African forage grasses

1991-1992 Science Officer, Society for Environmental Exploration, UK & Tanzania Coordinated biodiversity work of 18 volunteers in Tanzanian Coastal Forests

Research focus

My main research interests are in examining gene flow at different spatial, temporal and biological organisational scales, and the response of organisms to the „evil trio‟ of major environmental impactors; habitat fragmentation, invasive species and historical and ongoing climate change. To date my major scientific contributions of theoretical and societal importance are: Interspecific hybridisation and weed evolution, Biogeography and macroevolution, Historical range shifts and phenological change due to historical climate change, Landscape, conservation and restoration genetics, and Biodiversity discovery and ecosystem monitoring.

325 Evidence of impact

Publications and Presentations Published more than 100 papers and book chapters, many in high impact publications (including Science, Systematic Biology, TREE, TIPS, Molecular Ecology, Evolution) Lead author of a book Ecological Genetics; Design, Analysis and Application, published in 2004, which received an outstanding review in Trends in Ecology and Evolution. It is now in its third reprint (selling more than 5000 copies) with publisher Blackwells Commissioned to write and coordinate five review articles with international experts for journal Heredity, on population genetics in neotropical trees, published in 2005. Awarded Institute of Chartered Foresters‟ 2004 Silvicultural prize for Lowe et al 2004 Forestry 77: 335-347 „ an original and much valued contribution to the genetics of oak‟ Since 2005, have given 29 presentations at international and national meetings (23 of which were invited and 14 funded), 23 public, departmental and policy presentations (21 of which were invited and 5 funded), has been involved in organizing 14 scientific conferences or workshops. Regularly contributes to radio, TV and written media (including newspapers and scientific periodicals)

Research and Teaching Finalist for South Australian Scientist of the Year (in Research Collaboration category), 2010 Collaborated with 275 researchers (as evidenced by joint publications, funded projects or student supervision), from 86 institutes and 30 countries Since 2000, have been lead PI on 16 research grants worth more than $18M (equivalent), and has been a partner on a further 15 grants with a total income in excess of $78M (total combined income ~$96M) Scientific coordinator of several large research programmes (>$1M, PSRF, EU), and a partner in national and international programmes (TERN, NCCARF and EU) Currently supervising 4 postdocs and 14 PhD students. In total 20 postdoctoral researchers, research associates and fellowship holders have been through my labs, with 8 PhD, 4MSc and 7 BSc Honours students successfully completing Received high evaluations for teaching whilst at the University of Queensland (top 25% of teachers, the highest category in the evaluation system). Upon taking over coordination of the first year ecology and environment course (approx 350 students), increased student satisfaction rating by 26%

Editorial and Reviewing Service Serving on journal editorial boards of Diversity and Distributions (2007-onwards), Silvae Genetica (2004-onwards), Journal of the Adelaide Botanic Gardens (2006 –onwards) Invited PhD external examiner for vivas at Oxford University (2001, attended), University of Adelaide (2002, written), Uppsala University (2003, attended), James Cook University (2008, written), University of New England (2008, written). Internal reviewer for five PhDs whilst on staff at the University of Queensland Article and book reviewer for current Biology, Trends in Ecology and Evolution, Ecology Letters, Molecular Ecology, Heredity, Genome, Genetics, Diversity and Distributions, Journal of Biogeography, Conservation Genetics, American Journal of Botany Theoretical and Applied Genetics, Forest Ecology and Management, Silvae Genetica Grant reviewer for Natural Environment Research Council (NERC, UK), National Science Foundation (NSF, USA), EU, National Geographic Society (NGS, USA), Department for International Development (DfID UK Government), Department for Environment, Farming and Regions (DEFRA, UK Government), The Darwin Initiative, Scottish Executive

326 Funding Since 2000, Andrew has been lead PI on 17 research grants worth more than $30M (equivalent), and has been a partner on a further 16 grants with a total income in excess of $78M (total combined income ~$108M), and has included roles as scientific coordinator (7 projects >$1M, PSRF, EU, TERN), and partner in major national and international programs (TERN, NCCARF and EU).

Publications and written outputs Published more than 100 papers and book chapters, and over 40 reports, general article and websites. Andrew‟s work has been cited more than 1800 times (including 4 papers listed by Essential Science Indicators as Highly Cited). He has an h factor of 23, average number of citations per ISI listed reference of 26.2, 250-300 total citations per year since 2007, and has four ESI Highly Cited papers and one listed as Faculty of 1000 Must Read.

Articles in final draft form Dormontt E, Prentis P, Lowe AJ. Founder effects, adaptation or maladaptation? Explaining reduced diversity and increased differentiation during spread of Senecio madagascariensis in Australia Gardner MG, Breed M, Ottewell K, Navarro C, Lowe AJ. Lack of pollen diversity impacts long- term growth of mahogany. For Ecology Letters Lowe AJ, Cannon C, Loo J, Neale D, Taylor G, Vaillencourt R, Cavers S, Vendramin GG. Research Initiatives in Genomics and Conservation. For Science policy forum Davies SJ, Cavers S, Finegan B, White A, Lowe AJ. Mating system resilience and pollen- mediated genetic rescue following stand-replacing disturbance in a neotropical pioneer tree, Vochysia ferruginea Mart. For Heredity. Ottewell KM, Bickerton D, Lowe AJ. Genetic tools for population-level threatened species conservation management. For Biological Conservation

Articles - Recently Submitted Gardner MG, Bertozzi T, Fitch AJ, Lowe AJ. The proportions of microsatellite motif families in eukaryotes changes with genome size and differ between plants and animals. Evolution. Canon C, Lerdau M, Lowe AJ. Porous genomes increase intra-specific variation and enhance species co-existence. Ecology Letters. Pavlacky DC Jr, Possingham HP, Lowe AJ, Prentis PJ, Green DJ, Goldizen AW. Empirical evidence for the rescue effect in a rainforest bird metapopulation. American Naturalist. Sigg DP, Goldizen AW, Lowe AJ. Exceptionally high genetic diversity in a recently rediscovered but critically endangered macropod, the bridled nailtail wallaby, and options for maintaining social structure and recovery. Diversity and Distributions.

Published books, book chapters and articles Books and Edited Volumes Lowe A (2005) Population Genetics of Neotropical Trees. Focus issue of Heredity, vol. 95. Coordinated and edited 7 contributions to this dedicated Special Issue of the journal. Lowe AJ, Harris SA, Ashton P (2004) Ecological Genetics: Design, Analysis and Application. Blackwells, Oxford. 326 pp. Received highly complimentary reviews in Trends in Ecology and Evolution (Dhondt AA, 2004, 19: 292-293), Heredity, Annals of Botany.

327 Journal Articles Journal impact factor (IF), and article citation index, ISI (CI) or (GS), indicated.

2010 90. Biffin E, Brodribb T, Lowe AJ. Leaf evolution in Southern Hemisphere conifers: a response to the Cretaceous angiosperm radiation? Proceedings of the National Academy of Sciences, USA. Accepted October 2010 89. Lowe AJ, Wong KN, Tiong Y-S, Iyerh S, Chew F-T. A DNA Method to Verify The Integrity of Timber Supply Chains; Confirming The Legal Sourcing of Merbau Timber From Logging Concession to Sawmill. Silvae Genetica 59: 263-268 88. Spain CS, Lowe AJ. How well do genetic and species diversity parameters correlate for Macadamia tetraphylla and its component fragmented sub-tropical rainforest habitat? Silva Genetica. Accepted October 2010 87. Mellick R, Lowe A, Rossetto M. Historical dynamics and recent fragmentation in the distribution of a late successional rainforest conifer (Podocarpus elatus). Australian Journal of Botany. Accepted October 2010. 86. Keppel G, Prentis P, Biffin E, Hodgskiss PD, Tuisese S, Lowe AJ. Diversification history and hybridisation of Dacrydium (Podocarpaceae) in Remote Oceania. Australian Journal of Botany. Accepted Sept 2010. 85. Ottewell KM, Bickerton D, Lowe AJ. Can a seed bank provide demographic and genetic rescue in a declining population of the endangered shrub Acacia pinguifolia? Conservation Genetics. Accepted Sept 2010. 84. Prentis PJ Woolfit M, Thomas-Hall SR, Ortiz-Barrientos D, Schenk P, Lowe AJ. Massively parallel sequencing identifies gene expression differences between the native and introduced range of a globally invasive species. Annals of Botany. Accepted Aug 2010. 83. Breed MF, Ottewell K, Lowe AJ. Scattered trees: a complementary strategy for facilitating adaptive responses to climate change in modified landscapes? – a response. Journal of Applied Ecology. Accepted with revision, May 2010. 82. Molecular Ecology Resources Primer Development Consortium (Andris M, Aradottir GI, Arnau G, Audzijonyte A, Bess EC, Bonadonna F, Bourdel G, Bried JL, Bugbee GJ, Burger PA, Chair H, Charruau PC, Ciampi AY, Costet L, Debarro PJ, Delatte H, Dubois M-P, Eldridge MDB, England PR, Enkhbileg D, Fartek B, Gardner MG, Gray K-A, Gunasekera RM, Hanley SJ, Havil N, Hereward JP, Hirase S, Y Hong, Jarne P, Jianfei Q, Johnson RN, Kanno M, Kijima A, Kim HC, Kim KS, Kim W-J, Larue E, Lee JW, Lee J-H, Li C, Liao M, Lo N, Lowe AJ, Malausa T, Male P-JG, Marko MD, Martin J-F, Messing R, Miller KJ, Min B-W, Myeong J-I, Nibouche S, Noack AE, Noh JK, Orivel J, Park C-J, Petro D, Prapayotin- Riveros K, Quilichini A, Reynaud B, Riginos C, Risterucci AM, Rose HA, Sampaio I, Silbermayr K, Silva MB, Tero N, Thum RA, Vinson CC, Vorsino A, Vossbrinck CR, Walzer C, White JC, Wieczorek A, Wright A), (2010) Permanent Genetic Resources Note Permanent Genetic Resources Added To Molecular Ecology Resources Database 1 June 2010 – 31 July 2010. Molecular Ecology Resources 10: 1106–1108. doi: 10.1111/j.1755- 0998.2010.02916.x 81. Sgrò CM, Lowe AJ, Hoffmann AA. Building evolutionary resilience for conserving biodiversity under climate change. Evolutionary Applications. Published online doi: 10.1111/j.1752- 4571.2010.00157.x 80. Biffin E, Hill R, Lowe AJ (2010) Did Agathis (Araucariaceae: Coniferales) really survive the Oligocene drowning of New Zealand. Systematic Biology 59: 594–602. 79. Weeks AR, Endersby NM, Lange CL, Lowe A, Zalucki MP, Hoffmann AA (2010) Genetic variation among Helicoverpa armigera populations as assessed by microsatellites: a cautionary tale about accurate allele scoring. Bulletin of Entomological Research 100: 445- 450. 78. Pauku Rl, Lowe AJ, Leakey RRB (2010) Domestication of indigenous fruit and nut trees for agroforestry in the Solomon Islands. Forests, Trees and Livelihoods 19: 269–287. 77. Scoble J, Lowe AJ (2010) A case for incorporating phylogeography and landscape genetics into species distribution modelling approaches to improve climate adaptation and conservation planning. Diversity and Distributions 16: 343-353. IF 3.4, CI 1

328 76. Lowe AJ, Harris D, Dormontt E, Dawson IK (2010) Testing putative African tropical forest refugia using chloroplast and nuclear DNA Phylogeography. Tropical Plant Biology 3: 50- 58. 75. Lemes MR, Dick CW, Navarro C, Lowe AJ, Cavers S, Gribel R (2010) Chloroplast DNA microsatellites reveal contrasting phylogeographic structure in mahogany (Swietenia macrophylla King, Meliaceae) from Amazonia and Central America. Tropical Plant Biology 3: 40-49. 74. Davies SJ, Cavers S, Finegan B, Navarro C, Lowe AJ (2010) Genetic consequences of multigenerational and landscape colonisation bottlenecks for a neotropical forest pioneer tree, Vochysia ferruginea. Tropical Plant Biology 3:14-27. 2009 73. Wang J, Gao P, Kang M, Lowe A, Huang H (2009) Refugia within refugia: the case study of a canopy tree Eurycorymbus cavaleriei in subtropical China. Journal of Biogeography 36: 2156–2164. IF 4.6 72. Prentis PJ, Sigg DP, Raghu S, Dhileepan K Lowe AJ (2009) Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management. Diversity and Distributions 15: 822-830. IF 3.4 71. Wilson JRU, Dormontt EE, Prentis PJ, Lowe AJ, Richardson DM (2009) The importance of biogeography in defining invasion biology. Trends in Ecology and Evolution 24: 586 IF 11.9 70. Pavlacky DC, Goldizen AW, Prentis PJ, Nicholls JA, Lowe AJ (2009) A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird. Molecular Ecology 18: 2945– 2960. IF 5.3, CI 3, GS 1 69. Bacles CFE, Brooks J, Lee DJ, Schenk P, Lowe AJ, Kremer A (2009) Reproductive biology of Corymbia citriodora subsp. variegata and effective pollination across its native range in Queensland, Australia. Southern Forests 71:125–132. CI 1 68. Jamnadass R, Lowe AJ, Dawson IK (2009) Molecular markers and the management of tropical trees: the case of indigenous fruits. Tropical Plant Biology 2:1-12. 67. Ottewell KM, Donnellan SC, Lowe AJ, Paton DC (2009) Predicting reproductive success of insect- versus bird-pollinated scattered trees in agricultural landscapes. Biological Conservation 142: 888-898. IF 3.6, CI 2, GS 3 66. Keppel G, Lowe AJ, Possingham H (2009) Changing perspectives on the biogeography of the tropical South Pacific: influences of dispersal, vicariance and extinction. Journal of Biogeography 36:1035–1054. IF 4.6, CI 4, GS 1 65. Hardner C, Peace C, Lowe AJ, Neal J, Pisanu P, Powell M, Schmidt A, Spain C, Williams K (2009) Genetic Resources and Domestication of Macadamia. Horticultural Reviews 35:1- 125. 64. Wilson JRU, Dormontt EE, Prentis PJ, Lowe AJ, Richardson DM (2009) Something in the way you move: dispersal pathways affect invasion success. Trends in Ecology & Evolution 24: 136-144. IF 11.9, CI 13, GS 12 2008 63. Broadhurst, LM, Lowe, A, Coates, DJ, Cunningham, SA, McDonald, M, Vesk, PA and Yates, C (2008) Seed supply for broadscale restoration: maximising evolutionary potential. Evolutionary Applications 1: 587-597. CI 6 Listed by Faculty of 1000 Biology as Must Read:http://www.f1000biology.com/ article/id/1156950/evaluation, reviewed by Richard Hobbs, 25 Feb, http://www.f1000biology.com/article/id/1156950/evaluation and Ary Hoffmann, 10 Mar, 2009 http://www.f1000biology.com/article/id/1156950/evaluation. Most viewed article of journal during 2008. 62. Kang M, Huang HW, Jiang MX, Lowe AJ (2008) Understanding population structure and historical demography in a conservation context: population genetics of an endangered fern. Diversity and Distributions 14: 799-807. IF 3.4, CI 1 61. Prentis P, Dormontt E, Wilson A, Richardson D, Lowe AJ (2008) Adaptive evolution in invasive species. Trends in Plant Sciences 13: 288-294. IF 9.2, CI 22, GS 20 Listed on Essential Science Indicators (ESI) as Highly Cited Paper (top cited papers over the past 10 years in each of 22 scientific fields, based on percentile rankings).

329 2007 60 Kang M, Xu F, Lowe AJ, Huang H (2007) Protecting evolutionary significant units for the remnant populations of Berchemiella wilsonii var. pubipetiolata (). Conservation Genetics 8: 465-473. IF 2.4, CI 1 59. Kang M, Buckley Y, Lowe AJ (2007) Testing the role of genetic factors across multiple independent invasions of the shrub Scotch broom (Cytisus scoparius). Molecular Ecology. 16: 4662-4673. IF 5.3, CI 9, GS 8 58. Prentis P, White EM, Lowe AJ, Clarke AR. (2007) Can hybridization cause local extinction: a case for demographic swamping of the Australian native Senecio pinnatifolius by the invasive Senecio madagascariensis? New Phytologist 176: 902-912. IF 5.2, CI 10, GS 8 57. Wells JA, Gardner MG, Lowe AJ (2007) Development of eight polymorphic microsatellites for an Australasian rainforest tree species, Cryptocarya mackinnoniana (Lauraceae). Molecular Ecology Notes 7: 981-983. IF 1.6, GS 1 56. Kang M, Lowe A, Buckley Y (2007) Isolation and characterization of polymorphic microsatellite loci for the invasive plant Cytisus scoparius. Molecular Ecology Notes 7:100- 102. IF 1.6, CI 7 2006 55. Bacles CFE, Lowe AJ, Ennos RA (2006) Seed dispersal across a fragmented landscape. Science 311: 628. IF 28, CI 39, GS 46 54. Lowe A, Unsworth C, Gerber S, Davies S, Munro RC, Kelleher C, King A, Brewer S, White A, Cottrell J (2006) The route, speed and mode of oak postglacial colonisation across the British Isles; Integrating molecular ecology, palaeoecology and modelling approaches. Botanical Journal of Scotland 57: 59-82. 53. Schmidt AL, Scott L, Lowe AJ (2006) Isolation and characterization of microsatellite loci from Macadamia integrifolia. Molecular Ecology Notes 6: 1060-1063. IF 1.6, GS 3 2005 52. Navarro C, Cavers S, Colpaert N, Hernandez G, Breyne P, Lowe AJ (2005) Chloroplast and total genomic diversity in the endemic Costa Rican tree Lonchocarpus costaricensis (J.D.Smith) Pittier (Papilionaceae). Silvae Genetica 54: 293-300. IF 0.7, CI 2, GS 1 51. Navarro C, Cavers S, Pappinen A, Tigerstedt P, Lowe A, Merilä J (2005) Contrasting quantitative traits and neutral genetic markers for genetic resource assessment of Mesoamerican Cedrela odorata. Silvae Genetica 54: 281-292. IF 0.7, CI 3 50. Cavers S, Navarro C, Hopkins P, Ennos RA, Lowe AJ (2005) Regional and population-scale influences on genetic diversity partitioning within Costa Rican populations of the pioneer tree Vochysia ferruginea Mart. Silvae Genetica 54: 258-264. IF 0.7, CI 4, GS 7 49. Colpaert N, Cavers S, Bandou E, Caron H, Gheysen G, Lowe AJ (2005) Sampling tissue for DNA analysis of trees: trunk cambium as an alternative to canopy leaves. Silvae Genetica 54: 265-269. IF 0.7, CI 4, GS 4 48. Hannan-Jones MA, Lowe AJ, Scott KD, Graham GC, Playford JP, Zalucki MP (2005) Isolation and characterisation of microsatellite loci from mother-of-millions, Bryophyllum delagoense (Crassulaceae), and its hybrid with B. daigremontianum “Houghton‟s hybrid”. Molecular Ecology Notes 5: 770-773. IF 1.6, CI 2, GS 2 47. Lowe AJ, Hicks BJ, Worley K, Ennos RA, Morman JD, Stone G, Watt AD (2005) Dispersal, colonisation and host range expansion within Scottish populations of the pine beauty moth, Panolis flammea. Bulletin of Entomological Research 95: 517-526. IF 1.4, CI 2, GS 2 46. Lowe A (2005) Population genetics of neotropical trees focus issue. Heredity 95: 243-245. IF 3.8 45. Lowe AJ, Boshier D, Ward M, Bacles CFE, Navarro C (2005) Genetic resource loss following habitat fragmentation and degradation; reconciling predicted theory with empirical evidence. Heredity 95: 255-273. IF 3.8, CI 67 44. Ward M, Dick CW, Gribel R, Lemes M, Caron H, Lowe AJ (2005) To inbreed, or not to inbreed: A review of mating systems and pollen dispersal variance in neotropical trees. Heredity 95: 246-254. IF 3.8, CI 46, GS 54 43. Cavers S, Degen B, Caron H, Hardy O, Lemes M, Gribel R, Margis R, Salgueiro F, Lowe AJ (2005) Optimal sampling strategy for estimation of spatial genetic structure in tree populations. Heredity 95: 281-289. IF 3.8, CI 22

330 42. Kremer A, Caron H, Cavers S, Colpaert N, Gheysen L, Gribel R, Lemes M, Lowe AJ, Margis R, Navarro C, Salgueiro F (2005) Monitoring genetic diversity in tropical trees with multilocus dominant markers. Heredity 95: 274-280. IF 3.8, CI 14, GS 15 41. Taylor KJ, Lowe AJ, Hunter RJ, Ridgway T, Gresshoff PM, Rossetto M (2005) Genetic diversity and regional identity in the Australian remnant Nothofagus moorei. Australian Journal of Botany 53: 437-444. IF 1.5, CI 2 40. Bacles CFE, Burczyk J, Lowe AJ, Ennos RA (2005) Historical and contemporary mating patterns in remnant populations of the forest tree Fraxinus excelsior L. Evolution 59: 979- 990. IF 4.7, CI 40, GS 46 2004 39. Davies S, White A, Lowe A (2004) An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis. Heredity. 93: 566-576. IF 3.8, CI 16 38. Lowe A, Munro RC, Samuel S, Cottrell J (2004) The utility and drawbacks of chloroplast DNA for identifying native British oak stands. Forestry. 77: 335-347. IF 1.5, CI 2 37. Abbott RJ, Lowe AJ (2004) Origins, establishment and evolution of two new polyploid species of Senecio in the British Isles. Biological Journal of the Linnean Society. 82: 467-474. IF 2.9, CI 59, GS 63 36. Lowe AJ, Abbott RJ (2004) Reproductive isolation of a new hybrid species, Senecio eboracensis. Heredity. 92:386-395. IF 3.8, CI 11, GS 12 35. Scott KD, Wilkinson KS, Lawrence N, Lange CL, Scott LJ, Merritt MA, Lowe AJ, Graham GC (2004) Gene-flow between populations of cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is highly variable between years. Bulletin of Entomological Research 94: 381-392. IF 1.4, GS 8 34. Muir C, Lowe AJ, Fleming CC, Vogl C (2004) High nuclear genetic diversity, high levels of outcrossing and low differentiation among remnant populations of Quercus petraea at the margin of its range in Ireland. Annals of Botany. 93: 691-697. IF 271, CI 27, GS 27 33. Cavers S, Navarro C, Lowe AJ (2004) Targeting genetic resource conservation in widespread species: a case study of Cedrela odorata L. Forest Ecology and Management. 197: 285- 294. IF 2.1, CI 7, GS 7 32. Lowe AJ, Moule C, Trick M, Edwards KJ (2004) Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theoretical and Applied Genetics. 108: 1103-1112. IF 3.5, CI 76, GS 86 Listed on Essential Science Indicators (ESI) as Highly Cited Paper (top cited papers over the past 10 years in each of 22 scientific fields, based on percentile rankings). 31. Bacles CFE, Lowe AJ, Ennos RA (2004) Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape. Molecular Ecology 13: 573-584. IF 5.3, CI 36, GS 44 2003 30. Cottrell JE, Munro RC, Tabbener HE, Milner AD, Forrest GI & Lowe AJ (2003) Comparison of fine-scale genetic structure within two British oakwoods using microsatellites; consequences of recolonsiation dynamics and past management. Forest Ecology and Management 176: 287-303. IF 2.1, CI 23, GS 25 29. Menozzi P, Lowe AJ (2003) Spatial dynamics and natural regeneration: Dynamics and conservation of genetic diversity in forest ecosystems. Forest Genetics 9: 336-337. 28. Cavers S, Navarro C, Lowe AJ (2003) A combination of molecular markers (cpDNA PCR- RFLP, AFLP) identifies evolutionarily significant units in Cedrela odorata L. (Meliaceae) in Costa Rica. Conservation Genetics 4: 571-580. IF 2.4, CI 20, GS 24 27. Lowe AJ, Abbott RJ (2003) A new British species, Senecio eboracensis (Asteraceae), another hybrid derivative of S. vulgaris L. and S. squalidus L. Watsonia 24: 375-388. GS 14 26. Lowe AJ, Jourde B, Breyne P, Colpaert N, Navarro C, Wilson J, Cavers S (2003) Fine scale genetic structure and gene flow within Costa Rican populations of mahogany (Swietenia macrophylla). Heredity 90: 268-275. IF 3.8, CI 18, GS 17 25. Lowe AJ, Thorpe W, Teale A & Hanson J (2003) Characterisation of germplasm accessions of Napier grass (Pennisetum purpureum and P. purpureum x P. glaucum hybrids) and

331 comparison with farm clones using RAPD. Genetic Resources and Crop Evolution 50: 121- 132. IF 0.9, CI 5, GS 6 24. Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology 12: 1339-1348. IF 5.3, CI 77, GS 98 23. Cavers S, Navarro C, Lowe AJ (2003) Chloroplast DNA phylogeography reveals colonisation history of a Neotropical tree, Cedrela odorata L., in Mesoamerica. Molecular Ecology 12: 1451-1460. IF 5.3, CI 40, GS 58 22. Jensen JS, Olrik DC, Siegismund HR, Lowe AJ (2003) Population genetics and spatial autocorrelation in an unmanaged stand of Quercus petraea (Matt.) Liebl. in Denmark. Scandinavia Journal of Forestry 18: 295-304. IF 0.8, CI 9, GS 9 2002 21. Kremer A, Dupouey JL, Deans JD, Cottrell J, Csaikl U, Finkeldey R, Espinel S, Jensen J, Kleinschmit J, Dam BV, Ducousso A, Forrest I, Heredia ULD, Lowe AJ, Tutkova M, Munro RC, Steinhoff S, Badeau V. (2002) Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands. Annals of Forest Science 59: 777-787. CI 36 20. Cottrell J, Munro RC, Tabbener H, Gillies ACM, Deans D, Lowe AJ (2002) Distribution of Chloroplast DNA variation in British Oaks (Quercus robur and Q. petraea): the influence of postglacial colonisation and human management. Forest Ecology and Management (Special Issue) 156: 181-196. IF 2.1, CI 27, GS 33 19. Jensen JS, Gillies ACM, Csaikl U, Munro RC, Madsen SF, Roulund H, Lowe A (2002) Chloroplast DNA variation within the Nordic countries. Forest Ecology and Management (Special Issue) 156: 167-180. IF 2.1, CI 8 18. Petit RJ, Csaikl U, Bordacs S, Burg K, Coart E, Cottrell J, van Dam B, Deans JD, Glaz I, Dumolin-Lapègue S, Fineschi S, Finkelday R, Gillies ACM, Goicoechea PG, Jensen JS, König A, Lowe AJ, Madsen SF, Matyas G, Munro RC, Olalde M, Pemonge M-H, Popescu F, Slade D, Tabbener H, Taurchini D, de Vries SGM, Ziegenhagen B, Kremer A (2002) Chloroplast DNA variation in European white oaks: Phylogeography and patterns of diversity based on data from over 2,600 populations. Forest Ecology and Management (Special Issue) 156: 5-26. IF 2.1, CI 151, GS 149 Listed on Essential Science Indicators (ESI) as Highly Cited Paper (top cited papers over the past 10 years in each of 22 scientific fields, based on percentile rankings). 17. Petit RJ, Brewer S, Bordacs S, Burg K, Cheddadi R, Coart E, Cottrell J, Csaikl U, Fineschi S, Goicoechea P, Jensen JS, König A, Lowe AJ, Madsen SF, Matyas G, Oledska I, Popescu F, Slade D, Van Dam B, de Beaulieu J-L, Kremer A (2002) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. Forest Ecology and Management (Special Issue) 156: 49-74. IF 2.1, CI 179, GS 194 Listed on Essential Science Indicators (ESI) as Highly Cited Paper (top cited papers over the past 10 years in each of 22 scientific fields, based on percentile rankings). 16. Kremer A, Kleinschmit J, Koenig A, Cundall N, Deans JD, Lowe AJ, Munro RC, Petit RJ, Stephan R (2002) Is there a correlation between chloroplastic divergence and phenotypic or nuclear genetic divergence in European oaks? Forest Ecology and Management (Special Issue) 156: 75-88. IF 2.1, CI 33, GS 36 15. Lowe AJ, Goodall-Copestake WP, Caron H, Kremer A, Decroocq S (2002) A set of polymorphic microsatellites for Vochysia ferruginea, a promising tree for land reclamation in the Neotropics. Molecular Ecology Notes 2: 153-155. IF 1.6, CI 2, GS 3 14. Lowe AJ, Jones AE, Raybould AF, Trick M, Moule CJ, Edwards K (2002) Transferability and genome specificity of a new set of microsatellite primers among Brassica species of the U triangle. Molecular Ecology Notes. 2: 7-11. IF 1.6, CI 22, GS 34 13. Mariette S, Cottrell J, Csaikl UM, Goikoechea P, König A, Lowe AJ, Van Dam BC, Barreneche T, Bodénès C, Streiff R, Burg K, Groppe K, Munro RC, Tabbener H, Kremer A (2002) Comparison of levels of genetic diversity detected with AFLP and microsatellite markers within and among mixed Q. petraea (Matt.) Liebl. and Q. robur L. stands. Silvae Genetica 51: 72-79. IF 0.7, CI 32

332 2001 12. Lowe AJ, Bandou E, Breyne P, Caron H, Cavers S, Colpaert N, Degen B, Gribel R, Hernandez M, Kremer A, Labbe P, Lemes M, Margis R, Margis-Pinheiro M, van Montagu M, Navarro C, Wilson J (2001) Assessment of Levels and Dynamics of Intra-Specific Genetic Diversity of Latin American Tropical Trees for Conservation and Sustainable Management. European Tropical Forest Network Newsletter 34: 20-22. 2000 11. Lowe AJ, Wilson J, Gillies ACM, Dawson I (2000) Conservation genetics of bush mango from central/west Africa, implications from RAPD analysis. Molecular Ecology 9: 831-841. IF 5.3, CI 31, GS 46 10. Lowe AJ, Abbott RJ (2000) Routes of origin of two recently evolved hybrid taxa: Senecio vulgaris var. hibernicus and York radiate groundsel (Asteraceae). American Journal of Botany 87: 1159-1167. IF 2.6, CI 21, GS 20 1999 9. Newton AC, Allnutt T, Gillies ACM, Lowe AJ, Ennos RA (1999) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends in Ecology and Evolution 14: 140-145. IF 11.9, CI 178, GS 210 8. Gillies ACM, Navarro C, Lowe AJ, Newton AC, Hernandez M, Wilson J, Cornelius JP (1999) Genetic diversity in Mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs. Heredity 83: 722-732. IF 3.8, CI 61 1998 7. Lowe AJ, Sturrock GL (1998) Behaviour and diet of Colobus angolensis palliatus Peters, 1968, in relation to seasonality in a Tanzanian dry coastal forest. Folia Primatologica 69: 121-128. IF 1.5, CI 1 6. Lowe AJ, Russell JR, Powell W, Dawson IK (1998) Identification and characterization of nuclear, cleaved amplified polymorphic sequences (CAPS) loci in Irvingia gabonensis and I. wombolu, indigenous fruit trees of west and central Africa. Molecular Ecology 7: 1771- 1788. IF 5.3, CI 2, GS 6 1997 5. Abbott RJ, Harris SA, Lowe AJ (1997) Interspecific hybridization and the origin of new plant taxa in Scotland. Botanical Journal of Scotland 49: 247-256. 1996 4. Lowe AJ, Abbott RJ (1996) Origins of the new allopolyploid species Senecio cambrensis (Asteraceae) and its relationship to the Canary Islands endemic Senecio teneriffae. American Journal of Botany 83: 1365-1372. IF 2.6, CI 28, GS 27 3. Lowe AJ, Hanotte O, Guarino L (1996) Standardization of molecular genetic techniques for the characterisation of germplasm collections: The case for random amplified polymorphic DNA (RAPD). Plant Genetic Resources Newsletter 107: 50-54. GS 42 2. Lowe AJ, Hanson J, Teale A (1996) Molecular characterisation of Napier grass (Pennisetum purpureum) using random amplified polymorphic DNA (RAPD) markers. African Feed Resources Network Newsletter 6: 4-8. 1993 1. Gould MS, Lowe AJ, Clarke GP (1993) The frequency of termite (Isoptera) damage to tree species in Namakutwa Forest, Tanzania. Sociobiology 23: 189-198. IF 0.5, CI 1, GS 4

General and Promotional Articles Lowe AJ (2008) How many plant species do we have in South Australia? DEH Landscapes. Autumn Lowe AJ, Abbott RJ (2003) Evolution in action: Britain‟s newest plant species is an unparalleled opportunity to study evolution. Planet Earth (Summer) pp 24-25. Cottrell JE, Tabbener HE, Munro RC, Gillies ACM, Forrest GI, Deans JD, Lowe AJ (2000) Chloroplast DNA Variation in British Oak Populations. Forest Research Annual Report. pp 39-41. Cavers S, Navarro C, Wilson J, Lowe AJ (2000) Hidden in the trees: Genetic variation in tropical trees helping to inform forest conservation. NERC News. Autumn, pp 10-11.

333 Thomas Valqui Curriculum Vitae

8 Calle Sta Rita 105, of 2, Urb Huertos de San Antonio, Surco, Lima, Perú [email protected] http://www.corbidi.org

Personal Information

Full name: Thomas Holger Valqui Haase Cityzenship: Peruvian Date of birth: 27 of May, 1966 Languages: Spanish, German, English

Present position

Director and curator of the Bird Division and president of the Center for Ornithology and Biodiversity (CORBIDI)

Education

2009 Ph.D. Biological Sciences, Louisiana State University. Advisors: J. V. Remsen, PhD and R. Brumfield, PhD 1998 M.A. Ecology and Evolutionary Biology, Princeton University, New Jersey. Advisor: Henry Horn, PhD. 1995 Forestry Engineering, Universidad Nacional Agraria, La Molina, Lima. Pedro Vasquez, Eng. 1992 Bachelor in Forestry, Universidad Nacional Agraria, La Molina, Lima. 1985 German Abitur, Alexander von Humboldt School, Lima

Professional experience

2009 - Director of Ornithology and curator in CORBIDI. 2008-2008 Curatorial Assistant, LSUMNS Collection of 2007-2008 Teaching Assistant, Dept. Biological Sciences, LSU 2006-2007 Person in charge to design and execute the environmental ornithological impact study for the Rio Tinto company in the La Granja mine. 2000-2003 Curatorial Assistant, LSUMNS Collection of Birds 2005 Person in charge of the ornithological assesment of ERM for PlusPetrol in Camisea, central Amazonian Peru. Ornithological consultant for the environmental assessment of the Antamina

334 mine in high Andean central Peru. 2004 Ornithological consultant for the environmental assessment by ERM for PlusPetrol in Camisea, central Amazonian Peru. Ornithologival consultant for the review of conservation elements of the Peruvian Yungas, for The Nature Conservancy and CDC de la Universidad Agraria-La Molina. Ornithological consultant for the environmental assessment of the Antamina mine in high Andean central Peru. 1998 Ornithological consultant for the environmental study of oil drilling in Candamo, Southeastern Peru for Conservación Internacional. 1993- 2008 Free lance birdwatching guide in Perú.

Field expedition experience

2009 Museum of Natural Science-LSU/CORBIDI expedition to the department of Tumbes, northwestern Peru. 2 month. 2002 Museum of Natural Science-LSU expedition to Abra Patricia, departament of San Martin, northern Peru. 2 month. 2001 Museum of Natural Science-LSU expedition to Jeberos and the lower Morona, department of Loreto, northeastern Peru. 2 month. 2000 Museum of Natural Science-LSU expedition to the Cordillera Azul, upper Pauya river, departament of Loreto, central-eastern Peru. 2 month.

Publications:

Books: 2005 Valqui, T. Peru, Natural Eden of Birds. Graph&Consult.200 pags. 2004 Valqui, T. Where to Watch Birds in Peru. Graña Press. 381 pags. 2004 Plenge, H., R. Williams & T. Valqui.2004. Birds of the Clouds. Foto Natur SRL., Lima Peru. 104 pag.

Disertations: 2008 Phylogeograhy of Nothoprocta tinamous and the phylogeny of the TINAMDAE. Ph.D. dissertation.

1995 Evaluación del Impacto de la Extracción Selectiva de Madera en Comunidades de Aves en un Bosque Húmedo Tropical en el Bosque de Chimanes, Beni - Bolivia. Forestry Engineering thesis.

Scientífic papers:

335 in press Wilson, R. E., M. Eaton, T. Valqui, and K. G. McCracken. Ecogeographic variation within and among three Cinnamon Teal (Anas cyanoptera) subspecies along an elevational and latitudinal gradient. Ornithological Monographs (in press).

2009 Flanagan, J N., G. Engblom, I. Franke, T. Valqui, F. Angulo. 2009. Distribution of the Peruvian Phytotoma raimondii (Passeriformes: Cotingidae). Rev. Peru. Biol Vol 16(2): 175-182

McCracken, K., C. Barger, M. Bulgarella, M.K. Johnson, A. V. Kuhner, V. Moore, J. L. Peters, J. Trucco, T. Valqui, K. Winker, and R. Wilson. Signature of high-altitude adaaptation in the major hemoglobin of five species of Andean dabbling ducks. American naturalist 174 (5) 631-650

McCracken, K. G., C. Barger, M. Bulgarella, K.P. Johnson, S. Sonsthagen, J. Trucco, T. Valqui, R. E. Wilson, K. Winker, M.D. Sorensen. Parallel evolution in the major hemoglobin genes of eigth species of Andean waterfowl. Molecular Ecology 18: 3992-4005

Herzog, S. K., S. R. Ewing, , K. L. Evans, A. MacCormick, T. Valqui, R. Bryce, M. Kessler, MacLeod, R. “Vocalization, distribution, and ecology of the Cloud-forest Screech Owl (Megascops marshalli)”. The Wilson Journal of Ornithology 121 (2): 240-252.

McCracken, K. G., M. Bulgarella, K. Johnson, K., Kuhner, M. K., Trucco, T. Valqui, R. Wilson, Peters, J. Gene flow in the face of countervailing selection: adaptation to high-altitude hypoxia in the Beta-A Hemoglobin subunit of Yellow-billed Pintails in the Andes. Molecular Biology and Evolution 26: 815–827.

2008 Hernandez, P. A., I. Franke, S. K. Herzog, V. Pacheco, L. Paniagua, H. L. Quintana, A. Soto, J. J. Swenson, C. Tovar, T. Valqui, J. Vargas, & B. E. Young. Predicting species distributions in poorly-studied landscapes. Biodiversity and Conservation 17:1353-1366.

2007 Bulgarella, M., R. E. Wilson, C. Kopuchian, T. Valqui, and K. G. McCracken. Elevational variation in body size of Crested Ducks (Lophonetta specularioides) from the Central High Andes, Mendoza, and Patagonia. Ornitologia Neotropical 18:587-602.

Lane, D. F., G. P. Servat, T. Valqui, Frank R. Lambert. A distinctive new species of Tyrant Flycatcher (PASSERIFORMES: TYRANNIDAE: Cnipodectes) from Southeastern Peru. The Auk 124 (3): 762-772

Valqui, C. & T. Valqui, Modelos matemáticos para curvas de distribución

336 de especies. REVCIUNI, Revista de la facultad de ciencias de la UNI, 11 (1): 38-44.

2006 Lane, D., T. Valqui, J. Alvarez, J. Armenta, and K. Eckhardt The rediscovery and natural history of the White-masked Antbird (Pithys castaneus). Wilson Journ. Ornithol., 118 (1): 13-22.

Wilson, Robert E., T. Valqui & Kevin McCracken. Aberrant plumage in the Yellow-billed Pintail Anas georgica. Wildfowl 56:192-196

2002 Isler M.L., J. Alvarez, R.I. Isler, T. Valqui, A. Begazo, B.M. Whitney. Rediscovery of a cryptic species and description of a new subspecies in the Myrmeciza hemimelaena complex (Thamnophilidae) of the Neotropics. The Auk 119 (2): 362-378

Valqui, T. and B. Walker. Importance of mangrove forests in Peru with notes on Bare-throated Tiger Heron Tigrisoma mexicanum and Rufous- necked Wood-rail Aramides axillaris. 18: 58-60.

Valqui, T. and J. Fjeldså. Atlapetes melanopsis nom. nov. for the Black- faced Brush-. Ibis 144: 347.

2001 Begazo, A. , T. Valqui, M. Sokol, L. Longlois. Notes on some birds from central and northern Peru. Cotinga 15: 81-87.

Schulenberg, T. S., J. P. O'Neill, D. F. Lane, T. Valqui, & C. Albújar. Birds. Pp. 146-155, 206-225 in "Peru: Biabo Cordillera Azul" (, eds.). Rapid Biological Inventories: 1-228.

Valqui T. 2001. Rediscovery of the Royal Cinclodes (Cinclodes aricomae) for Bolivia. Cotinga 14: 104

2000 & before: Begazo, A. & T. Valqui. 2000. Notes on three cracid species of northern Peru and southern Ecuador. Bulletin of the UICN/Birdlife/WPA Cracid specialist group Vol. 10: 9-10.

Valqui T. & J. Fjeldså (1999) A new species of Brush-Finch (Atlapetes) for central Perú. Ibis. Vol.141. No.2.: 194-198.

Begazo A., T. Valqui. 1998. Birds of Pacaya-Samiria National Reserve with a new population (Myrmotherula longicauda) and new record for Perú (Hylophilus semicinereus). Bull. B.O.C. 118 (3): 159-166

Castro, G., V. Pulido, T. Valqui, J. Chavez, B. . 1996. The Huanchaco

337 Extractive Reserve: Integrating Environmental Conservation and Sustainable development in Perú – A Report. Ethnobiology in Human Welfare. Ed. S. K. Jain. 1996, Deep Publications, New Delhi: 239-242.

Valqui Thomas. 1994. The extinction of the Junin Flightless Grebe?. COTINGA No.1: 42-44.

Wust Walter, Anthony Luscombe, Thomas Valqui. 1994. Las aves de los Pantanos de Villa y alrededores." Asocición de Ecología y Conservación (ECCO). 37 pages.

Wust W., T. Valqui, C. Guillen. 1990. Aves registradas en Jenaro Herrera, Boletin de Lima No.69: 23-26.

338 Curriculum vitae Gisella ORJEDA

Address: Genomics Research Unit [email protected] Universidad Peruana Cayetano Heredia Av Honorio Delgado 430 Tel: (51) 1 319 0000 Ext. 2701 Urb Ingenieria, SMP, Lima, Peru Cell: (51) 997 58 29 24 tel: (51) 1 319 0000 anex 2413 Date of birth: 4 January 1960. fax: (51) 1 319 0016 Civil status: Divorced. Home: Nationality: Peruvian Calle Ocharan 779 Children: Catalina (31) and Rafael (29). Lima 18, Peru

Languages

Spanish: Mother tongue; English: completely fluent; French: completely fluent.

Studies

Doctoral (Ph.D.) 1990 - 1995 University of Birmingham, Birmingham, United Kingdom. Thesis subject: Ploidy manipulation for sweet potato breeding and genetic studies. Thesis supervisor: Dr. Michael Lawrence Master of Sciences (M.Sc.) 1988 - 1989 Universidad Nacional Agraria "La Molina", Lima, Peru. “Plant breeding”. Thesis subject: Development of tetraploid interspecific hybrids between Ipomoea batatas Lam. (2n =2x=90) and I.trifida (H.B.K.) G. Don. (2n=2x=30) as testers for diploid and tetraploid wild species. Approved with “Outstanding”. Bachelor of Sciences (B.Sc.) 1981 - 1987 Universidad Nacional Agraria "La Molina" Lima, Peru. Faculty of Sciences, Biology. Emphasis in Genetics upper quartile, approved with “Excellent”.

Professional Experience

Scientist: Jan 2005 to present. Universidad Peruana Cayetano Heredia – Genomics Research Unit. Lima, Peru. Responsibilities:  Head of the Unit: My responsibilities in the lab are: getting the necessary funds for the work according to national priorities, linking with possible partners and directing the research. I have returned definitely to Peru on May 2, 2005 to set up the first genomics research facility in Peru.

Responsibilities  In charge of the Research Unit (research and admin.).  Identify, write, and submit research projects to funding agencies

1/ 6 339  Hire personnel for the projects

Achievements:

So far I have been able to leverage 3’000,000 USD. I have 28 people under my responsibility. I have the following projects running in the lab.

 2006. PI. “Towards the positional cloning of 4HL stripe rust resistance quantitative trait loci in barley: Saturation of the 4H QTL region with molecular markers from various Triticacea species” ICGEB. 60,000 USD  2006. co- PI. “Towards the positional cloning of 4HL stripe rust resistance quantitative trait loci in barley: Generation of doubled haploid population to map 4HL QTL.” Concytec. 12,000 USD  2006. Towards the positional cloning of 4HL stripe rust resistance quantitative trait loci in barley: Saturation of 4HL region using sinteny with triticacea species. Fondo concursable UPCH. 10,000 USD  2006. PI. Preparation to initiate the Potato genome sequencing. Concytec. 40,000 USD  2007. co-PI: Identification and utilisation of durable resistance to barley diseases in Latin America. FONTAGRO 484,000 USD.  2007. PI: Capacity building and tools acquisition for potato structural and functional genomics. STC-CGIAR. 450,000 USD  2007. PI: “Protocol standardization to order and improve Pisco grapes and pisco” Concytec, 40,000 USD  2007. PI. Molecular fingerprint, in Vitro propagation viral detection and viral cleaning of Pisco grapes. Fincyt. 150,000 USD  2008. Co-PI “International Collaborations in Cyberinfrastructure-enabled Genomics” conference organiser.  2008. PI: Plant Genomics and Capacity Building in Latin America, Perez Guerrero Fund, 38,000 USD.  2008. co-PI. “Towards the positional cloning of 4HL stripe rust resistance quantitative trait loci in barley: Development of BAc library.  2008. PI.: Strengthening of regional capacities in biotechnology through the exploration and valorization of the potato genome: an American crop. OEA, 1’750,000, USD  2008. PI. Sequencing and using the potato genome for the discovery and utilisation of genes involved in biotic and abiotic resistances. Fincyt, 300,000 USD  2008. PI. DNA bar-coding of medicinal plants of productive and commercial importance in Peru I: Identification of species of the Rubiacea family (Cinchona) and Piperaceae (Piper and Peperomia). Fincyt, 300,000 USD.  2008. PI. Technological equipment project. Fincyt. 100,000 USD.  2009. PI. Catedra Cruzada : Organisation génomique et diversification des gènes de résistance des plantes auxbioagresseurs : Analyse comparative au sein des Euastéridées I. IRD. 80,000 euros.  2010. PI. Waiting reply: La tecnología del siglo 21 al servicio de la seguridad alimentaria y del agricultor andino: un desafío para el mejoramiento de la Quinua en el Perú. KWS. 750,000 Euros

2/6 Last updated: 7-Feb-11 340 Foreign Scientist: 2002 to Oct 2004 INRA- Unité de Recherche en Génomique végétale. Evry, France. I worked in the positional cloning laboratory. In the team of Abdel Bendahmane Responsibilities:  Positional cloning of the Melon necrotic spot virus (MNSV) recessive gene using high throughput technology: o Generation of a segregating population. o Screening for recombination events linked to the target gene. o Screening for linked DNA markers. o Construction of a high resolution genetic map. o Construction of a BAC library. o Construction of a physical map.  Isolation of the cDNA of the candidate gene  Identification of the target locus by transgenic expression in a plant that lacks the character or by sequence comparison to a number of mutants alleles  Functional analysis of the plant-virus interaction using Yeast-3-hybrid technique  Sequencing and annotation of the BAC containing the gene.

Achievements: 3000 Back cross segregating genotypes have been produced, their phenotype screened and DNA extracted. Flanking markers to the gene have been obtained. A fine genetic map using flanking markers has been established using chromosome walking and physical mapping. A BAC library is under construction. A candidate gene that co-segregates has been identified and its cDNA cloned Yeast –3-hybrid interaction studies have identified several sequences responsible for interaction between the virus and the resistance protein. Complementation studies were performed 2 articles as first author (first authorship shared) have been published

Scientist: 2000 to 2002 Genoscope. Centre National de Sequençage. Evry, France.

Responsibilities: Sequencing of rice chromosome 12 Establishment of the physical map and minimum tiling path merging by Bacs coming from various international collaborators. Participate to the project set-up, and all decisions concerning the project. Achievements: Chromosome 12 has been completely sequenced in two years. The physical map has been finished. Sequences are submitted to GeneBank. Article in Nature.

Genetic Improvement and Evaluation Scientist: 1996 -1999 The International Network for the Improvement of the Banana and Plantain (INIBAP), Montpellier, France.

Responsibilities: Responsible for The International Musa Testing Programme (IMTP) phase II and III (37 experimental sites around the world for evaluating new banana and plantain varieties). Responsible for Global Programme for Musa Improvement, PROMUSA. (Consortium of researchers on Musa). Achievements: Set up of PROMUSA, Establishment of research priorities and co-ordination of working groups, set-up of collaborative projects between partners. Organisation of 5 international meetings of more than 100 researchers. Set up of various experimental protocols according to the technological conditions of partner institutions.

3/6 Last updated: 7-Feb-11 341 Project set-up, in-vitro plantlet distribution, follow up of essays, local researcher training, collecting data. Finalising IMTP phase II and publishing of results. Statistical analysis (GxE) multiple locations. Creation of a database that contains passport data of the improved hybrids and reference clones, their photographs, fingerprint patterns, averages and coefficients of variance for all their important agronomic traits and their resistance/tolerance data to Fusarium, Sigatoka, nematodes, information on post-harvest characteristics and information on the breeding programme that produced the hybrids as well as weather and experimental design information under which the hybrids were evaluated. Started IMTP phase III. 2 books published

Post doctoral scientist: Sept. 1995 - April 1996 International Potato Center . Lima, Peru.

Responsibilities : To screen wild potato species for nematode resistance. Achievements:

Initiation of germplasm screening for nematode resistance using wild tuber-bearing Solanum.

Sub-project leader : 1989 - 1995 International Potato Center. Lima, Peru.

Responsibilities: Responsible of project: Ploidy manipulations for exploitation and enhancement of sweet potato germplasm .

Achievements: Got several populations with high dry matter content. Got genetically equivalent populations at different ploidy levels. Developed several introgression pathways for using diploid and tetraploid wild species on sweet potato improvement . Got several tetraploid populations with high dry matter content, high yields and wide genetic background.

Research assistant : 1986 - 1989. International Potato Center. Lima, Peru.

Responsibilities : Technical responsible: Project title: “Development of cytological techniques to facilitate exploitation of sweet potato germplasm”. Project leader: Dr. M. Iwanaga.

Achievements : Coordination of all the activities in the field and greenhouse. 7 people under my responsibility. Production of interspecific hybrids, field experiment planning and data recording for yield, earliness and other phenotypic traits. Set-up of all experimental trials follow up of statistical evaluation of results (quantitative traits). Cytological studies of 2n pollen production in wild species. Practical supervision of an MSc thesis on embryo rescue. Cytological studies on abortion of interspecific hybrids.

Other professional activities

Fund raising:

4/6 Last updated: 7-Feb-11 342  Funds obtained from the Peruvian government for the Musa Latin American Network (LACNET) of INIBAP.-IPGRI. The amount that the Peruvian government gives to the CGIAR systems is 500,000 USD annually.  Funds obtained from the European Molecular Biology Organisation (EMBO), UNESCO, the Welcome Trust, the GENOPOLE, the Peruvian Science and Technology Council (CONCYTEC) and the International Cell Research Organisation (ICRO) to organise an International course in Bioinformatics, data mining and analysis of genome sequence data in collaboration with the Peruvian University Cayetano Heredia. The amount raised was 70,000 USD.  Funds obtained for several research projects at the Genomics research Unit. Universidad Peruana Cayetano Heredia. 3 million USD in three years.

Teaching:

 Coordinator and lecturer of the general genetics course for third year Science students, UPCH.  Coordinator and lecturer of the Advanced genetics and genomics course for fourth year Science students, UPCH.  Lecturer of the Genetics and molecular biology laboratory course for third year students, UPCH.  Director of 4 Biologist thesis projects :  New enucleation points in the potato physical map using novel markers from various genetic maps in chromosome III of Solanum tuberosum.  ¨Setting up the barcoding methodology in plants and study of loci Diversity in: matK, rbcL and trnH- pbsA for the delimitation of specific differences in genus Piper and Peperomia¨  Identification and anchoring of new Bacs in the Solanum tuberosum physical map using sinteny with Solanum lycopersicum  ¨Study of loci Diversity in: matK, rbcL and trnH-pbsA for the delimitation of specific differences in genus Cinchona”  Teaching of genomics to medicine students : June 2005. Universidad Peruana Cayetano Heredia. Lima Peru.  Main organiser and lecturer of an EMBO Practical Course in Bioinformatics, data mining and analysis of Genome Sequence data. 3-5November 2003 UPCH.  Teaching of practical courses to third year students : Nov 2001 . University of Evry, France Plant genetics course. Professor Dr. Francis Quetier (DDG Genoscope).  MSc thesis supervisor: 1994 - 1995 International Potato Center/ Universidad Peruana “Cayetano Heredia”, Lima, Peru. Inheritance and cytological mechanisms of 2n pollen production in 2 Ipomoea species: I. batatas Lam. (2n=4x=60) and I. triloba L. (2n=2x=30). Student: Augusto Becerra. Universidad Peruana “Cayetano Heredia” thesis approved with “Outstanding”.  Invited lecturer: 1993 Universidad Nacion31/01/200707/02/2011al Agraria “La Molina”. Lima, Peru. Course: Plant genetics.  Teacher : 1992 Los Reyes Rojos School. Lima, Peru. Natural sciences working group

Scientific popularization  Film Scientific advisor: June 2001 „La revanche de la Pomme de Terre‟: Director Pierre Bressiant.. Production Alan Sedouy. Price MIF-Sciences at the Portuguese Villa Real Festival. Official selection 2008 seventh art and Sciences Festival at Noirmoutier, France.

 Collaborator for the scientific page of the Peruvian journal “El comercio”. Editor Mr. Omar Swayne.

Stages - Courses

2002 Cold Spring Harbor Laboratory. New York, USA. Course on “Acquiring and analyzing genomic sequence data”. 1999 June- Dec CIRAD-FLHOR Montpellier, France. Cytogenetic characterisation of Musa somatic hybrids using molecular markers.

5/6 Last updated: 7-Feb-11 343 1993 Cold Spring Harbor Laboratory. New York, USA. Course on “Molecular markers for plant breeding and genetics”. 1993 USDA ARS, Charleston. South Carolina USA. Flow cytometry studies on sweetpotato interspecific hybrids. 1984 - 1986 Pre-professional stage. International Potato Center. Lima, Peru. Cytological studies on the mode of formation of apomictic seed. Involved with different cytological techniques such as chromosome counts, microtechnique, tissue culture, and in vitro ovary and ovule culture in Solanum tuberosum.

6/6 Last updated: 7-Feb-11 344