DOCSLIB.ORG

CV 2015 Sharpton, Thomas.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
CV 2015 Sharpton, Thomas.Pdf THOMAS JEFFERSON SHARPTON Department of Microbiology [email protected] Oregon State University lab.sharpton.org 226 Nash Hall, Corvallis, OR 97331 @tjsharpton tel: (541) 737-8623 fax: (541) 737-0496 github.com/sharpton EDUCATION 2009 University of California, Berkeley, CA Ph.D., Microbiology, Designated Emphasis in Computational Biology 2003 Oregon State University, Corvallis, OR B.S. (Cum Laude), Biochemistry and Biophysics. APPOINTMENTS 2013- Assistant Professor Departments of Microbiology and Statistics, Oregon State University 2009-2013 Bioinformatics Fellow Gladstone Institute of Cardiovascular Disease, Gladstone Institutes Mentors: Katherine Pollard & Jonathan Eisen (UC Davis) 2003-2009 Graduate Student Researcher Department of Microbiology, University of California, Berkeley Mentors: John Taylor & Sandrine Dudoit 2005 Bioinformatics Research Intern The Broad Institute Mentor: James Galagan 2002-2003 Research Assistant Department of Zoology, Oregon State University 2001 Research Assistant International Arctic Research Center, University of Alaska, Fairbanks, AK HONORS & AWARDS 2013 Gladstone Scientific Leadership Award 2007 Dean’s Council Student Research Representative 2007 Effectiveness in Teaching Award, UC Berkeley 2006-2008 Chang-Lin Tien Graduate Research Fellowship 2002 Student Leadership Fellowship 2002 HHMI Undergraduate Research Fellowship 2002-2003 Dr. Donald MacDonald Excellence in Science Scholarship 2002 OSU College of Science's Excellence in Science Scholarship 1999-2003 Provost Scholarship 1999 American Legion Student Ethics Award PUBLICATIONS Refereed Journal Articles 17. O’Dwyer JP, Kembel SW, Sharpton TJ (In Review) Backbones of Evolutionary History Test Biodiversity Theory for Microbes 16. Quandt AC, Kohler A, Hesse C, Sharpton TJ, Martin F, Spatafora JW. (In Print) Metagenomic sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria rich microbiome. Environmental Microbiology. 15. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. (2014) Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLOS ONE 9(8): e105067. 14. Kent M, Soderlund K, Thomann E, Schreck CB, Sharpton TJ. (2014) Post-mortem sporulation of Ceratomyxa Shasta (Myxozoa) after dealth in adult Chinook salmon. Journal of Parasitology. Published online April 11, 2014. [PMCID – In progress]. 13. Sharpton TJ^. (2014) An Introduction to the Analysis of Shotgun Metagenomic Data Frontiers in Plant Genetics and Genomics. 5(209) PMCID: PMC4059276. 12. Kidd JM*, Sharpton TJ*, Norman PJ, Carpenter M, Sikora M, Gignoux CR, Gorgani NN, Agilent Technologies, Pollard KS, Parham P, Feldman MW, Wall J, Bustamante CD, Henn BM. (2014) Exome Capture from Saliva Produces High Quality Genomic and Metagenomic Data. BMC Genomics. 15(262). PMCID: PMC4051168 11. Finucane M, Sharpton TJ, Laurant T, Pollard KS (2014) A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter PLOS ONE. 9(1): e84689. PMCID: PMC3885756 10. Ladau J, Sharpton TJ, Jospin G, Kembel SW, O'Dwyer JP, Koeppel A, Green JL, Pollard KS. (2013) Global marine bacterial diversity peaks at high latitudes in winter. International Society of Microbial Ecology Journal. Published online March 21, 2013; DOI: 10.1038/ismej.2013.37. PMCID: PMC3749493 9. Sharpton TJ*^, Jospin G*, Wu D, Langille MG, Pollard KS, Eisen JA (2012). Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource, BMC Bioinformatics, 13(1): 264. PMCID: PMC3481395 8. Whiston E, Wise HZ, Jui G, Sharpton TJ, Cole GT, Taylor JW. (2012) “Comparative Transcriptomics of the Saprobic and Parasitic Growth Phases in Coccidioides spp.” PLOS ONE. 7(7): e41034. PMCID: PMC3401177 7. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS (2012). Novel bacterial taxa in the human microbiome, PLOS ONE, 7(6): e3529. PMCID: PMC3374617 6. The Human Microbiome Project Consortium (2012) A Framework for Human Microbiome Research, Nature, 486: 215–221. PMCID: PMC3377744 5. The Human Microbiome Project Consortium (2012). Structure, function and diversity of the human microbiome in an adult reference population, Nature, 486: 207-214. PMCID: PMC3564958 4. Sharpton TJ^, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS (2011). PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data, PLOS Computational Biology, 7(1): e1001061. PMCID: PMC3024254 3. Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park D, Whiston E, Hung C, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, Bessette D, Brown A, FitzGerald M, Lui A, Macdonald JP, Priest M, Orbach MJ, Galgiani JN, Kirkland TN, Cole GT, Birren BW, Henn MR, Taylor JW, Rounsley SD. (2010) Population Genomic Sequencing of Coccidioides Fungi Reveals Recent Hybridation and Transposon Control, Genome Research, 20: 938–946. PMCID: PMC2892095 2. Sharpton TJ^, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung C, McMahan C, Muszewksa A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, Taylor JW. (2009) Comparative Genomic Analyses of the Human Fungal Pathogens Coccidioides and their Relatives, Genome Research, 19: 1722– 1731. PMCID: PMC2765278 1. Sharpton TJ^, Neafsey DE, Galagan JE, and Taylor JW. (2008) Mechanisms of Intron Gain and Loss in Cryptococcus, Genome Biology, 9(1): R24. PMCID: PMC2395259 *Indicates co-first author ^Indicates corresponding author Other Publications Sharpton TJ, Jhaveri AA. (2006) Leveraging the Knowledge of Our Peers: Online Communities Hold the Promise to Enhace Scientific Research. PLOS Biology, 4(6): e199. PROFESSIONAL MEMBERSHIP & SERVICE ACADEMIC SERVICE 2014- Committee Member. Microbiology Graduate Admissions, OSU 2014- Committee Member. (Under)graduate Bioinformatics Curriculum Task Force, OSU 2014- Subcommittee Co-Chair. Graduate Bioinformatics Curriculum Task Force, OSU 2014- Review Editor. Frontiers in Systems Microbiology 2013-2014 Committee Member. Center for Genome Research and Biocomputing Spring Colloquium Steering Committee, OSU 2013- Biological Consultant. Informal advisor for statisticians, OSU 2013- Statistical Consultant. Informal advisor for microbiologists, OSU 2010- Member. The Human Microbiome Project Consortium 2009- Journal Referee. Science, PLoS Computational Biology, BMC Genomics, Molecular Ecology, FEMS Microbial Ecology, Microbiome, Bioinformatics, PLoS ONE 2010 Advisor. UCSF Biomedical Informatics Graduate Program Review 2007 President. Plant and Microbial Graduate Group, UC Berkeley 2007 President. Microbiology Student Group, UC Berkeley 2006 Chair. Microbiology Student Symposium, UC Berkeley 2006-2008 Webmaster. Microbiology Student Group, UC Berkeley 2005 Reviewer. Joint Genome Institute’s IUMS Genome Browser Review TEACHING AND TRAINING Academic Courses 2014 Introduction to Quantitative Genomics. ST599 Course Developer and Instructor (Fall Quarter) 2014 Molecular Host-Microbe Interactions. MCB637 Guest Lecture – “The Human Gut Microbiome” (5/30) 2014 Microbial Bioinformatics and Genome Evolution. OSU MB668 Course Developer and Lead Instructor. (Spring Quarter) 2014 Neuroendrocrine Regulation of Energy Metabolism. OSU NUTR 599/699 Guest Lecture – “The Human Gut Microbiome” (4/14) 2014 Nucleic Acid Bioinformatics. OSU BB499/599 CS419/519 Guest Lecture – “Inferring functional elements from conservation” (2/17) 2013 Microbial Systems. OSU MB511 Guest Lecture - “Mapping the Diversity of Marine Bacteria” (11/25) 2013 Microbiomes and Host-Microbiome Interactions. OSU HC407 Guest Lecture - “The Human Gut Microbiome” (11/12) 2007 Comparative Genomics Seminar UC Berkeley PMB290 Course Organizer 2006 The Diversity of Fungi. UC Berkeley PMB110 Graduate Student Assistant Instructor 2004 Introduction to Biology. UC Berkeley BIO1B Graduate Student Assistant Instructor 2003 Cell and Molecular Biology. OSU BI314 Undergraduate Student Assistant Instructor ADVISING 2014- Melissa Conley, PhD Co-Advisor, Nutrition 2014 Martin Guyer. MS Co-Advisor, Statistics 2014- Nicole Kirchoff, PhD Advisor, Microbiology 2014- Christopher Gaulke, Postdoctoral Fellow, Microbiology 2014- Kyle Duyck, Undergraduate Researcher, Biochemistry/Biophysics 2014- Holman Jue, Undergraduate Researcher, Microbiology 2014- Sean McNall, Undergraduate Researcher, Microbiology 2014 Courtney Armour, Rotation Student, MCB MENTORSHIP: INFORMAL 2013 Dr. Mariel Finucane – The obesity-associated gut microbiome 2013 Timothy Laurent – Ascertaining protein family quality and function 2012 Rachel Radnor – Computational analysis of marine microbial diversity 2012 Guillaume Jospin – Iterative clustering to identify novel proteins 2012 Stephen Nayfach – Assessing microbial functional diversity estimations 2011 Peter Skews-Cox – Building Viral HMMs for metagenomic data analysis 2011 Aram Avila-Herrera – Identification of CRISPRs in metagenomic data 2010 Dr. Rebecca Truty – Quantifying novel human microbiota THESIS/DISSERTATION COMMITTEE MEMBER AND SERVICE 2014- Trevor Tivey, Dept. Integrative Biology, PhD Committee Member 2014- Kimberly Kenny, Honors Thesis Committee Member 2014 Krista Soderlund, Honors Thesis Committee Member 2014 Martin Guyer, Dept. Statistics, MS Committee Member 2014- Edward Davis, Dept. Botany
Load more

Recommended publications
  • CV Page 1 THOMAS JEFFERSON SHARPTON Rank
    THOMAS JEFFERSON SHARPTON Rank: Associate Professor Department: Department of Microbiology, Oregon State University Department of Statistics, Oregon State University Date Hired: October 15, 2013 Address: 226 Nash Hall, Corvallis, OR 97331 Phone: (541) 737-8623 Email: [email protected] Web: lab.sharpton.org A. EDUCATION AND EMPLOYMENT INFORMATION Education 2009 Ph.D. Microbiology, Designated Emphasis in Computational Biology, University of California, Berkeley, CA, USA Dissertation: “Investigations of Natural Genomic Variation in the Fungi” Advisors: John W. Taylor & Sandrine Dudoit 2003 B.S. (Cum Laude) Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA Employment history 2019- Associate Professor Department of Microbiology, Oregon State University Department of Statistics, Oregon State University 2016- Founding Director Oregon State University Microbiome Initiative 2013-2019 Assistant Professor Department of Microbiology, Oregon State University Department of Statistics, Oregon State University 2013- Center Investigator Center for Genome Research and Biocomputing, Oregon State University 2009-2013 Bioinformatics Fellow Gladstone Institute of Cardiovascular Disease, Gladstone Institutes Advisors: Katherine Pollard & Jonathan Eisen (UC Davis) 2003-2009 Graduate Student Researcher Department of Microbiology, University of California, Berkeley Advisors: John Taylor & Sandrine Dudoit 2005 Bioinformatics Research Intern The Broad Institute Advisor: James Galagan Additional Affiliations 2017-2018 Scientific Advisory Board Member Thomas J. Sharpton – CV Page 1 Resilient Biotics, Inc. B. AWARDS 2019 Phi Kappa Phi Emerging Scholar Award 2018 OSU College of Science Research and Innovation Seed Program Award 2017 OSU College of Science Early Career Impact Award 2014 Finalist: Carter Award in Outstanding & Inspirational Teaching in Science 2013 Gladstone Scientific Leadership Award 2007 Dean’s Council Student Research Representative 2007 Effectiveness in Teaching Award, UC Berkeley 2006-2008 Chang-Lin Tien Graduate Research Fellowship C.
    [Show full text]
  • Jonathan Eisen at AAAS 2012 206 Items
    Created by JonathanEisen Powered by Jonathan Eisen at AAAS 2012 206 Items Notes from my trip to the AAAS Meeting in Vancouver 2012 Try #1 - heading to AAAS in Vancouver. My first time at AAAS. Going up to session on the Earth Microbiome Project organized by Jack Gilbert. Session: The Earth Microbiome Project: Modeling the Microbial Planet (2012 AAAS… Confex Jonathan Eisen @phylogenomics On my way to Vancouver for my first #AAASmtg - not sure if tweeting is embargoed or not - phylogenomics.blogspot.com/2012/01/aaas-m… 5:54 PM - Feb 16, 2012 · California, USA See Jonathan Eisen's other Tweets AAAS meeting - is this one for embargo watch? Phylogenomics Giving a talk at the AAAS meeting in February in Vancouver. I have avoided AAAS meetings previously because I do not like AAAS's position on open access issues. Given that AAAS is at least… Jonathan Eisen @phylogenomics · Feb 16, 2012 On my way to Vancouver for my first #AAASmtg - not sure if tweeting is embargoed or not - phylogenomics.blogspot.com/2012/01/aaas-m… DNLee @DNLee5 @phylogenomics I've tweeted and live blogged in the past. As long as you can get a wifi signal you should be fine #AAASmtg 5:56 PM - Feb 16, 2012 See DNLee's other Tweets Ginger Pinholster @gingerpin Replying to @mrgunn @mrgunn @phylogenomics Tweet away, guys. Watch our live webcasts! Pass it on. eurekalert.org/aaasnewsroom #aaasmtg 1 7:22 PM - Feb 16, 2012 See Ginger Pinholster's other Tweets Jonathan Eisen @phylogenomics Well I may be stuck in an airport but at least I have Jack #AAASmtg cc: @gilbertjacka 8:54 PM - Feb 16, 2012 · California, USA See Jonathan Eisen's other Tweets Jennifer Gardy @jennifergardy · Feb 14, 2012 Replying to @phylogenomics @phylogenomics Awesome! My weekend is a bit crazy but late Thurs (9pm-10ish) is good, Fri early PM, Sat and Sun late afternoon.
    [Show full text]
  • CASSANDRA LANE ETTINGER [email protected] • ORCID: 0000-0001-7334-403X • Casett.Github.Io
    CASSANDRA LANE ETTINGER [email protected] • ORCID: 0000-0001-7334-403X • casett.github.io EDUCATION & TRAINING UNIVERSITY OF CALIFORNIA, RIVERSIDE 2020 – present • Postdoctoral scholar, Dept. of Microbiology & Plant Pathology • Advisor: Dr. Jason Stajich UNIVERSITY OF CALIFORNIA, DAVIS 2013 – 2020 • Ph.D., Integrative Genetics & Genomics • Dissertation: Taxonomic diversity of the bacterial and fungal communities associated with the seagrass, Zostera marina • Advisor: Dr. Jonathan Eisen UNIVERSITY OF CALIFORNIA, BERKELEY 2009 – 2013 • B.A., Molecular & Cell Biology – Genetics, Genomics & Development Emphasis • Honors thesis: Genetic variation in abiotic tolerance and symbiotic quality among wild rhizobium bacteria • Advisor: Dr. Ellen Simms UNIVERSITY OF YORK, UNITED KINGDOM 2012 • Visiting Scholar, Biology & Archaeology Departments • Research project: Investigation of the role of dopamine in Drosophila vision and its relation to Parkinson’s disease • Advisor: Dr. Christopher Elliot PUBLICATIONS IN REVIEW LaForgia ML, Kang H* & Ettinger CL. Submitted. Competitive outcomes between native and invasive plants are linked to shifts in the bacterial rhizosphere microbiome. Available on bioRxiv; DOI: 10.1101/2021.01.07.425800 *undergraduate author Ettinger CL, Vann LE & Eisen JA. Submitted. Global diversity and biogeography of the Zostera marina mycobiome. Available on bioRxiv; DOI: 10.1101/2020.10.29.361022 PEER-REVIEWED PUBLICATIONS Ettinger CL & Eisen JA. 2020. Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina. PLoS One. DOI: 10.1371/journal.pone.0236135 Selbmann S, Coleine C, de Hoog S, Donati C, Druzhinina I, Ettinger CL, Gladfelter AS, Gorbushina AA, Grigoriev IV, Grube M, Gunde-Cimerman N, Muggia L, Northen T, Pennacchio C, Pòcsi I, Prigione V, Riquelme M, Segata N, Schumacher J, Shelest E, CASSANDRA LANE ETTINGER Sterflinger K, Tesei D, U’Ren J, Varese GC, Vázquez- Campos X, Vicente VA, Souza EM, Walker AL & Stajich JE.
    [Show full text]
  • UNIVERSITY of CALIFORNIA, SAN DIEGO the Comparative Genomics
    UNIVERSITY OF CALIFORNIA, SAN DIEGO The Comparative Genomics of Salinispora and the Distribution and Abundance of Secondary Metabolite Genes in Marine Plankton A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Kevin Matthew Penn Committee in charge: Paul R. Jensen, Chair Eric Allen Lin Chao Bradley Moore Brian Palenik Forest Rohwer 2012 UMI Number: 3499839 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent on the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI 3499839 Copyright 2012 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 Copyright Kevin Matthew Penn, 2012 All rights reserved The Dissertation of Kevin Matthew Penn is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2012 iii DEDICATION I dedicate this dissertation to my Mom Gail Penn and my Father Lawrence Penn they deserve more credit then any person could imagine. They have supported me through the good times and the bad times. They have never given up on me and they are always excited to know that I am doing well. They just want the best for me.
    [Show full text]
  • 2018 Annual Report Alfred P
    2018 Annual Report Alfred P. Sloan Foundation $ 2018 Annual Report Contents Preface II Mission Statement III From the President IV The Year in Discovery VI About the Grants Listing 1 2018 Grants by Program 2 2018 Financial Review 101 Audited Financial Statements and Schedules 103 Board of Trustees 133 Officers and Staff 134 Index of 2018 Grant Recipients 135 Cover: The Sloan Foundation Telescope at Apache Point Observatory, New Mexico as it appeared in May 1998, when it achieved first light as the primary instrument of the Sloan Digital Sky Survey. An early set of images is shown superimposed on the sky behind it. (CREDIT: DAN LONG, APACHE POINT OBSERVATORY) I Alfred P. Sloan Foundation $ 2018 Annual Report Preface The ALFRED P. SLOAN FOUNDATION administers a private fund for the benefit of the public. It accordingly recognizes the responsibility of making periodic reports to the public on the management of this fund. The Foundation therefore submits this public report for the year 2018. II Alfred P. Sloan Foundation $ 2018 Annual Report Mission Statement The ALFRED P. SLOAN FOUNDATION makes grants primarily to support original research and education related to science, technology, engineering, mathematics, and economics. The Foundation believes that these fields—and the scholars and practitioners who work in them—are chief drivers of the nation’s health and prosperity. The Foundation also believes that a reasoned, systematic understanding of the forces of nature and society, when applied inventively and wisely, can lead to a better world for all. III Alfred P. Sloan Foundation $ 2018 Annual Report From the President ADAM F.
    [Show full text]
  • Nandita R. Garud
    NANDITA R. GARUD Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E. Young Drive South Los Angeles, CA 90095-1606 [email protected] Curriculum Vitae January 2020 EDUCATION 2015 Ph.D. in Genetics Stanford University, Stanford, CA Focus on adaptation in natural populations 2012 MS in Statistics Stanford University, Stanford, CA 2008 BS in Biometry & Statistics and Biological Sciences, (Magna Cum Laude) Cornell University, Ithaca, NY EMPLOYMENT 2019- current Assistant Professor University of California, Los Angeles, CA Department of Ecology and Evolutionary Biology Department of Human Genetics Member, Interdepartmental Program in Bioinformatics Member, Genetics & Genomics Home Area 2015-2019 Bioinformatics Fellow Postdoctoral Position The Gladstone Institutes at the University of California, San Francisco, CA Advisor: Katherine Pollard 2015 summer Data Scientist Intern Intuit Inc., Mountain View, CA PREVIOUS RESEARCH 2010-2015 Ph.D. Candidate Department of Genetics, Stanford University, Stanford, CA Advisor: Dmitri Petrov 2008-2009 Fulbright Scholar The Bioinformatics Centre, University of Copenhagen, Denmark Advisor: Jakob Pedersen 2006-2008 Undergraduate Honors Researcher Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY Advisor: Andrew Clark 2006 Cold Spring Harbor Summer Undergraduate Research Intern Cold Spring Harbor, NY Advisor: Doreen Ware AWARDS AND HONORS 2014-2015 Stanford Center for Evolution and Human Genomics Fellow 2013 Walter Fitch Finalist, Society for Molecular Biology and Evolution, Chicago. 2010-2013 National Science Foundation Graduate Research Fellow 2008-2009 Fulbright Scholar, Denmark 2009-2010 Stanford Genome Training Program Grant 2007-2008 Cornell Hughes Scholar 2007-2008 CALS Charitable Trust Grant and Morley Grant for Undergraduate Research 2004-2008 Dean’s List, Cornell University 2004-2008 Byrd Undergraduate Scholarship 2004-2008 New York Lottery Undergraduate Scholarship PUBLICATIONS 1.
    [Show full text]
  • MSTATNEWS Athe Membership Magazine of the American Statistical Association What Makes Y O U R V O T E Matter?
    April 2008 • Issue #370 MSTATNEWS AThe Membership Magazine of the American Statistical Association What Makes Y o u r V o t e Matter? Publications Agreement No. 41544521 Board of Directors Meeting Highlights Making Statistics Delicious, Not Just Palatable April 2008 • Issue #370 VISION STATEMENT To be a world leader in promoting statistical practice, applications, and research; publishing statistical journals; improving statistical education; FEATURES and advancing the statistics profession. Executive Director 2 Longtime Members Ron Wasserstein: [email protected] 10 President’s Invited Column Associate Executive Director and Director of Operations Stephen Porzio: [email protected] 11 Highlights of the March 2008 Board of Directors Meeting Director of Programs 12 ASA Board Calls for Audits To Increase Confidence in Martha Aliaga: [email protected] Electoral Outcomes Director of Science Policy Steve Pierson: [email protected] 12 ASA Position on Electoral Integrity Managing Editor Megan Murphy: [email protected] 13 Wise Elders Program Production Coordinators/Graphic Artists 14 What Makes Your Vote Matter? Colby Johnson: [email protected] Lidia Vigyázó: [email protected] 16 Canadian Model for Accrediting Professional Statisticians Publications Coordinator Valerie Snider: [email protected] 17 Proposals Sought for NSF-CBMS Conferences Advertising Manager 18 Making Statistics Delicious, Not Just Palatable Claudine Donovan: [email protected] Contributing Staff Members 20 Big Science and Little Statistics Keith Crank • Ron Wasserstein 21 Free Textbook Offered to Stats Teachers Amstat News welcomes news items and let- 22 Success of Statistical Service Leads to Expanded Network ters from readers on matters of interest to the asso- ciation and the profession. Address correspondence 22 NHIS Paradata Released to Public to Managing Editor, Amstat News, American Statistical Association, 732 North Washington Street, Alexandria VA 22314-1943 USA, or email amstat@ 23 Staff Spotlight amstat.org.
    [Show full text]
  • Cvauc: Cross- Validated Area Under the ROC Curve Confidence Intervals
    CURRICULUM VITAE and BIBLIOGRAPHY CONTACT INFORMATION Name: Mark Johannes van der Laan. Nationality: Dutch. Marital status: Married to Martine with children Laura, Lars, and Robin. University address: University of California Division of Biostatistics School of Public Health 108 Haviland Hall Berkeley, CA 94720-7360 email: [email protected]. Telephone number: office: 510-643-9866 fax: 510-643-5163 Web address: www.stat.berkeley.edu/ laan Working Papers, Division of Biostatistics: www.bepress.com/ucbbiostat EDUCATION 1990-1993: Department of Mathematics, Utrecht University. Ph.D student of Prof. Dr. R.D. Gill. Position included 25% teaching, 75% research and education. Specialization in Estimation in Semiparametric and Censored Data Models. 1991-1992: University of California, Berkeley. Statistics Program at M.S.R.I.: \Semiparametric Models and Survival Analysis". Research with guidance by second Promotor Prof. Dr. P.J. Bickel. Subject: “Efficient Estimation in the Bivariate Censoring Model". December 13, 1993: Official Public Defense of Ph.D Thesis. 1985-1990: Masters degree in Mathematics at the University of Utrecht, The Netherlands. Statistics Major. 1988-1989: One year study, Masters degree courses at the Department of Statistics, North Carolina State University, Raleigh, North Carolina, U.S.A. G.P.A 4.0, Dean's List. 1989-1990: Masters thesis under guidance of Prof. Dr. R.D. Gill. Subject: The Dabrowska Estimator and the Functional Delta method. Grade (from 1-10, 10=top): 9.5. Official Completion: May 1, 1990. 1 ACADEMIC POSITIONS 2006-present: Jiann-Ping Hsu/Karl E. Peace Endowed Chair in Biostatistics. 2013-2018: Investigator and core leader of the methods workgroup of the Sustainable East African Research in Community Health (SEARCH).
    [Show full text]
  • Downloaded from NCBI Genbank Or Sequence
    Lind and Pollard Microbiome (2021) 9:58 https://doi.org/10.1186/s40168-021-01015-y METHODOLOGY Open Access Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing Abigail L. Lind1 and Katherine S. Pollard1,2,3,4,5* Abstract Background: Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded. Results: Here, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients.
    [Show full text]
  • Patrick J. H. Bradley
    (415) 734-2745 Patrick J. H. Bradley Gladstone Institutes, GIDB [email protected] 1650 Owens Street Pronouns: he/him/his Bioinformatics Fellow San Francisco, CA 94158 Current Position ······················································································· 2013— J. David Gladstone Institutes at UCSF Bioinformatics Fellow, Prof. Katherine S. Pollard Lab Academic History ····················································································· 2012—13 Lewis-Sigler Institute for Integrative Genomics, Princeton University Postdoctoral Fellow, Prof. Olga G. Troyanskaya Lab 2005—12 Dept. of Molecular Biology, Princeton University Ph.D. in Molecular Biology, Specialization in Quantitative and Computational Biology Thesis: Inferring Metabolic Regulation from High-Throughput Data Advisors: Prof. Joshua D. Rabinowitz, Prof. Olga G. Troyanskaya Committee: Prof. Ned S. Wingreen, Prof. David Botstein 2005 Dept. of Biology, Harvard College A.B. in Biology Peer-Reviewed Publications ·········································································· 1. Patrick H. Bradley, Katherine S. Pollard. “phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.” Bioinformatics, 2019; btz722.∗;z 2. Patrick H. Bradley, Patrick A. Gibney, David Botstein, Olga G. Troyanskaya, Joshua D. Rabinowitz. “Minor isozymes tailor yeast metabolism to carbon availability.” mSystems, 2019; 4:e00170-18.∗;y 3. Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard. “Phylogeny-corrected identification
    [Show full text]
  • External Review Research at University of California, Davis
    CONFIDENTIAL Report of The Washington Advisory Group an LECG Company on External Review of Research at University of California, Davis May 27, 2010 External Review of Research University of California, Davis May 27, 2010 The Washington Advisory Group an LECG company The Washington Advisory Group, founded in 1996, serves the science and technology advisory and institutional needs of U.S. and foreign companies, universities, governmental and non-governmental organizations, and other interested and affected parties. The Washington Advisory Group provides authoritative advisory and other services to institutions affected by the need to institute and improve research and education programs, by the press of the competitive marketplace, and by changing programs and policies of the federal science and technology enterprise. In October 2004, LECG Corporation, a provider of expert services, acquired substantially all of the assets of The Washington Advisory Group, which continues to operate as a company within LECG. University consulting is a major field of activity for The Washington Advisory Group. A common thread in our university engagements is the improvement of an institution’s national standing as a university that engages in both education and research so it can thereby contribute more to the cultural and economic growth of their community and the nation. Concomitant with this goal is improved ability to raise funds from federal and state agencies, philanthropic foundations, and industry. The directors of The Washington Advisory Group are: Erich Bloch Frank Press Jack Breese Mitchell T. Rabkin, M.D. Purnell Choppin, M.D. Frank Rhodes Jordan J. Cohen, M.D. Maxine Savitz Peter A. Freeman Robert M.
    [Show full text]
  • Open Access: a Model for Sharing Published Conservation Research
    May 2014 Vol. 39, No. 3 Inside From the Executive Director 2 AIC News 7 Annual Meeting 9 FAIC News 13 Open Access: A Model for Sharing JAIC News 16 Published Conservation Research Allied Organizations 17 By Priscilla Anderson, Whitney Baker, Beth Doyle, and Peter Verheyen Health & Safety 18 The conservation field has articulated the importance of publishing our research to disseminate information and further the aims of conserva- New Publications 20 tion. Article X of AIC’s Code of Ethics states that conservators should “contribute to the evolution and growth of the profession, a field of People 21 study that encompasses the liberal arts and the natural sciences” in part COLUMN In Memoriam 21 by “sharing of information and experience with colleagues, adding to SPONSORED the profession’s written body of knowledge.” Our Guidelines for Practice BY BP G Specialty Group Columns 23 state “the conservation professional should recognize the importance of published information that has undergone formal peer review,” because, as Commentary Network Columns 29 2.1 indicates, “publication in peer-reviewed literature lends credence to the disclosed information.” Furthermore, our Guidelines for Practice state that the “open exchange of Courses, Conferences, & Seminars 31 ideas and information is a fundamental characteristic of a profession.” In publishing our research, we can increase awareness of conservation and confidence in our research methods among allied professionals as well as the general public. However, current publication models limit the free flow of information by making access expensive and re-use complicated. An alternative to traditional subscription publishing is the Open Access movement, which strives to remove barriers to access and re-use of published information by reducing the costs of publishing and rethinking permissions issues.
    [Show full text]