AFP / Biosapiens 2008 SIG Meeting Program Toronto, Canada, July 2008

Total Page:16

File Type:pdf, Size:1020Kb

AFP / Biosapiens 2008 SIG Meeting Program Toronto, Canada, July 2008 AFP / Biosapiens 2008 SIG Meeting Program Toronto, Canada, July 2008 Dear AFP / Biosapiens 2008 attendee, Welcome to the joint Automated Function Prediction / Biosapiens meeting in ISMB 2008. This is the second time AFP and Biosapiens are joining forces to bring you an engaging and stimulating program. As usual, we strive to bring you the latest in cutting-edge research in computational gene and protein function prediction and annotation delivered by leading international researchers. This year we are holding a joint session with the 3D SIG on predicting function from protein structure. “Structure to Function” is a problem that is rapidly moving to the forefront of life science due to the increasing number of unannotated structures coming from structural genomics projects. We are also addressing a need voiced by the community to learn more about computational function prediction. Kimmen Sjölander from the University of California Berkeley will conduct a workshop on function prediction using phylogenomics. Yanay Ofran from Bar Ilan University, Israel and Predrag Radivojac from Indiana University will present a variety of components, tools and techniques for computational function prediction. Those tutorials are intended for researchers and students that are entering the field, and for those in the field to gain more knowledge and expertise. This is a rare opportunity to interact informally with leading experts in the field and enhance your own research. We would like to thank the members of the Program Committee for carefully reviewing the abstracts sent to this meeting. Thanks to the International Society for Computational Biology for hosting this meeting at ISMB 2008. A special thanks to Prof. Sean Mooney and his lab at the Indiana University School of Medicine for maintaining the conference website. Iddo Friedberg (Chair), Michal Linial (Co-chair), Adam Godzik and Ying Zhang Organizing committee: Iddo Friedberg, University of California San Diego, USA Michal Linial, The Hebrew University of Jerusalem, Israel Ying Zhang, Burnham Institute for Medical Research, La Jolla CA, USA Program Committee: Iddo Friedberg (Chair) Sarah Boyd Priti Talwar Jeffrey Chang Mallika Veeramalai Barry Grant Mark Wass Thomas Hamelryck Daniela Wieser Piotr Kozbial Shirley Wu Michal Linial Yuzhen Ye Marc Marti-Renom Ying Zhang Mary Pacold Ana Rodrigues Ariel Schwartz AFP / Biosapiens 2008 Conference Program Time Speaker Title 8:30-8:45 Opening remarks Day 1 - Friday, July 18, 2008 University of California, 8:45-9:30 Patricia Babbitt San Francisco TBA Los Alamos National Prediction of Functional Sites in SCOP Domains using 9:30-9:50 Judith Cohn Laboratory Dynamics Perturbation Analysis Partial Order Optimal Likelihood (POOL): A New Approach 9:50-10:15 Mary Jo Ondrechen Northeastern University to High Performance Functional Site Prediction 10:15-10:35 Break Howard Hughes Medical 10:35-11:15 Barry Honig Institute & Columbia On the nature of protein fold space: extracting functional Joint Session with University information from apparently remote structural neighbors 3D Sig Assessing functional novelty of PSI structures via structure- Joint Session with 11:15-11:35 Benoît H Dessailly University College London function analysis of large and diverse superfamilies 3D Sig Joint Session with 11:35-11:55 TBD TBD TBD 3D Sig Prediction of functional characteristics based on sequence and Joint Session with 11:55-12:35 Alfonso Valencia CNIO, Spain structure 3D Sig 12:35-13:30 Lunch University of California, A Systematic Approach to Identifying Protein-Ligand Binding 13:30-14:15 Philip Bourne San Diego Profiles on a Proteome Scale LabelHash: A Flexible and Extensible Method for Matching 14:15-14:35 Mark Moll Rice University Structural Motifs Analysis of Genetic Interaction Maps Reveals Functional 14:35-15:00 Shuye Pyu University of Toronto Pleiotropy Poster Session (Coffee 15:00-17:00 break 15:30-16:00) Research Laboratories of 17:00-17:20 Philip Groth Bayer Schering Pharma Hunting for gene function: Using phenotype data mining as a AG, Berlin, Germany largescale discovery tool Centre de Regualció 17:20-18:00 Roderic Guigo Genòmica, Spain Transcriptional complexity in the human genome Day 2 - Saturday, July 19, 2008 8:30-8:40 Rally Investigating the biological role(s) of the functional orphan 8:40-9:20 Andrew Emili University of Toronto protein repertoire of Escherichia coli: Integrating experimental data with genomic inference to make testable predictions Workshops (Coffee break 9:30-12:00 10:15-10:45) 1) Kimmen Sjölander; 2)Yanay Ofran and Predrag Radivojac University of California, 12:00-12:25 Steven Brenner Berkeley Assessment of Molecular Function Prediction 12:30-13:30 Lunch The European Molecular 13:30-14:15 Peer Bork Biology Laboratory Predicting biological functions at different spatial scales ESG: Extended Similarity Group method for automated 14:15-14:35 Daisuke Kihara Purdue University protein function prediction The Hebrew University of 14:35-15:00 Michal Linial Jerusalem Safe Functional Inference for Uncharacterized Viral Proteins 15:05-15:30 David Horn Tel Aviv University Data mining of protein families using common peptides. 15:30-16:00 Coffee break Predicting Protein-Disease Relationships Using Sequence, 16:00-16:20 Predrag Radivojac Indiana University Physicochemical Properties, and Molecular Function Information University of Minnesota, Association Analysis Techniques for Discovering Functional 16:20-16:40 Gaurav Pandey Twin Cities Modules from Microarray Data Computationally-driven experimental identification of protein 16:40-17:20 Olga Troyanskaya Princeton University function 17:20-17:30 Closing remarks Talk Abstracts Conserved Substrate Substructures & Protein Similarity Networks for Automated Annotation of Enzymes Patricia Babbitt*, Ranyee Chiang, Shoshana Brown, Holly Atkinson Univerisity of California, 1700 4th St., MC 2550, San Francisco, CA 94158-2330, USA *Correspondence: [email protected] 1. INTRODUCTION While many methods are available for inference of functional properties for uncharacterized proteins, homology-based analysis remains a major approach for assignment of molecular function by annotation transfer. For enzymes, organization of homologous proteins into superfamilies related by structural similarities in the catalytic machinery required to catalyze a fundamental aspect of the chemical reactions represented is a powerful way to assign functional characteristics to newly discovered members. Yet many such superfamilies include multiple reactions evolved to catalyze different overall reactions using broadly dissimilar substrates, challenging the effectiveness of annotation transfer between diverse sequences and structures, particularly for automated function prediction. To address some of these issues, we have developed two new approaches to aid in functional annotation of members of enzyme superfamilies. The first, identification of conserved substrate substructures associated with common aspects of catalysis across all diverse members of a superfamily allows annotation using information that is orthogonal to that obtained from sequence and structural conservation patterns. The second approach uses protein similarity networks to facilitate annotation via mapping of functional properties to superfamily member proteins that have been clustered using simple sequence similarity metrics. 2. RESULTS 2.1 Conservation of substrate substructures for automated annotation of functional characteristics of enzyme superfamilies. Just as conservation patterns across sequences and structures of homologous proteins can reveal clues about their functions, conservation patterns across their cognate substrates identify aspects of function associated with all member reactions, even when the substrates and overall reactions across a superfamily vary greatly. We analyzed graph isomorphisms among enzyme substrates for 42 SCOP superfamilies to establish the substrate conservation pattern for each. The chemical substructures conserved among all known substrates of each superfamily, the substructures that are reacting, and the relationship between the two were determined (1). This information can be used to annotate new sequences and structures identified as members of these superfamilies (Fig. 1). The results define an obligate substructure for the substrate of uncharacterized members, thereby restricting the reaction space to be explored for annotation of reaction specificity or to identify featues of ligands useful for screening or co-crystallization Fig. 1. Examples of uncharacterized structures from the PSI that can be annotated with the substrate substructure conserved in all members of the superfamily to which it belongs. studies. The method is automated, enabling large-scale identification of fundamental functional capabilities of new superfamilies provided sufficient diverse members have already been functionally characterized. 2.2 Protein similarity networks for facile mapping of functional properties to sequence clusters in protein superfamilies. To improve annotation of specific molecular function on a large scale, we have explored and validated the use of protein similarity networks (2) for visualization of functional trends across large and diverse protein superfamilies. Using pairwise comparisons of large sets of homologous sequences in superfamilies representing many different molecular functions, we show that even such simple approaches to clustering sequences in networks provide satisfactory depictions of high-dimensional similarity
Recommended publications
  • • La Gestion Efficace De L’Énergie • Le Réseautage Planétaire • Les Processus Géophysiques • L’Économie Globale, La Sécurité Et La Stabilité
    SupérieureS atiqueS athéM e M inaire D SéM The planet on which we live and the challenges that we face on this planet become increasingly complex as ecological, economic and social systems are large intertwined networks governed by dynamic processes and feedback loops. Mathematical models are indispensable in understanding and managing such systems since they provide insight into governing processes; they help predict future behavior; and they allow for risk-free evaluation of possible interventions. The goal of this thematic program is to tackle pressing and emerging challenges in population and ecosystem health, including understanding and controlling major transmissible diseases, optimizing and monitoring vaccination, predicting the impacts of climate change on invasive species, protecting biodiversity and managing ecosystems sustainably. This pan-Canadian program will bring together the international community of researchers who work on these topics in a series of workshops to foster exchange and stimulate cross-disciplinary research between all scientific areas involved, to discuss perspectives and directions for future advances in the field, including new models and methods and to foster tighter links between the research community, government agencies and policy makers. Three summer schools will introduce graduate students and postdoctoral fellows to the art of modeling living systems and to the latest tools and techniques to analyze these models. SCIENTIFIC COMMITTEE Jacques Bélair Mark Lewis (Montréal) Models and Methods in Ecology (Alberta) Frithjof Lutscher and Epidemiology Mathematical Modeling James Watmough (Ottawa) February 6-8, 2013 (UNB) of Indigenous Population Jianhong Wu CRM, Montréal (York) Organizers: Jacques Bélair (Montréal), Health Jianhong Wu (York) September 28-29, 2013 AISENSTADT CHAIRS BIRS Bryan Grenfell (Princeton), May 2013 Graphic Design: www.neograf.ca Simon A.
    [Show full text]
  • Fall 2016 Is Available in the Laboratory of Dr
    RNA Society Newsletter Aug 2016 From the Desk of the President, Sarah Woodson Greetings to all! I always enjoy attending the annual meetings of the RNA Society, but this year’s meeting in Kyoto was a standout in my opinion. This marked the second time that the RNA meeting has been held in Kyoto as a joint meeting with the RNA Society of Japan. (The first time was in 2011). Particular thanks go to the local organizers Mikiko Siomi and Tom Suzuki who took care of many logistical details, and to all of the organizers, Mikiko, Tom, Utz Fischer, Wendy Gilbert, David Lilley and Erik Sontheimer, for putting together a truly exciting and stimulating scientific program. Of course, the real excitement in the annual RNA meetings comes from all of you who give the talks and present the posters. I always enjoy meeting old friends and colleagues, but the many new participants in this year’s meeting particularly encouraged me. (Continued on p2) In this issue : Desk of the President, Sarah Woodson 1 Highlights of RNA 2016 : Kyoto Japan 4 Annual Society Award Winners 4 Jr Scientist activities 9 Mentor Mentee Lunch 10 New initiatives 12 Desk of our CEO, James McSwiggen 15 New Volunteer Opportunities 16 Chair, Meetings Committee, Benoit Chabot 17 Desk of the Membership Chair, Kristian Baker 18 Thank you Volunteers! 20 Meeting Reports: RNA Sponsored Meetings 22 Upcoming Meetings of Interest 27 Employment 31 1 Although the graceful city of Kyoto and its cultural months. First, in May 2016, the RNA journal treasures beckoned from just beyond the convention instituted a uniform price for manuscript publication hall, the meeting itself held more than enough (see p 12) that simplifies the calculation of author excitement to keep ones attention! Both the quality fees and facilitates the use of color figures to and the “polish” of the scientific presentations were convey scientific information.
    [Show full text]
  • The 7Th White Coat Ceremony at SSPPS by Binh Tran, Pharmd
    The 7th White Coat Ceremony at SSPPS By Binh Tran, PharmD The White Coat Ceremony at the Skaggs School of Pharmacy and Pharmaceutical Sciences (SSPPS) on September 25th held special meaning as the University of California - San Diego celebrates its 50th Anniversary this year. SSPPS faculty, alumni, student pharmacists, the incoming class of 2014, their families and their friends listened to Dean Palmer Taylor’s welcoming address in the spacious Health Sciences auditorium modeled with panels made of eucalyptus wood. Dr Rita Shane, Director of Pharmacy Services at Cedars-Sinai Medical Center and Assistant Dean of Clinical Pharmacy at the UCSF School of Pharmacy delivered an energizing speech on The Power of Differentiation: Will you be a Brand or Generic? Attributes mentioned were competency, responsibility and accountability, intellectual curiosity, being able to seize opportunities, and establishing credibility. Dr. Anthony Manoguerra, Associate Dean for Student Affairs, reported that the class of 2014’s grade point average of 3.71 broke the record set by the previous class which averaged 3.70. The White Coat hooding by Dean Taylor was a moving ceremony with Justine Abella being last due to a recent foot injury. The class recited the Pharmacist’s Oath, which brought back memories of our own experiences. The Student Welcome by second- year student, Ammar Zanial, was heartfelt and reminiscent of his comments during pharmacy conference class. Little did I know at the time that the student pharmacist who volunteered at many outreaches in the community and helped backstage during Cultural Fusion Night was the President of his class. In closing, Dean Taylor commented on the ingeniousness of the class when he observed them tacitly move their seats in order to step closer to the stage.
    [Show full text]
  • Are You an Invited Speaker? a Bibliometric Analysis of Elite Groups for Scholarly Events in Bioinformatics
    Are You an Invited Speaker? A Bibliometric Analysis of Elite Groups for Scholarly Events in Bioinformatics Senator Jeong, Sungin Lee, and Hong-Gee Kim Biomedical Knowledge Engineering Laboratory, Seoul National University, 28–22 YeonGeon Dong, Jongno Gu, Seoul 110–749, Korea. E-mail: {senator, sunginlee, hgkim}@snu.ac.kr Participating in scholarly events (e.g., conferences, work- evaluation, but it would be hard to claim that they have pro- shops, etc.) as an elite-group member such as an orga- vided comprehensive lists of evaluation measurements. This nizing committee chair or member, program committee article aims not to provide such lists but to add to the current chair or member, session chair, invited speaker, or award winner is beneficial to a researcher’s career develop- practices an alternative metric that complements existing per- ment.The objective of this study is to investigate whether formance measures to give a more comprehensive picture of elite-group membership for scholarly events is represen- scholars’ performance. tative of scholars’ prominence, and which elite group is By one definition (Jeong, 2008), a scholarly event is the most prestigious. We collected data about 15 global “a sequentially and spatially organized collection of schol- (excluding regional) bioinformatics scholarly events held in 2007. We sampled (via stratified random sampling) ars’ interactions with the intention of delivering and shar- participants from elite groups in each event. Then, bib- ing knowledge, exchanging research ideas, and performing liometric indicators (total citations and h index) of seven related activities.” As such, scholarly events are communica- elite groups and a non-elite group, consisting of authors tion channels from which our new evaluation tool can draw who submitted at least one paper to an event but were its supporting evidence.
    [Show full text]
  • Olga G. Troyanskaya - Sciencewatch.Com
    Olga G. Troyanskaya - ScienceWatch.com Home About Scientific Press Room Contact Us ● ScienceWatch Home ● Interviews Featured Interviews Author Commentaries Institutional Interviews 2008 : September 2008 - Author Commentaries : Olga G. Troyanskaya Journal Interviews Podcasts AUTHOR COMMENTARIES - 2008 ● Analyses September 2008 Featured Analyses Olga G. Troyanskaya What's Hot In... Featured Scientist from Essential Science IndicatorsSM Special Topics Dr. Olga Troyanskaya has been named a Rising Star in the field of Computer ● Data & Rankings Science, according to an analysis published by ScienceWatch.com in May. Her citation record in this field in Essential Science Indicators from Thomson Sci-Bytes Reuters includes 31 papers cited a total of 1,533 times between January 1, 1998 and April 30, 2008. She also has Highly Cited Papers in the field of Fast Breaking Papers Clinical Medicine. Dr. Troyanskaya is an Assistant Professor in the New Hot Papers +enlarge Department of Computer Science and the Lewis-Sigler Institute for Integrative Emerging Research Fronts Genomics at Princeton University. Fast Moving Fronts Research Front Maps In the interview below, she talks with us about her highly cited work. Current Classics Top Topics Please tell us a little about your research and educational background. Rising Stars My background is interdisciplinary—I have a Ph.D. in Biomedical Informatics and undergraduate New Entrants degrees in both Computer Science and Biology. My research has always reflected this—I have been involved in bioinformatics research since undergraduate days, first working with Steven Salzberg, then at Country Profiles Johns Hopkins University and The Institute for Genomic Research, and then with Gad Landau and Alex Bolshoy at Haifa University in Israel.
    [Show full text]
  • EYAL AKIVA, Phd
    Eyal Akiva CV, Nov. 2017 EYAL AKIVA, PhD Department of Bioengineering and Therapeutic Sciences Phone +1-650-504-9008 University of California at San Francisco Email [email protected] 1700 4th street, San Francisco, Web www.babbittlab.ucsf.edu/eakiva CA, USA EDUCATION 2012-2017 Post-doctoral fellowship at UCSF, Dept. Of Bioengineering and Therapeutic Sciences. Host: Prof. Patricia Babbitt. 2010-2012 Post-doctoral fellowship at UCSF, Dept. Of Bioengineering and Therapeutic Sciences. Host: Prof. Tanja Kortemme. 2004-2010 PhD at The Hebrew University of Jerusalem (Israel), bioinformatics. Host: Prof. Hanah Margalit. “Various Aspects of Modularity in Protein-Protein Interaction". 2001-2004 MSc at The Hebrew University of Jerusalem (Israel), bioinformatics and human genetics. Host: Prof. Muli Ben-Sasson. “Exploiting the Exploiters: Identification of Virus-Host Pep- tide Mimicry as a Source for Modules of Functional Significance”. MAGNA CUM LAUDE. 1997-2000 BSc at Bar-Ilan University (Israel), biology (major) and computer science (minor). Final project advisor: Prof. Ramit Mehr “Modeling the Evolution of the Immune System: a Sim- ulation of the Evolution of Genes that Encode the Variable Regions of Immunoglobulins”. MAGNA CUM LAUDE. 1996-1997 First year of "Industrial Engineering and Management" studies, Tel-Aviv University, Israel. OTHER WORK EXPERIENCE 2000-01 ‘Do-coop technologies’: Team leader and chemistry/microbiology researcher; development of biological applications and manufacture of proprietary nanoparticles (Or Yehuda, Israel and Tel-Aviv University (Prof. Eshel Ben-Jacob’s lab at the school of physics)). FUNDING, HONORS AND AWARDS 2017 Grant: Co-PI, “Utilizing metagenomic sequences for enzyme function prediction”, Joint Genome Institute (US Department of Energy) (http://jgi.doe.gov/doe-user-facilities-ficus- join-forces-to-tackle-biology-big-data/).
    [Show full text]
  • Celebrate Princeton Invention 2017
    CELEBRATE PRINCETON INVENTION 2017 850016-cpi-booklet September 8, 2017 9:44 AM Office of the Dean for Research Celebrating the journey from research to impact 91 Prospect Ave. Princeton, NJ 08540 609-258-5500 rinceton University is a place where deep thinkers and visionaries [email protected] have the latitude to push basic discoveries into new realms. At research.princeton.edu this year’s Celebrate Princeton Invention, we honor both those researchers who start with a problem and look for a solution, To learn more about the researchers and Pand those who make fundamental technologies in this brochure, contact: discoveries that they then apply John Ritter in new areas. Director, Technology Licensing An example of this latter type 87 Prospect Ave., 3rd Floor of inventor is Herschel Rabitz, Princeton, NJ 08544 the Charles Phelps Smyth ’16 *17 609-258-1001 [email protected] Professor of Chemistry. His www.princeton.edu/patents work on optimization theory has led to new ways to develop For information on fostering industry- and formulate new medicines. faculty collaborations, contact: Another example is Jeroen Tromp, Coleen Burrus the Blair Professor of Geology Director, Corporate Engagement and and a professor of geosciences Foundation Relations and applied and computational 91 Prospect Ave. mathematics. Tromp has adopted Princeton, NJ 08540 methods he created for studying the 609-258-3277 Earth’s interior to the problem of [email protected] improving medical imaging. cefr.princeton.edu These pioneering projects complement the many avenues of invention featured this year, ones that For inquiries regarding sponsored research, contact: are making buildings more energy efficient, ramping up the production of biofuels, bringing molecular diagnosis to remote locations with a new Jeff Friedland “lab on a chip,” and helping to find the genes that contribute to autism.
    [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]
  • Seq-Setnet: Exploring Sequence Sets for Inferring Structures
    Seq-SetNet: Exploring Sequence Sets for Inferring Structures Fusong Ju1,2, Jianwei Zhu1,2, Guozheng Wei1,2, Qi Zhang1,2, Shiwei Sun1,2, Dongbo Bu1,2 1Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China 2University of Chinese Academy of Sciences, Beijing, 100049, China {jufusong, zhujianwei, weiguozheng, zhangqi, dwsun, dbu}@ict.ac.cn Abstract Sequence set is a widely-used type of data source in a large variety of fields. A typical example is protein structure prediction, which takes an multiple sequence alignment (MSA) as input and aims to infer structural information from it. Almost all of the existing approaches exploit MSAs in an indirect fashion, i.e., they transform MSAs into position-specific scoring matrices (PSSM) that represent the distribution of amino acid types at each column. PSSM could capture column- wise characteristics of MSA, however, the column-wise characteristics embedded in each individual component sequence were nearly totally neglected. The drawback of PSSM is rooted in the fact that an MSA is essentially an unordered sequence set rather than a matrix. Specifically, the interchange of any two sequences will not affect the whole MSA. In contrast, the pixels in an image essentially form a matrix since any two rows of pixels cannot be interchanged. Therefore, the traditional deep neural networks designed for image processing cannot be directly applied on sequence sets. Here, we proposed a novel deep neural network framework (called Seq-SetNet) for sequence set processing. By employing a symmetric function module to integrate features calculated from preceding layers, Seq-SetNet are immune to the order of sequences in the input MSA.
    [Show full text]
  • Your Scientific Reputation Class Slides
    Your Scientific Reputation and Being a Responsible Member of Society Peter D Sottile, MD October 2020 • Silence personal devices. • Stay muted when not talking. • Set up in a quiet location. Housekeeping: Zoom • Remain attentive. Avoid checking Etiquette: email/phone/web. • Use the Chat function to ask questions or get technical help. • Use your full name, not an alias. Receiving credit for attendance: To satisfy the NIH Requirement for Instruction in the Responsible Conduct of Research, the following are required in order to receive credit for attendance: Attend the full 90 minutes of the training. Attending any 8 out of the 9 RCR seminars we offer will satisfy the NIH requirement. Keep your video camera on throughout the session. NIH requirements for RCR training specify face- to-face discussion. Participate interactively throughout the session. Participate in discussions, respond to polls, and sign the attendance sheet (link will be distributed in the Chat). Raise your Hand to participate in discussions: In order to participate in discussions, raise your hand. Try it now! • Click “Participants” at the bottom of your screen. • Click “Raise Hand” in the popup window. • Click “Lower Hand” to stop raising your hand. 3 Objectives: • Explain why a good scientific reputation is important in academia • Describe the factors that contribute to a good scientific reputation • Identify the components to being a responsible member of the scientific community • Describe threats that may harm one’s scientific reputation, and responses to challenges
    [Show full text]
  • Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by Pickeringhutchins Ltd
    European Bioinformatics Institute EMBL-EBI Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by PickeringHutchins Ltd www.pickeringhutchins.com EMBL member states: Austria, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland, United Kingdom. Associate member state: Australia EMBL-EBI is a part of the European Molecular Biology Laboratory (EMBL) EMBL-EBI EMBL-EBI EMBL-EBI EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD United Kingdom Tel. +44 (0)1223 494 444, Fax +44 (0)1223 494 468 www.ebi.ac.uk EMBL Heidelberg Meyerhofstraße 1 69117 Heidelberg Germany Tel. +49 (0)6221 3870, Fax +49 (0)6221 387 8306 www.embl.org [email protected] EMBL Grenoble 6, rue Jules Horowitz, BP181 38042 Grenoble, Cedex 9 France Tel. +33 (0)476 20 7269, Fax +33 (0)476 20 2199 EMBL Hamburg c/o DESY Notkestraße 85 22603 Hamburg Germany Tel. +49 (0)4089 902 110, Fax +49 (0)4089 902 149 EMBL Monterotondo Adriano Buzzati-Traverso Campus Via Ramarini, 32 00015 Monterotondo (Rome) Italy Tel. +39 (0)6900 91402, Fax +39 (0)6900 91406 © 2012 EMBL-European Bioinformatics Institute All texts written by EBI-EMBL Group and Team Leaders. This publication was produced by the EBI’s Outreach and Training Programme. Contents Introduction Foreword 2 Major Achievements 2011 4 Services Rolf Apweiler and Ewan Birney: Protein and nucleotide data 10 Guy Cochrane: The European Nucleotide Archive 14 Paul Flicek:
    [Show full text]
  • Curtis Huttenhower Associate Professor of Computational Biology
    Curtis Huttenhower Associate Professor of Computational Biology and Bioinformatics Department of Biostatistics, Chan School of Public Health, Harvard University 655 Huntington Avenue • Boston, MA 02115 • 617-432-4912 • [email protected] Academic Appointments July 2009 - Present Department of Biostatistics, Harvard T.H. Chan School of Public Health April 2013 - Present Associate Professor of Computational Biology and Bioinformatics July 2009 - March 2013 Assistant Professor of Computational Biology and Bioinformatics Education November 2008 - June 2009 Lewis-Sigler Institute for Integrative Genomics, Princeton University Supervisor: Dr. Olga Troyanskaya Postdoctoral Researcher August 2004 - November 2008 Computer Science Department, Princeton University Adviser: Dr. Olga Troyanskaya Ph.D. in Computer Science, November 2008; M.A., June 2006 August 2002 - May 2004 Language Technologies Institute, Carnegie Mellon University Adviser: Dr. Eric Nyberg M.S. in Language Technologies, December 2003 August 1998 - November 2000 Rose-Hulman Institute of Technology B.S. summa cum laude, November 2000 Majored in Computer Science, Chemistry, and Math; Minored in Spanish August 1996 - May 1998 Simon's Rock College of Bard A.A., May 1998 Awards, Honors, and Scholarships • ISCB Overton PriZe (Harvard Chan School, 2015) • eLife Sponsored Presentation Series early career award (Harvard Chan School, 2014) • Presidential Early Career Award for Scientists and Engineers (Harvard Chan School, 2012) • NSF CAREER award (Harvard Chan School, 2010) • Quantitative
    [Show full text]