DOCSLIB.ORG

Annual Report 2016 ELIXIR Annual Report 2016

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Annual Report 2016 ELIXIR Annual Report 2016 ELIXIR Annual Report 2016 Report Annual ELIXIR Annual Report 2016 ELXIR Annual Report 2016 1 Contents 2 Foreword by Torsten Schwede, Chair of ELIXIR Board (2015–2016) 3 Foreword by ELIXIR Director 5 ELIXIR Platforms and Use Cases 6 Structure of ELIXIR activities 8 Tools: Services and connectors to drive access and exploitation 10 Data: Sustaining Europe’s life science data infrastructure 11 Compute: Access, exchange and storage 12 Interoperability: Integration of data and services 14 Training: Professional skills for managing and exploiting data 16 Human data: Use case 17 Rare diseases: Use case 18 Marine metagenomics: Use case 19 Plant sciences: Use case 20 Platfrom and Use case leaders 23 ELIXIR members 24 Introducing ELIXIR UK 25 Introducing ELIXIR Germany 26 ELIXIR Nodes updates 32 2016 highlights 35 EU projects 36 ELIXIR-EXCELERATE 39 Collaboration with other Research Infrastructures 41 Supporting activities 42 Capacity building and Node development 43 Governance 44 Industry engagement 46 International collaboration 47 ELIXIR Working Groups 49 ELIXIR Hub activities 50 ELIXIR Communications 52 ELIXIR Hub staff 53 Governance Committees and financial data 54 ELIXIR Committees 57 Financial data 60 Commissioned Services: ELIXIR Implementation studies Foreword by Torsten Schwede I have watched ELIXIR develop since its conception and have been delighted to see its continued growth, year on year, since the Preparatory Phase. Yet 2016 was in many ways transformative for ELIXIR. The number of activities taking place in ELIXIR Nodes and across ELIXIR Platforms and Use Cases simply exploded. Four new Implementation Studies were initiated, five ELIXIR Node applications were approved and three Collaboration Agreements concluded. ELIXIR’s first ELSI (Ethical, Legal and Societal Issues) policy was developed in 2016, and the work to define indicators for ELIXIR Core Data Resources concluded. ELIXIR became the largest ESFRI research infrastructure in terms of membership, with 20 members in 2016. This rapid expansion of activities and membership is a clear indication of ELIXIR’s success, and shows the increasingly widespread recognition of bioinformatics as a driving force in the life sciences. 2016 also marked the maturity of ELIXIR: the European Strategy Forum on Research Infrastructures (ESFRI) recognised ELIXIR as a ‘landmark’ infrastructure in its 2016 Roadmap. I have had the privilege of sitting on the ELIXIR Board since its formation in 2014, serving the past two years as Chair. ELIXIR has achieved a great deal during that time, and I am looking forward to seeing it build and develop further. To realise the potential of computational biology to address the most pressing challenges we face, we must continue to develop ELIXIR at pace so that it may support new and emerging communities. Looking at the energy and commitment of our members, I continue to be enthusiastic about the achievements we can make together in 2017 and beyond. Torsten Schwede Chair of ELIXIR Board, 2015–2016 2 ELXIR Annual Report 2016 Foreword by ELIXIR Director The year 2016 marked the midway point in ELIXIR’s first Scientific Programme (2014– 2018), and was indeed transformational. Our two flagship projects, ELIXIR- EXCELERATE and CORBEL, were in full swing, allowing us to concentrate fully on infrastructure delivery and integration. This Annual Report highlights major achievements that illustrate the growth and maturity of our research infrastructure, which represents the combined efforts of 20 members. Integrated services Our goal is to establish a coordinated, integrated infrastructure for life-science data, and in 2016 we took major steps towards achieving just that. Our work on ELIXIR Core Data Resources was strategically important. These resources are essential to the wider life- science community, and to the long-term preservation of biological data. The ELIXIR Data Platform defined criteria for identifying Core Data Resources as well as the process by which they will be selected in 2017. These Core Data Resources will drive ELIXIR’s sustainability strategy, and serve as a basis for policy-level discussions. We launched the ELIXIR Authorisation and Authentication Infrastructure (AAI), a critical component of the ELIXIR Compute Platform for both users and service providers. AAI facilitates seamless access to ELIXIR services for researchers, and it gives ELIXIR service providers better control and management of access rights. Our Intranet was among the first services to use the ELIXIR AAI, so our partners can now share information more easily with one another from over 180 institutes. Other services that integrated the ELIXIR AAI were ELIXIR Beacons, discovery services that make human genomic datasets and cohorts discoverable and accessible by the global biomedical research community. The Beacons, developed in collaboration with the Global Alliance for Genomics and Health, define a global standard in data discovery. By the end of 2016, ELIXIR Beacons facilitated access to genomics data from six ELIXIR Nodes. In 2016 our members will engage more deeply in the Beacons project, new Nodes will participate and the ELIXIR-GA4GH collaboration will be expanded. ELXIR Annual Report 2016 3 Expanding membership Five new members joined ELIXIR in 2016: Italy, Slovenia, Ireland, Luxembourg and Germany. With these additions, we became the largest ESFRI Research Infrastructure in terms of membership. In the three years since our December 2013 launch, our membership has surged from the six founding members to 20. Looking ahead The second half of our current Scientific Programme focuses on expanding our efforts to accelerate the exploitation of open biological data. In 2017 we will further consolidate the ELIXIR's portfolio of services and initiate discussions about the next programming period (2019–2023). There are over 600 people actively contributing to ELIXIR, and each one has played a part in its success. We owe a lot to those whose hard work and dedication contributed to the development of ELIXIR in 2016: the ELIXIR Heads of Node, Technical and Training Coordinators, Platform and Use Case Leaders and everyone in ELIXIR Nodes. The achievements of 2016 have laid the foundations for accelerated progress in 2017 and beyond, and I look forward to continued success in this transformative era in the life sciences. Niklas Blomberg ELIXIR Director 4 ELXIR Annual Report 2016 ELIXIR Platforms and Use Cases Structure of ELIXIR activities ELIXIR activities are structured according ELIXIR Platforms are built on the real and changing to five Platforms and four Use Cases. needs of established research communities. The four Use Cases drive the work of the ELIXIR Platforms by defining These form the basic units of operation their bioinformatics needs and requirements. This close within ELIXIR, and draw on expertise and collaboration ensures that the services developed by the resources from ELIXIR Nodes. ELIXIR Platforms are fit for purpose. Senior scientists at the ELIXIR Nodes lead each of the The ELIXIR Platforms comprise: Platforms and Use Cases, which are primarily funded by • Data: Sustaining Europe’s life-science the ELIXIR-EXCELERATE project, in which each Platform data infrastructure and Use Case is represented by a Work Package. Additional activities are funded through other grants and through the • Tools: Services and connectors to drive access ELIXIR Hub as Implementation Studies. and exploitation • Interoperability: Supporting the discovery, integration and analysis of biological data • Compute: Storage, compute and authentication/ access services • Training: Professional skills for managing and exploiting data The four Use Cases service domain-specific research communities: • Human data: Developing long-term strategies for managing and accessing sensitive human data • Rare diseases: Supporting the development of new therapies for rare diseases • Marine metagenomics: Developing a sustainable metagenomics infrastructure to nurture research and innovation in marine science • Plant science: Developing an infrastructure to facilitate genotype-phenotype analyses for crop and tree species 6 ELXIR Annual Report 2016 Human data Rare diseases USE CASES Tools Data Compute PLATFORMS Inter- operability Training Marine Plant science metagenomics ELXIR Annual Report 2016 7 Tools Services and connectors for access and exploitation The Tools Platform is working to deliver Benchmarking a discovery portal that collects and curates Bioinformatics methods must be assessed for quantitative computational tools and data services performance and user friendliness to ensure they are fit for purpose. Benchmarking is thus a basic element of the for the life sciences. It is also developing ELIXIR infrastructure. These methods are so diverse in a framework for benchmarking and their design and purpose that it is necessary to abstract the evaluating bioinformatics tools from a scientific benchmark and technical monitoring processes in order to design an effective approach. This is an important scientific and technical perspective. part of the ELIXIR Tools Platform work programme, which is developing guidance and infrastructure for Bio.tools: ELIXIR tools and services registry benchmarking and monitoring bioinformatics tools, web In 2016 the Tools Platform focused on developing content, servers and algorithms. the underlying ontology (EDAM), portal software, In 2016, the Tools Platform mapped the needs of relevant sustainability strategy and applications for the bio.tools stakeholders and selected
Load more

Recommended publications
  • Ismb/Eccb 2015
    Research Collection Journal Article ISMB/ECCB 2015 Author(s): Moreau, Yves; Beerenwinkel, Niko Publication Date: 2015 Permanent Link: https://doi.org/10.3929/ethz-b-000102416 Originally published in: Bioinformatics 31(12), http://doi.org/10.1093/bioinformatics/btv303 Rights / License: Creative Commons Attribution-NonCommercial 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Bioinformatics, 31, 2015, i1–i2 doi: 10.1093/bioinformatics/btv303 ISMB/ECCB 2015 Editorial ISMB/ECCB 2015 This special issue of Bioinformatics serves as the proceedings of the 175 external reviewers recruited as sub-reviewers by program com- joint 23rd annual meeting of Intelligent Systems for Molecular mittee members. Table 1 provides a summary of the areas, area Biology (ISMB) and 14th European Conference on Computational chairs and a review summary by area. The conference used a two- Biology (ECCB), which took place in Dublin, Ireland, July 10–14, tier review system—a continuation and refinement of a process that 2015 (http://www.iscb.org/ismbeccb2015). ISMB/ECCB 2015, the begun with ISMB/ECCB 2013 in an effort to better ensure thorough official conference of the International Society for Computational and fair reviewing. Under the revised process, each of the 241 sub- Biology (ISCB, http://www.iscb.org/), was accompanied by nine missions was first reviewed by at least three expert referees, with a Special Interest Group meetings of 1 or 2 days each, and two satel- subset receiving between four and six reviews, as needed. lite meetings.
    [Show full text]
  • Computational Biology and Bioinformatics
    Vol. 30 ISMB 2014, pages i1–i2 BIOINFORMATICS EDITORIAL doi:10.1093/bioinformatics/btu304 Editorial This special issue of Bioinformatics serves as the proceedings of The conference used a two-tier review system, a continuation the 22nd annual meeting of Intelligent Systems for Molecular and refinement of a process begun with ISMB 2013 in an effort Biology (ISMB), which took place in Boston, MA, July 11–15, to better ensure thorough and fair reviewing. Under the revised 2014 (http://www.iscb.org/ismbeccb2014). The official confer- process, each of the 191 submissions was first reviewed by at least ence of the International Society for Computational Biology three expert referees, with a subset receiving between four and (http://www.iscb.org/), ISMB, was accompanied by 12 Special eight reviews, as needed. These formal reviews were frequently Interest Group meetings of one or two days each, two satellite supplemented by online discussion among reviewers and Area meetings, a High School Teachers Workshop and two half-day Chairs to resolve points of dispute and reach a consensus on tutorials. Since its inception, ISMB has grown to be the largest each paper. Among the 191 submissions, 29 were conditionally international conference in computational biology and bioinfor- accepted for publication directly from the first round review Downloaded from matics. It is expected to be the premiere forum in the field for based on an assessment of the reviewers that the paper was presenting new research results, disseminating methods and tech- clearly above par for the conference. A subset of 16 papers niques and facilitating discussions among leading researchers, were viewed as potentially in the top tier but raised significant practitioners and students in the field.
    [Show full text]
  • A Systematic, Label-Free Method for Identifying RNA-Associated Proteins in Vivo Provides Insights Into Vertebrate Ciliary Beatin
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.966754; this version posted March 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 A systematic, label-free method for identifying RNA- associated proteins in vivo provides insights into vertebrate ciliary beating Kevin Drew*, Chanjae Lee*, Rachael M. Cox, Vy Dang, Caitlin C. Devitt, Ophelia Papoulas, Ryan L. Huizar, Edward M. Marcotte** and John B. Wallingford** Dept. of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78712 *These authors contributed equally **To whom correspondence should be addressed: John Wallingford Patterson Labs 2401 Speedway Austin, Texas 78712 [email protected] 512-232-2784 Edward Marcotte 2500 Speedway, MBB 3.148BA Austin, Texas 78712 [email protected] 512-471-5435 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.966754; this version posted March 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 2 Abstract: Cell-type specific RNA-associated proteins (RAPs) are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RAPs, we currently have few comprehensive rosters of cell-type specific RAPs in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-interacting proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method.
    [Show full text]
  • Trouble with Testosterone Test
    Trouble with testosterone test Annual Meeting Special Section CONTENTS NEWS FEATURES PERSPECTIVES 2 14 36 EDITOR’S NOTE THE TROUBLE WITH PUBLIC AFFAIRS It’s time THE TESTOSTERONE TEST Are postdocs still invisible? 3 18 38 PRESIDENT’S MESSAGE MASTERS OF PHYSIOLOGY MINORITY AFFAIRS Celebrating serendipity 38 Exemplifying Sewer’s commitment to diversity 22 40 Diversifying the scientic 4 THE 2017 ANNUAL MEETING NEWS FROM THE HILL workforce with IMAGE 23 Expand your scientic horizons A lot at stake 42 Cultivating a focus on diversity 29 e spotlight is on you as a community 30 Promoting lifelong learning 5 34 Advance your careers, grad students MEMBER UPDATE 44 and postdocs! TRANSITIONS 35 Reminders for the 2017 ASBMB 7 Undergraduate Poster Competition Wrestling with life RETROSPECTIVE 7 Roscoe Owen Brady (1923–2016) 14 48 9 Roger Tsien (1952–2016) Experts are OPEN CHANNELS grappling with what constitutes 10 high testosterone 42 blood levels in elite NEWS track and eld Blind wins Tabor award women athletes. for work on nuclear lipids 11 JOURNAL NEWS 11 Blocking potato blight’s ability 22 to set up shop 12 Infant gut microbes’ thirst for milk proteins 13 How a single-cell marine organism makes fatty acids 12 44 TRANSITION STATES NOVEMBER 2016 ASBMB TODAY 1 EDITOR’S NOTE THE MEMBER MAGAZINE OF THE AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY It’s time By Angela Hopp OFFICERS COUNCIL MEMBERS Natalie Ahn Squire J. Booker President Victoria J. DeRose Wayne Fairbrother. recently saw a documen- Ben Corb, in his “News Steven McKnight Karen G. Fleming tary on Netix about from the Hill” column, Past President Rachel Green uncontacted tribes in writes about the count- Jennifer DuBois Susan Marqusee I Secretary Jared Rutter the rainforest on the border down to a new American Celia A.
    [Show full text]
  • MICROBIOLOGY Graduate Program
    MICROBIOLOGY Graduate Program Student Handbook 2020-21 THE UNIVERSITY OF TEXAS AT AUSTIN Welcome! .............................................................................................................................................................. 4 Responsibilities of a Microbiology Graduate Student ........................................................................................ 4 The Graduate School ......................................................................................................................................... 4 The College of Natural Sciences (CNS) ............................................................................................................ 5 The Institute for Cell and Molecular Biology (ICMB) ......................................................................................... 5 The Microbiology Graduate Program (MIC) ...................................................................................................... 5 Microbiology Graduate Program Administration ................................................................................................ 6 The Microbiology Graduate Studies Committee (GSC) .................................................................................... 6 Degrees Offered ................................................................................................................................................... 7 Doctor of Philosophy (Ph.D.) ............................................................................................................................
    [Show full text]
  • An Aging-Independent Replicative Lifespan in a Symmetrically Dividing
    TOOLS AND RESOURCES An aging-independent replicative lifespan in a symmetrically dividing eukaryote Eric C Spivey1,2†, Stephen K Jones Jr1,2†, James R Rybarski1, Fatema A Saifuddin1, Ilya J Finkelstein1,2,3* 1Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States; 2Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, United States; 3Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States Abstract The replicative lifespan (RLS) of a cell—defined as the number of cell divisions before death—has informed our understanding of the mechanisms of cellular aging. However, little is known about aging and longevity in symmetrically dividing eukaryotic cells because most prior studies have used budding yeast for RLS studies. Here, we describe a multiplexed fission yeast lifespan micro-dissector (multFYLM) and an associated image processing pipeline for performing high-throughput and automated single-cell micro-dissection. Using the multFYLM, we observe continuous replication of hundreds of individual fission yeast cells for over seventy-five generations. Surprisingly, cells die without the classic hallmarks of cellular aging, such as progressive changes in size, doubling time, or sibling health. Genetic perturbations and drugs can extend the RLS via an aging-independent mechanism. Using a quantitative model to analyze these results, we conclude that fission yeast does not age and that cellular aging and replicative lifespan can be uncoupled in a eukaryotic cell. DOI: 10.7554/eLife.20340.001 *For correspondence: [email protected] †These authors contributed Introduction equally to this work Aging is the progressive decrease of an organism’s fitness over time.
    [Show full text]
  • The International Conference on Intelligent Biology
    The Author(s) BMC Genomics 2017, 18(Suppl 6):703 DOI 10.1186/s12864-017-4018-6 INTRODUCTION Open Access The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics Zhongming Zhao1,2*, Zhandong Liu3, Ken Chen4, Yan Guo5, Genevera I. Allen3,6, Jiajie Zhang7, W. Jim Zheng7 and Jianhua Ruan8* From The International Conference on Intelligent Biology and Medicine (ICIBM) 2016 Houston, TX, USA. 08-10 December 2016 Abstract In this editorial, we first summarize the 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) that was held on December 8–10, 2016 in Houston, Texas, USA, and then briefly introduce the ten research articles included in this supplement issue. ICIBM 2016 included four workshops or tutorials, four keynote lectures, four conference invited talks, eight concurrent scientific sessions and a poster session for 53 accepted abstracts, covering current topics in bioinformatics, systems biology, intelligent computing, and biomedical informatics. Through our call for papers, a total of 77 original manuscripts were submitted to ICIBM 2016. After peer review, 11 articles were selected in this special issue, covering topics such as single cell RNA-seq analysis method, genome sequence and variation analysis, bioinformatics method for vaccine development, and cancer genomics. Introduction more than 150 scientists or trainees across the world with The 2016 International Conference on Intelligent Biology diverse backgrounds and training ranging from biology, and Medicine (ICIBM 2016) was held from December 8th medicine, computer science, bioengineering, bioinformat- to 10th, 2016 in Houston, Texas, USA. This is the fifth ics, statistics, mathematics, and genomics, among others.
    [Show full text]
  • ISMB/ECCB Rebooted: 2015 Brings Major Update to the Meeting Program
    MESSAGE FROM ISCB ISMB/ECCB Rebooted: 2015 Brings Major Update to the Meeting Program Christiana N. Fogg1, Diane E. Kovats2* 1 Freelance Science Writer, Kensington, Maryland, United States of America, 2 International Society for Computational Biology, La Jolla, California, United States of America * [email protected] The 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology (ISMB/ECCB 2015) is shaping up to be a phenomenal meeting, with world-renowned keynote speakers and changes in the meeting format that aim to make it a more streamlined and user-friendly conference. The joint ISMB/ ECCB conference is held biennially and is the flagship meeting of the International Society for Computational Biology (ISCB). The meeting will take place at the Convention Center Dublin, Ireland, from July 10–14, 2015, and will bring together scientists from across the globe working in a broad range of computational biology—related disciplines, including genomics, structural biology, proteomics, data mining, machine learning, and systems biology. Online registration is open until June 26: https://www.iscb.org/ismbeccb2015-registration. In the past, presentations at the meeting have been organized according to tracks, namely, the Proceedings, Highlights, and Late Breaking Research tracks. In 2015, all oral presentations will be presented in broad thematic areas. As in the past, submissions accepted into the highly selective Proceedings track will be published in a special ISMB/ECCB Proceedings issue of Bioinformatics. Conference co-chairs Alex Bateman, Janet Kelso, and Des Higgins and the conference com- mittee undertook the reorganization effort and came up with five thematic areas: Genes, Pro- teins, Systems, Disease, and Data.
    [Show full text]
  • Curriculum Vitae
    Curriculum vitae NAME Martin Kircher BORN 1983 in Erfurt, Germany STUDIES 09/2007 - 07/2011: Dr. rer. nat. (PhD) in Computer Sciences (summa cum laude) at Universität Leipzig, Germany Thesis: Understanding and improving high-throughput sequencing data production and analysis 04/2006 - 07/2007: Master of Science (Honor's Degree) at Saarland University, Germany Computational Molecular Biology Thesis: In silico analysis of microRNA genes on human chr. 14 and mouse chr. 12 10/2003 - 03/2006: Bachelor of Science at Saarland University, Germany Bioinformatics AFFILIATIONS since 04/2012: Jay Shendure, PhD, MD Department of Genome Sciences, University of Washington, Seattle, WA, USA Senior fellow 06/2012 - 11/2015: Center for Mendelian Genomics at the University of Washington, Seattle, WA, USA Lead data analyst 09/2007 - 03/2012: Janet Kelso, PhD & Prof. Dr. Svante Pääbo Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany PhD student (Bioinformatics, Evolutionary Genetics) (09/2007 - 02/2011) Research scientist (Bioinformatics, Evolutionary Genetics) (03/2011 – 03/2012) 05/2007 - 07/2007: Professor Dr. Thomas Lengauer, PhD Max Planck Institute for Informatics, Saarbrücken, Germany Student assistant 09/2006 - 10/2006: Professor Dr. Andreas Zeller Software Engineering Chair, Saarland University, Germany Tutor of practical training in software design 08/2005 - 01/2006: Professor Dr. Hans-Peter Lenhof Center for Bioinformatics, Saarland University, Germany Student assistant VISITS 09/2010 - 11/2010, 11/2009: Dr. Philipp Khaitovich CAS-MPG Partner institute for Computational Biology, Shanghai, China Analysis of Illumina Digital Gene Expression data Consultant for high-throughput sequencing 03/2008: Dr. Dirk Schübeler Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Measuring DNA methylation using MeDIP [email protected] 1/12 Dr.
    [Show full text]
  • Program Book
    The Genetics Society of America Conferences 15th International Xenopus Conference August 24-28, 2014 • Pacific Grove, CA PROGRAM GUIDE LEGEND Information/Guest Check-In Disabled Parking E EV Charging Station V Beverage Vending Machine N S Ice Machine Julia Morgan Historic Building W Roadway Pedestrian Pathway Outdoor Group Activity Area Program and Abstracts Meeting Organizers Carole LaBonne, Northwestern University John Wallingford, University of Texas at Austin Organizing Committee: Julie Baker, Stanford Univ Chris Field, Harvard Medical School Carmen Domingo, San Francisco State Univ Anna Philpott, Univ of Cambridge 9650 Rockville Pike, Bethesda, Maryland 20814-3998 Telephone: (301) 634-7300 • Fax: (301) 634-7079 E-mail: [email protected] • Web site: genetics-gsa.org Thank You to the Following Companies for their Generous Support Platinum Sponsor Gold Sponsors Additional Support Provided by: Carl Zeiss Microscopy, LLC Monterey Convention & Gene Tools, LLC Visitors Bureau Leica Microsystems Xenopus Express 2 Table of Contents General Information ........................................................................................................................... 5 Schedule of Events ............................................................................................................................. 6 Exhibitors ........................................................................................................................................... 8 Opening Session and Plenary/Platform Sessions ............................................................................
    [Show full text]
  • CV Burkhard Rost
    Burkhard Rost CV BURKHARD ROST TUM Informatics/Bioinformatics i12 Boltzmannstrasse 3 (Rm 01.09.052) 85748 Garching/München, Germany & Dept. Biochemistry & Molecular Biophysics Columbia University New York, USA Email [email protected] Tel +49-89-289-17-811 Photo: © Eckert & Heddergott, TUM Web www.rostlab.org Fax +49-89-289-19-414 Document: CV Burkhard Rost TU München Affiliation: Columbia University TOC: • Tabulated curriculum vitae • Grants • List of publications Highlights by numbers: • 186 invited talks in 29 countries (incl. TedX) • 250 publications (187 peer-review, 168 first/last author) • Google Scholar 2016/01: 30,502 citations, h-index=80, i10=179 • PredictProtein 1st Internet server in mol. biol. (since 1992) • 8 years ISCB President (International Society for Computational Biology) • 143 trained (29% female, 50% foreigners from 32 nations on 6 continents) Brief narrative: Burkhard Rost obtained his doctoral degree (Dr. rer. nat.) from the Univ. of Heidelberg (Germany) in the field of theoretical physics. He began his research working on the thermo-dynamical properties of spin glasses and brain-like artificial neural networks. A short project on peace/arms control research sketched a simple, non-intrusive sensor networks to monitor aircraft (1988-1990). He entered the field of molecular biology at the European Molecular Biology Laboratory (EMBL, Heidelberg, Germany, 1990-1995), spent a year at the European Bioinformatics Institute (EBI, Hinxton, Cambridgshire, England, 1995), returned to the EMBL (1996-1998), joined the company LION Biosciences for a brief interim (1998), became faculty in the Medical School of Columbia University in 1998, and joined the TUM Munich to become an Alexander von Humboldt professor in 2009.
    [Show full text]
  • Copyright by Blake Charles Borgeson 2016
    Copyright by Blake Charles Borgeson 2016 The Dissertation Committee for Blake Charles Borgeson certifies that this is the approved version of the following dissertation: All-by-all discovery of conserved protein complexes by deep proteome fractionation Committee: Edward Marcotte, Supervisor Andrew Ellington John Wallingford Claus Wilke Vishwanath Iyer All-by-all discovery of conserved protein complexes by deep proteome fractionation by Blake Charles Borgeson, B.S.E.E. DISSERTATION Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY THE UNIVERSITY OF TEXAS AT AUSTIN December 2016 Dedicated to all those whose life and health we are too late to save. And to my parents, who instilled in me the belief that we can do anything we set our minds to. Acknowledgments I want to thank the numerous people in my life without whom my journey into biology would have been so much less valuable and enjoyable. First, Edward Marcotte has found a way to combine and embody so many of the most wonderful things about science, in particular the boundless curiosity and excitement that draw us to it in the first place. I could not have found a better place to discover how biology, math, and computation can play together to such wonderful ends. I thank my committee members for their understanding, support, and encouragement along my unusual trajectory. I must heartily thank Cedric and Martin for teaching me and inspiring me in this new art of scientific computing and machine learning, and Taejoon, who greatly sped my understanding of mass spectrometry processing and computing on UT’s enormous cluster.
    [Show full text]