DOCSLIB.ORG

2019 ISCB Overton Prize: Christophe Dessimoz[Version 1; Peer Review

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

F1000Research 2019, 8(ISCB Comm J):722 Last updated: 05 AUG 2021 EDITORIAL 2019 ISCB Overton Prize: Christophe Dessimoz [version 1; peer review: not peer reviewed] Diane Kovats 1, Ron Shamir1,2, Christiana Fogg3 1International Society for Computational Biology, Leesburg, USA 2Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel 3Freelance Writer, Kensington, USA v1 First published: 23 May 2019, 8(ISCB Comm J):722 Not Peer Reviewed https://doi.org/10.12688/f1000research.19220.1 Latest published: 23 May 2019, 8(ISCB Comm J):722 https://doi.org/10.12688/f1000research.19220.1 This article is an Editorial and has not been subject to external peer review. Abstract Any comments on the article can be found at the Each year the International Society for Computational Biology (ISCB) end of the article. honors the achievements of an early- to mid-career scientist with the Overton Prize. This prize was instituted in 2001 to honor the untimely loss of Dr. G. Christian Overton, a respected computational biologist and founding member of the ISCB Board of Directors. The Overton Prize recognizes early or mid-career phase scientists who have made significant contributions to computational biology or bioinformatics through their research, teaching, and service. In 2019, ISCB recognized Dr. Christophe Dessimoz, Swiss National Science Foundation (SNSF) Professor at the University of Lausanne, Associate Professor at the University College London, and Group Leader at the Swiss Institute for Bioinformatics. Dessimoz receives his award and is presenting a keynote address at the 2019 Joint Intelligent Systems for Molecular Biology/European Conference on Computational Biology held in Basel, Switzerland on July 21-25, 2019. Keywords ISCB, Christophe Dessimoz, Award This article is included in the International Society for Computational Biology Community Journal gateway. Page 1 of 5 F1000Research 2019, 8(ISCB Comm J):722 Last updated: 05 AUG 2021 Corresponding authors: Diane Kovats ([email protected]), Ron Shamir ([email protected]) Author roles: Kovats D: Writing – Review & Editing; Shamir R: Writing – Review & Editing; Fogg C: Conceptualization, Data Curation, Resources, Validation, Writing – Original Draft Preparation Competing interests: No competing interests were disclosed. Grant information: The International Society for Computational Biology paid for the writing of this article. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2019 Kovats D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite this article: Kovats D, Shamir R and Fogg C. 2019 ISCB Overton Prize: Christophe Dessimoz [version 1; peer review: not peer reviewed] F1000Research 2019, 8(ISCB Comm J):722 https://doi.org/10.12688/f1000research.19220.1 First published: 23 May 2019, 8(ISCB Comm J):722 https://doi.org/10.12688/f1000research.19220.1 Page 2 of 5 F1000Research 2019, 8(ISCB Comm J):722 Last updated: 05 AUG 2021 Christophe Dessimoz: Learning to Stop Resisting Christophe Dessimoz grew up in Switzerland and was deeply drawn to computers from a young age, right around the dawn of the web and widespread internet access. As a teenager, he spent a lot of time programming and developing websites. To avoid spending too much time in front of computers, he decided instead to pursue a first degree in Biology at ETH (Eidgenös- sische Technische Hochschule) Zurich, Switzerland. During and after his studies, he traveled and spent several months doing biology research at Northwestern University in the United States, Tsinghua University in China, and Chulalongkorn University in Thailand. Dessimoz recalled his struggles at the bench and feared he was just too clumsy to pursue a career in biology. He was also still drawn to computers, and he said, “I just stopped resisting,” and returned to ETH Zurich to complete a PhD in Computer Science under the mentorship of Gaston Gonnet. Gonnet had expertise in symbolic and algebraic computation and helped develop a computer algebra system that became a founda- tion of the Maple system. Gonnet also cofounded the New Oxford Christophe Dessimoz English Dictionary Project, which created an electronic version of the Oxford English Dictionary that included a full text searching system. By the early nineties, this expertise in text searching and of Genetics, Evolution & Environment and the Department of string algorithms led him to bioinformatics. Computer Science. He was promoted to Reader in 2015, and he also joined the University of Lausanne (UNIL) as SNSF Dessimoz joined Gonnet’s team in 2004 to purse a PhD research Professor. Dessimoz became a group leader at the Swiss Insti- project in comparative genomics, right at the time when genomes tute of Bioinformatics in 2015, and he continues to maintain his were starting to become routinely available. There was an obvi- UCL and UNIL labs. Beyond his contributions to benchmarking, ous need to compare these genomes, and in particular to identify Dessimoz has made critical contributions to phylogenetics tests the corresponding genes in different species—the orthologs. of sequence alignment accuracy. Despite the decades of work in Dessimoz’s first scientific paper introduced the “Orthologous this area, he said, “We still struggle to assess the correctness of Matrix” (OMA) algorithm. The work provided the foundation alignments.” Dessimoz developed a novel assessment paradigm for the OMA database, which he kept working on ever since and based on the plausibility of trees reconstructed from inferred which has become a well-regarded resource. alignments, and through this work, he showed that the common practice of inferring trees from “high-confidence” alignment After completing his PhD and working as a teaching faculty columns only is counterproductive. Dessimoz has also made member and senior research associate at ETH Zurich, Dessimoz valuable contributions to methods used for Gene Ontology (GO) received a fellowship from the Swiss National Science Founda- annotation, particularly with the development of a technique tion (SNSF) to be a visiting scientist at the European Molecular using historical time series to track the fate of inferred annota- Biology Laboratory (EMBL)-European Bioinformatics Insti- tions over time. This approach has changed the way the GO tute (EBI) in Hinxton, UK. He joined Nick Goldman’s group consortium tracks annotation quality and has been adapted for to collaborate on large-scale phylogenetic methods. During other projects. Dessimoz continues to be drawn to research his stint at EBI, Dessimoz became increasingly interested in focused on evolutionary biology and orthology inference, and he benchmarking and developed an appreciation for this often also fascinated by the challenges of handling huge heterogeneous overlooked but critical methodological process. This interest is datasets. exemplified in his leadership role in the Quest for Orthologs Consortium, a community effort to improve orthology meth- Outside of the lab, Dessimoz has served the computational ods and their applications. Together with Adrian Altenhoff, biology community in many capacities, including service on his close associate since their days in Gonnet’s lab, Dessimoz multiple editorial and advisory boards and conference commit- developed a more direct approach to benchmarking orthology tees. Dessimoz’s groundbreaking research has been recognized inference methods based on congruence tests between genes by several other awards, including the 2017 Sentinel of Sci- and species trees, which has become a definitive method for ence Award, 2016 (European Molecular Biology Organization) orthology benchmarking. He has continued to advocate for the EMBO Young Investigator, 2015 Google Faculty Research importance of benchmarking and standardization for progress Award, and 2012 Swiss Institute of Bioinformatics (SIB) Early in bioinformatics. Career Bioinformatician Award. Dessimoz feels deeply hon- ored by his selection as the 2019 Overton Prize winner, and he In 2013, Dessimoz moved to University College London as a acknowledges that the support and relative independence that Lecturer and held a joint appointment between the Department his mentors gave, as well as the productive partnerships with his Page 3 of 5 F1000Research 2019, 8(ISCB Comm J):722 Last updated: 05 AUG 2021 staff, trainees and collaborators have been instrumental to his success as an independent investigator. Grant information The International Society for Computational Biology paid for the writing of this article. Data availability Underlying data The funders had no role in study design, data collection and No data are associated with this article analysis, decision to publish, or preparation of the manuscript. Page 4 of 5 F1000Research 2019, 8(ISCB Comm J):722 Last updated: 05 AUG 2021 The benefits of publishing with F1000Research: • Your article is published within days, with no editorial bias • You can publish traditional articles, null/negative results, case reports, data notes and more • The peer review process is transparent and collaborative • Your article is indexed in PubMed after passing peer review • Dedicated customer support at every stage For pre-submission enquiries, contact [email protected] Page 5 of 5.
Recommended publications
  • Applied Category Theory for Genomics – an Initiative

    Applied Category Theory for Genomics – an Initiative

    Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4].
  • Department of Computer Science

    Department of Computer Science

    Department of Computer Science Content Research Overview of the Computer Science Department This brochure gives an overview of the ongoing research activities at the Department of Computer Science of ETH Zurich. It is a collection of the two-page research summaries given by every professor of the Department. The following pages are in alphabetical order of the names of the professors. Gustavo Alonso Information and Communication Systems Research Group Armin Biere Formal Methods for Solving Complexity and Quality Problems Walter Gander From Numerical Analysis to Scientific Computing Gaston Gonnet Computational Biochemistry and Computer Algebra Markus Gross Computer Graphics Laboratory Thomas Gross Laboratory for Software Technology Jürg Gutknecht Program Languages and Runtime Systems Petros Koumoutsakos Computational Sciences Friedemann Mattern Ubiquitous Computing Infrastructures Ueli Maurer Information Security and Cryptography Bertrand Meyer Chair of Software Engineering Kai Nagel Modeling and Simulation Jürg Nievergelt Algorithms, Data Structures, and Applications Moira Norrie Constructing Global Information Spaces Hans-Jörg Schek Realizing the Hyperdatabase Vision Bernt Schiele Perceptual Computing and Computer Vision Robert Stärk Computational Logic Thomas Stricker Parallel- and Distributed Systems Group Roger Wattenhofer Distributed Computing Group Emo Welzl Theory of Combinatorial Algorithms Peter Widmayer Algorithms, Data Structures, and Applications Carl August Zehnder Development and Application Group The most up-to-date research summaries can be found under Û research in the Web presentation of the Department. This version is as of June 12, 2002. Information and Communication Systems Research Group Information Systems Prof. Gustavo Alonso http://www.inf.ethz.ch/department/IS/iks/ [email protected] Figure 1 to 4 BiOpera, a develop- ment and run time environment for cluster and grid computing The motivation behind our research uted at a large scale and heterogeneous.
  • UNIVERSITY of CALIFORNIA SAN DIEGO Making Sense of Microbial

    UNIVERSITY of CALIFORNIA SAN DIEGO Making Sense of Microbial

    UNIVERSITY OF CALIFORNIA SAN DIEGO Making sense of microbial populations from representative samples A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by James T. Morton Committee in charge: Professor Rob Knight, Chair Professor Pieter Dorrestein Professor Rachel Dutton Professor Yoav Freund Professor Siavash Mirarab 2018 Copyright James T. Morton, 2018 All rights reserved. The dissertation of James T. Morton is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2018 iii DEDICATION To my friends and family who paved the road and lit the journey. iv EPIGRAPH The ‘paradox’ is only a conflict between reality and your feeling of what reality ‘ought to be’ —Richard Feynman v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . .v Table of Contents . vi List of Abbreviations . ix List of Figures . .x List of Tables . xi Acknowledgements . xii Vita ............................................. xiv Abstract of the Dissertation . xvii Chapter 1 Methods for phylogenetic analysis of microbiome data . .1 1.1 Introduction . .2 1.2 Phylogenetic Inference . .4 1.3 Phylogenetic Comparative Methods . .6 1.4 Ancestral State Reconstruction . .9 1.5 Analysis of phylogenetic variables . 11 1.6 Using Phylogeny-Aware Distances . 15 1.7 Challenges of phylogenetic analysis . 18 1.8 Discussion . 19 1.9 Acknowledgements . 21 Chapter 2 Uncovering the horseshoe effect in microbial analyses . 23 2.1 Introduction . 24 2.2 Materials and Methods . 34 2.3 Acknowledgements . 35 Chapter 3 Balance trees reveal microbial niche differentiation . 36 3.1 Introduction .
  • A Phylogenomic Study of Human, Dog, and Mouse

    A Phylogenomic Study of Human, Dog, and Mouse

    A Phylogenomic Study of Human, Dog, and Mouse Gina Cannarozzi, Adrian Schneider, Gaston Gonnet* Institute of Computational Science, ETH Zurich, Zurich, Switzerland In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria—distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate–carnivore clade with the exclusion of rodents. Citation: Cannarozzi G, Schneider A, Gonnet G (2007) A phylogenomic study of human, dog, and mouse. PLoS Comput Biol 3(1): e2. doi:10.1371/journal.pcbi.0030002 Introduction Long branch attraction (LBA) may occur when an ingroup has a faster rate of evolution, thereby promoting migration of A correct interpretation of the direction of evolution in the long branch with accelerated evolution toward the long basal parts of the mammalian tree has important implications branch of the outgroup.
  • Fundamentación De La Propuesta De Otorgar El T´Itulo De Doctor Honoris Causa De La Facultad De Ingenier´Ia Al Dr. Gaston Go

    Fundamentación De La Propuesta De Otorgar El T´Itulo De Doctor Honoris Causa De La Facultad De Ingenier´Ia Al Dr. Gaston Go

    Fundamentaci´onde la propuesta de otorgar el t´ıtulode Doctor Honoris Causa de la Facultad de Ingenier´ıaal Dr. Gaston Gonnet. Gaston Henry Gonnet naci´oen Uruguay en setiembre de 1948. En 1968, habiendo concluido sus estudios secundarios, ingres´ocomo do- cente al reci´encreado CECUR (Centro de Computaci´onde la Universidad de la Rep´ublica).Al mismo tiempo, fue estudiante de la nueva carrera de Computador Universitario, habi´endosegraduado en agosto de 1973. A pesar de su juventud, Gonnet ya ten´ıacontacto con las grandes compu- tadoras de esa ´epoca gracias a su trabajo en la empresa IBM en Uruguay. Poco tiempo despu´esde la intervenci´onde la UDELAR en 1973, Gonnet se radic´oen Canad´a. En 1977, se doctor´oen la Universidad de Waterloo transform´andose r´api- damente en un cient´ıficodestacado internacionalmente en el ´areade Algorit- mos y Computabilidad. En 1980, Gonnet co-fund´oel Grupo de Computaci´onSimb´olicaen la Uni- versidad de Waterloo. De ese grupo surgi´oel proyecto Maple, que produjo el conocido Sistema de Algebra Computacional de amplio uso en el ´ambito cient´ıfico-tecnol´ogico.En 2011, Gaston Gonnet y Keith Geddes recibieron el Premio ACM Richard Jenks a la Excelencia en Ingenier´ıade Software apli- cada al Algebra Computacional en el Proyecto Maple. En 1984, Gonnet fue uno de los miembros fundadores del proyecto New Oxford English Dictionary. Este proyecto permiti´ocrear la primer versi´on electr´onicadel Oxford English Dictionary. En 1985, utiliz´osu a~nosab´aticopara retornar al Uruguay y ayudar al Instituto de Computaci´onen su reconstrucci´onluego de la dictadura.
  • Standardised Benchmarking in the Quest for Orthologs

    Standardised Benchmarking in the Quest for Orthologs

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Standardised Benchmarking in the Quest for Orthologs The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Altenhoff, A. M., B. Boeckmann, S. Capella-Gutierrez, D. A. Dalquen, T. DeLuca, K. Forslund, J. Huerta-Cepas, et al. 2016. “Standardised Benchmarking in the Quest for Orthologs.” Nature methods 13 (5): 425-430. doi:10.1038/nmeth.3830. http://dx.doi.org/10.1038/ nmeth.3830. Published Version doi:10.1038/nmeth.3830 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:29408292 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Methods Manuscript Author . Author manuscript; Manuscript Author available in PMC 2016 October 04. Published in final edited form as: Nat Methods. 2016 May ; 13(5): 425–430. doi:10.1038/nmeth.3830. Standardised Benchmarking in the Quest for Orthologs Adrian M. Altenhoff1,2, Brigitte Boeckmann3, Salvador Capella-Gutierrez4,5,6, Daniel A. Dalquen7, Todd DeLuca8, Kristoffer Forslund9, Jaime Huerta-Cepas9, Benjamin Linard10, Cécile Pereira11,12, Leszek P. Pryszcz4, Fabian Schreiber13, Alan Sousa da Silva13, Damian Szklarczyk14,15, Clément-Marie Train1, Peer Bork9,16,17, Odile Lecompte18, Christian von Mering14,15, Ioannis Xenarios3,19,20, Kimmen Sjölander21, Lars Juhl Jensen22, Maria J.
  • Multiscale Modeling in Systems Biology

    Multiscale Modeling in Systems Biology

    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2051 Multiscale Modeling in Systems Biology Methods and Perspectives ADRIEN COULIER ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1225-5 UPPSALA URN urn:nbn:se:uu:diva-442412 2021 Dissertation presented at Uppsala University to be publicly examined in 2446 ITC, Lägerhyddsvägen 2, Uppsala, Friday, 10 September 2021 at 10:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Mark Chaplain (University of St Andrews). Abstract Coulier, A. 2021. Multiscale Modeling in Systems Biology. Methods and Perspectives. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2051. 60 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1225-5. In the last decades, mathematical and computational models have become ubiquitous to the field of systems biology. Specifically, the multiscale nature of biological processes makes the design and simulation of such models challenging. In this thesis we offer a perspective on available methods to study and simulate such models and how they can be combined to handle biological processes evolving at different scales. The contribution of this thesis is threefold. First, we introduce Orchestral, a multiscale modular framework to simulate multicellular models. By decoupling intracellular chemical kinetics, cell-cell signaling, and cellular mechanics by means of operator-splitting, it is able to combine existing software into one massively parallel simulation. Its modular structure makes it easy to replace its components, e.g. to adjust the level of modeling details. We demonstrate the scalability of our framework on both high performance clusters and in a cloud environment.
  • OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements

    OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements

    OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, and Gaston H. Gonnet ETH Zurich, Institute of Computational Science, CH-8092 Z¨urich [email protected] Abstract. The OMA project is a large-scale effort to identify groups of orthologs from complete genome data, currently 150 species. The algo- rithm relies solely on protein sequence information and does not require any human supervision. It has several original features, in particular a verification step that detects paralogs and prevents them from being clustered together. Consistency checks and verification are performed throughout the process. The resulting groups, whenever a comparison could be made, are highly consistent both with EC assignments, and with assignments from the manually curated database HAMAP. A highly ac- curate set of orthologous sequences constitutes the basis for several other investigations, including phylogenetic analysis and protein classification. Complete genomes give scientists a valuable resource to assign functions to se- quences and to analyze their evolutionary history. These analyses rely heavily on gene comparison through sequence alignment algorithms that output the level of similarity, which gives an indication of homology. When homologous sequences are of interest, care must often be taken to distinguish between orthologous and paralogous proteins [1]. Both orthologs and paralogs come from the same ancestral sequence, and therefore are homologous, but they differ in the way they arise: paralogous se- quences are the product of gene duplication, while orthologous sequences are the product of speciation.
  • REST API and the Packages for R and Python Omadb

    REST API and the Packages for R and Python Omadb

    F1000Research 2019, 8:42 Last updated: 12 APR 2019 SOFTWARE TOOL ARTICLE Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved] Klara Kaleb1, Alex Warwick Vesztrocy 1,2, Adrian Altenhoff 2,3, Christophe Dessimoz 1,2,4-6 1Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK 2Swiss Institute of Bioinformatics, Lausanne, Switzerland 3Department of Computer Science, ETH Zurich, Zurich, Switzerland 4Department of Computer Science, University College London, London, WC1E 6BT, Switzerland 5Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland 6Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland First published: 10 Jan 2019, 8:42 ( Open Peer Review v2 https://doi.org/10.12688/f1000research.17548.1) Latest published: 29 Mar 2019, 8:42 ( https://doi.org/10.12688/f1000research.17548.2) Referee Status: Abstract Invited Referees The Orthologous Matrix (OMA) is a well-established resource to identify 1 2 orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly R and Python packages called OmaDB. These should further facilitate the incorporation of version 2 report report OMA data into computational scripts and pipelines. The REST API can be published freely accessed at https://omabrowser.org/api. The R OmaDB package is 29 Mar 2019 available as part of Bioconductor at http://bioconductor.org/packages/OmaDB/, and the omadb Python package is available from the Python Package Index version 1 (PyPI) at https://pypi.org/project/omadb/.
  • Daniel Aalberts Scott Aa

    Daniel Aalberts Scott Aa

    PLOS Computational Biology would like to thank all those who reviewed on behalf of the journal in 2015: Daniel Aalberts Jeff Alstott Benjamin Audit Scott Aaronson Christian Althaus Charles Auffray Henry Abarbanel Benjamin Althouse Jean-Christophe Augustin James Abbas Russ Altman Robert Austin Craig Abbey Eduardo Altmann Bruno Averbeck Hermann Aberle Philipp Altrock Ferhat Ay Robert Abramovitch Vikram Alva Nihat Ay Josep Abril Francisco Alvarez-Leefmans Francisco Azuaje Luigi Acerbi Rommie Amaro Marc Baaden Orlando Acevedo Ettore Ambrosini M. Madan Babu Christoph Adami Bagrat Amirikian Mohan Babu Frederick Adler Uri Amit Marco Bacci Boris Adryan Alexander Anderson Stephen Baccus Tinri Aegerter-Wilmsen Noemi Andor Omar Bagasra Vera Afreixo Isabelle Andre Marc Baguelin Ashutosh Agarwal R. David Andrew Timothy Bailey Ira Agrawal Steven Andrews Wyeth Bair Jacobo Aguirre Ioan Andricioaei Chris Bakal Alaa Ahmed Ioannis Androulakis Joseph Bak-Coleman Hasan Ahmed Iris Antes Adam Baker Natalie Ahn Maciek Antoniewicz Douglas Bakkum Thomas Akam Haroon Anwar Gabor Balazsi Ilya Akberdin Stefano Anzellotti Nilesh Banavali Eyal Akiva Miguel Aon Rahul Banerjee Sahar Akram Lucy Aplin Edward Banigan Tomas Alarcon Kevin Aquino Martin Banks Larissa Albantakis Leonardo Arbiza Mukul Bansal Reka Albert Murat Arcak Shweta Bansal Martí Aldea Gil Ariel Wolfgang Banzhaf Bree Aldridge Nimalan Arinaminpathy Lei Bao Helen Alexander Jeffrey Arle Gyorgy Barabas Alexander Alexeev Alain Arneodo Omri Barak Leonidas Alexopoulos Markus Arnoldini Matteo Barberis Emil Alexov
  • 1. Introduction

    1. Introduction

    Reviews in Computational Biology 1. Introduction ! Christophe Dessimoz and James Smith January 2012 1 Today Course introduction Review writing 2 About Christophe • Diploma in Biology • PhD in Computer Science • Now: Visiting Scientist at EBI • Relevant experience: ~25 research articles ~50 peer-reviews for 14 journals ~15 funding proposals Guest editor of Briefings in Bioinformatics 3 - ETH Zurich, Northwestern, Tsinghua University, Chulalongkorn (Bangkok) About James • Biological Sciences & Pathway Biochemistry • PhD in Comp. Pharmacology (Drug Design) • Now: Scientist in Comp. Biochemistry • Previous experience: Research Fellow in Comp. Systems Biology ~20 research articles ~20 peer-reviews for 8 journals 12 funding proposals (myself & students) Experience as a technical editor 4 - BSc(Hons) Biological Sciences (Leicester) – halfway into a DPhil Biochemistry (Oxford) was lured to Pharmacology in Cambridge on an industrial scholarship, so jumped :-) – collaborations with universities/institutes in the USA, UK, Germany (inc EMBL), France and some pharmaceutical companies. What is doctoral training? • Mechanism for interdisciplinary research eg. at the interface between life and physical/computational sciences • CCBI http://en.wikipedia.org/wiki/Doctoral_Training_Centredoesn't have a DTC so we are piloting this course module 5 What is a Academic Training & Transferable Skills Course? Doctoral training has been around in diferent forms other European countries In the UK, doctoral training is a strategic mechanism for interdisciplinary research at the interface between the life and physical sciences or between disciplines DTC modules are conventionally for 1st/2nd years of a 3 or 4-year programme that augment the background of interdisciplinary projects and help researchers interact in new domains. They act as bridges between disciplines.
  • Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by Pickeringhutchins Ltd

    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: