2019 IMAC Report
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Gene Prediction: the End of the Beginning Comment Colin Semple
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central http://genomebiology.com/2000/1/2/reports/4012.1 Meeting report Gene prediction: the end of the beginning comment Colin Semple Address: Department of Medical Sciences, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK. E-mail: [email protected] Published: 28 July 2000 reviews Genome Biology 2000, 1(2):reports4012.1–4012.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2000/1/2/reports/4012 © GenomeBiology.com (Print ISSN 1465-6906; Online ISSN 1465-6914) Reducing genomes to genes reports A report from the conference entitled Genome Based Gene All ab initio gene prediction programs have to balance sensi- Structure Determination, Hinxton, UK, 1-2 June, 2000, tivity against accuracy. It is often only possible to detect all organised by the European Bioinformatics Institute (EBI). the real exons present in a sequence at the expense of detect- ing many false ones. Alternatively, one may accept only pre- dictions scoring above a more stringent threshold but lose The draft sequence of the human genome will become avail- those real exons that have lower scores. The trick is to try and able later this year. For some time now it has been accepted increase accuracy without any large loss of sensitivity; this deposited research that this will mark a beginning rather than an end. A vast can be done by comparing the prediction with additional, amount of work will remain to be done, from detailing independent evidence. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Exploring the Structure and Function Paradigm Oliver C Redfern, Benoit Dessailly and Christine a Orengo
Available online at www.sciencedirect.com Exploring the structure and function paradigm Oliver C Redfern, Benoit Dessailly and Christine A Orengo Advances in protein structure determination, led by the Figure 1 shows that as the international genomics initiat- structural genomics initiatives have increased the proportion of ives gather pace, both the number of sequences and novel folds deposited in the Protein Data Bank. However, these protein families are still growing at an exponential rate, structures are often not accompanied by functional annotations although the rate of expansion of protein families is with experimental confirmation. In this review, we reassess the substantially less. This trend is also observed among meaning of structural novelty and examine its relevance domain families, which are 10-fold fewer (<10 000) than to the complexity of the structure-function paradigm. the number of protein families. By targeting these, the Recent advances in the prediction of protein function from structural genomics initiatives can aim to characterise the structure are discussed, as well as new sequence-based major building blocks of whole proteins and since these methods for partitioning large, diverse superfamilies into domains recur in different combination in the genomes, it biologically meaningful clusters. Obtaining structural data for will be an important step towards understanding the these functionally coherent groups of proteins will allow us to complete structural repertoire in nature. Furthermore, better understand the relationship between structure and the complement of molecular functions found within function. an organism is likely to be even fewer. For example, 97% of proteins in yeast can be assigned one or more of Address 4000 unique GO terms. -
EMBO Facts & Figures
excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology. -
Download Final Programme
Session Overview Saturday 17 September 2011 11:15 - 13:15 Arrival and Registration ATC Main Entrance 13:15 - 13:30 Welcome and Opening Remarks Klaus Tschira Auditorium 13:30 - 18:00 Session 1: Somatic Genetics I Chaired by David Tuveson and Ewan Birney Klaus Tschira Auditorium 18:00 - 19:00 Keynote Lecture: Lynda Chin Klaus Tschira Auditorium 19:00 - 20:30 Dinner ATC Canteen Sunday 18 September 2011 09:00 - 12:30 Session 2: Somatic Genetics II / Epigenetics Chaired by James R. Downing Klaus Tschira Auditorium 12:30 - 14:30 Poster Session I and Lunch ATC Foyer and Helix A 14:30 - 18:30 Session 3: Mouse Genetics Chaired by Lynda Chin Klaus Tschira Auditorium 18:30 - 23:00 Gala Dinner and Live Music ATC Canteen and ATC Rooftop Lounge Page 1 EMBO|EMBL Symposium: Cancer Genomics Monday 19 September 2011 09:00 - 13:00 Session 4: Computational Chaired by Peter Lichter Klaus Tschira Auditorium 13:00 - 15:00 Poster Session II and Lunch ATC Foyer and Helix A 15:00 - 16:00 Session 5: Somatic Genetics III Chaired by Andy Futreal Klaus Tschira Auditorium 16:00 - 17:00 Keynote Lecture: Michael Stratton Klaus Tschira Auditorium 17:00 - 17:15 Closing Remarks and Poster Prize Klaus Tschira Auditorium Page 2 Programme Saturday 17 September 2011 11:15 - 13:15 Arrival and Registration ATC Main Entrance 13:15 - 13:30 Welcome and Opening Remarks Klaus Tschira Auditorium 13:30 - 18:00 Session 1: Somatic Genetics I Chaired by David Tuveson and Ewan Birney Klaus Tschira Auditorium 13:30 - 14:00 Somatic genomic alterations in chronic lymphocytic 1 leukemia Elias -
Phenotype Inference in an Escherichia Coli Strain Panel
TOOLS AND RESOURCES Phenotype inference in an Escherichia coli strain panel Marco Galardini1, Alexandra Koumoutsi2, Lucia Herrera-Dominguez2, Juan Antonio Cordero Varela1, Anja Telzerow2, Omar Wagih1, Morgane Wartel2, Olivier Clermont3,4, Erick Denamur3,4,5, Athanasios Typas2*, Pedro Beltrao1* 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Hinxton, United Kingdom; 2Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; 3INSERM, IAME, UMR1137, Paris, France; 4Universite´ Paris Diderot, Paris, France; 5APHP, Hoˆpitaux Universitaires Paris Nord Val-de-Seine, Paris, France Abstract Understanding how genetic variation contributes to phenotypic differences is a fundamental question in biology. Combining high-throughput gene function assays with mechanistic models of the impact of genetic variants is a promising alternative to genome-wide association studies. Here we have assembled a large panel of 696 Escherichia coli strains, which we have genotyped and measured their phenotypic profile across 214 growth conditions. We integrated variant effect predictors to derive gene-level probabilities of loss of function for every gene across all strains. Finally, we combined these probabilities with information on conditional gene essentiality in the reference K-12 strain to compute the growth defects of each strain. Not only could we reliably predict these defects in up to 38% of tested conditions, but we could also directly identify the causal variants that were validated through complementation assays. Our work demonstrates the power of forward predictive models and the possibility of precision genetic interventions. DOI: https://doi.org/10.7554/eLife.31035.001 *For correspondence: [email protected] (AT); [email protected] (PB) Introduction Competing interests: The Understanding the genetic and molecular basis of phenotypic differences among individuals is a authors declare that no long-standing problem in biology. -
Molecular Genetics & Genomics
page 46 Lab Times 5-2010 Ranking Illustration: Christina Ullman Publication Analysis 1997-2008 Molecular Genetics & Genomics Under the premise of a “narrow” definition of the field, Germany and England co-dominated European molecular genetics/genomics. The most frequently citated sub-fields were bioinformatical genomics, epigenetics, RNA biology and DNA repair. irst of all, a little science history (you’ll soon see why). As and expression. That’s where so-called computational biology is well known, in the 1950s genetics went molecular – and and systems biology enter research into basic genetic problems. Fdid not just become molecular genetics but rather molec- Given that development, it is not easy to answer the question ular bio logy. In 1963, however, Sydney Brenner wrote in his fa- what “molecular genetics & genomics” today actually is – and, mous letter to Max Perutz: “[...] I have long felt that the future of in particular, what is it in the context of our publication analy- molecular biology lies in the extension of research to other fields sis of the field? It is obvious that, as for example science historian of biology, notably development and the nervous system.” He Robert Olby put it, a “wide” definition can be distinguished from appeared not to be alone with this view and, as a consequence, a “narrow” definition of the field. The wide definition includes along with Brenner many of the leading molecular biologists all fields, into which molecular biology has entered as an exper- from the classical period redirected their research agendas, utilis- imental and theoretical paradigm. The “narrow” definition, on ing the newly developed molecular techniques to investigate un- the other hand, still tries to maintain the status as an explicit bio- solved problems in other fields. -
Statistical and Computational Methods for Analyzing High-Throughout Genomic Data
Statistical and Computational Methods for Analyzing High-Throughout Genomic Data by Jingyi Li A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Biostatistics and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Peter J. Bickel, Chair Professor Haiyan Huang Professor Sandrine Dudoit Professor Steven E. Brenner Spring 2013 Statistical and Computational Methods for Analyzing High-Throughput Genomic Data Copyright 2013 by Jingyi Li 1 Abstract Statistical and Computational Methods for Analyzing High-Throughput Genomic Data by Jingyi Li Doctor of Philosophy in Biostatistics and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Professor Peter J. Bickel, Chair In the burgeoning field of genomics, high-throughput technologies (e.g. microarrays, next-generation sequencing and label-free mass spectrometry) have enabled biologists to perform global analysis on thousands of genes, mRNAs and proteins simultaneously. Ex- tracting useful information from enormous amounts of high-throughput genomic data is an increasingly pressing challenge to statistical and computational science. In this thesis, I will address three problems in which statistical and computational methods were used to analyze high-throughput genomic data to answer important biological questions. The first part of this thesis focuses on addressing an important question in genomics: how to identify and quantify mRNA products of gene transcription (i.e., isoforms) from next- generation mRNA sequencing (RNA-Seq) data? We developed a statistical method called Sparse Linear modeling of RNA-Seq data for Isoform Discovery and abundance Estimation (SLIDE) that employs probabilistic modeling and L1 sparse estimation to answer this ques- tion. -
Janet Thornton Ing for Future Research Needs
THIS MONTH are dedicated to developing and maintaining services THE AUTHOR FILE for the scientific community, including databases such as the genome portal Ensembl, the proteomic data- base UniProt and more, all of which requires strategiz- Janet Thornton ing for future research needs. “These resources don’t Finding ways to navigate the reactions happen overnight; they’re big teams and they have to of life and herd tigers are all part of her think carefully,” she says. workday. Fostering collaborative science internally and across organizational and national boundaries such as for The wealth of available sequenced genomes invites sci- the project ELIXIR—the European life sciences infra- entists to explore the molecular basis of life, to browse structure for biological information, a pan-European and parse the beautiful infrastructure she has spearheaded to help scientists complexity of this now share data—is hard work, especially in times of fiscal “open book,” says Janet belt-tightening. At times, Thornton says, the task can Thornton. feel more like “herding tigers” than cats. A physicist turned Overall she sees the role of computational biology computational shifting, she says. In physics, work by experimentalists biologist, Thornton led to theoretical lines of inquiry. Biology is in its data- directs the European gathering stage, and rapidly moving toward the ability Bioinformatics to model processes such as the effect of a drug on the Institute (EBI), where human body. “We’re only a fraction of the way towards she has cultivated being able to do that,” she says, but she believes the EBI interdisciplinary EBI’s resources help to create the “bedrock” for this teamwork since 2001. -
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: -
I S C B N E W S L E T T
ISCB NEWSLETTER FOCUS ISSUE {contents} President’s Letter 2 Member Involvement Encouraged Register for ISMB 2002 3 Registration and Tutorial Update Host ISMB 2004 or 2005 3 David Baker 4 2002 Overton Prize Recipient Overton Endowment 4 ISMB 2002 Committees 4 ISMB 2002 Opportunities 5 Sponsor and Exhibitor Benefits Best Paper Award by SGI 5 ISMB 2002 SIGs 6 New Program for 2002 ISMB Goes Down Under 7 Planning Underway for 2003 Hot Jobs! Top Companies! 8 ISMB 2002 Job Fair ISCB Board Nominations 8 Bioinformatics Pioneers 9 ISMB 2002 Keynote Speakers Invited Editorial 10 Anna Tramontano: Bioinformatics in Europe Software Recommendations11 ISCB Software Statement volume 5. issue 2. summer 2002 Community Development 12 ISCB’s Regional Affiliates Program ISCB Staff Introduction 12 Fellowship Recipients 13 Awardees at RECOMB 2002 Events and Opportunities 14 Bioinformatics events world wide INTERNATIONAL SOCIETY FOR COMPUTATIONAL BIOLOGY A NOTE FROM ISCB PRESIDENT This newsletter is packed with information on development and dissemination of bioinfor- the ISMB2002 conference. With over 200 matics. Issues arise from recommendations paper submissions and over 500 poster submis- made by the Society’s committees, Board of sions, the conference promises to be a scientific Directors, and membership at large. Important feast. On behalf of the ISCB’s Directors, staff, issues are defined as motions and are discussed EXECUTIVE COMMITTEE and membership, I would like to thank the by the Board of Directors on a bi-monthly Philip E. Bourne, Ph.D., President organizing committee, local organizing com- teleconference. Motions that pass are enacted Michael Gribskov, Ph.D., mittee, and program committee for their hard by the Executive Committee which also serves Vice President work preparing for the conference.