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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. -
Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I
EMBL-European Bioinformatics Institute Annual Scientific Report 2013 On the cover Structure 3fof in the Protein Data Bank, determined by Laponogov, I. et al. (2009) Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nature Structural & Molecular Biology 16, 667-669. © 2014 European Molecular Biology Laboratory This publication was produced by the External Relations team at the European Bioinformatics Institute (EMBL-EBI) A digital version of the brochure can be found at www.ebi.ac.uk/about/brochures For more information about EMBL-EBI please contact: [email protected] Contents Introduction & overview 3 Services 8 Genes, genomes and variation 8 Molecular atlas 12 Proteins and protein families 14 Molecular and cellular structures 18 Chemical biology 20 Molecular systems 22 Cross-domain tools and resources 24 Research 26 Support 32 ELIXIR 36 Facts and figures 38 Funding & resource allocation 38 Growth of core resources 40 Collaborations 42 Our staff in 2013 44 Scientific advisory committees 46 Major database collaborations 50 Publications 52 Organisation of EMBL-EBI leadership 61 2013 EMBL-EBI Annual Scientific Report 1 Foreword Welcome to EMBL-EBI’s 2013 Annual Scientific Report. Here we look back on our major achievements during the year, reflecting on the delivery of our world-class services, research, training, industry collaboration and European coordination of life-science data. The past year has been one full of exciting changes, both scientifically and organisationally. We unveiled a new website that helps users explore our resources more seamlessly, saw the publication of ground-breaking work in data storage and synthetic biology, joined the global alliance for global health, built important new relationships with our partners in industry and celebrated the launch of ELIXIR. -
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 -
The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data Hinxton, Cambridge, UK, 19–20 October 2002
Comparative and Functional Genomics Comp Funct Genom 2003; 4: 16–19. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.232 Feature Meeting Review: The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data Hinxton, Cambridge, UK, 19–20 October 2002 Sandra Orchard, Paul Kersey, Henning Hermjakob* and Rolf Apweiler EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK *Correspondence to: Abstract Henning Hermjakob, EMBL Outstation–European The Proteomics Standards Initiative (PSI) aims to define community standards Bioinformatics Institute, for data representation in proteomics and to facilitate data comparison, exchange Wellcome Trust Genome and verification. Initially the fields of protein–protein interactions (PPI) and mass Campus, Hinxton, Cambridge, spectroscopy have been targeted and the inaugural meeting of the PSI addressed the UK. questions of data storage and exchange in both of these areas. The PPI group rapidly E-mail: reached consensus as to the minimum requirements for a data exchange model; an [email protected] XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to Received: 14 November 2002 advance both these projects. Copyright 2003 John Wiley & Sons, Ltd. Accepted: 14 November 2002 Keywords: proteomics; spectroscopy; protein–protein interactions Introduction process, before splitting into two working parties to address the issues facing their respective fields. The Proteomics Standards Initiative was estab- lished following a meeting in April 2002, jointly organized by HUPO and NAS, at which the urgent Protein–protein interactions (PPI) group need for standardization of proteomics data was recognized. -
The European Bioinformatics Institute in 2020: Building a Global Infrastructure of Interconnected Data Resources for the Life Sciences Charles E
Published online 8 November 2019 Nucleic Acids Research, 2020, Vol. 48, Database issue D17–D23 doi: 10.1093/nar/gkz1033 The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences Charles E. Cook *, Oana Stroe, Guy Cochrane ,EwanBirney and Rolf Apweiler European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received September 21, 2019; Revised October 18, 2019; Editorial Decision October 21, 2019; Accepted November 06, 2019 ABSTRACT ature. EMBL-EBI’s data resources collate, integrate, curate and make freely available to the public the world’s scientific Data resources at the European Bioinformatics In- data. stitute (EMBL-EBI, https://www.ebi.ac.uk/)archive, Our resources (www.ebi.ac.uk/services) include archival organize and provide added-value analysis of re- or deposition databases that store primary experimental search data produced around the world. This year’s data submitted by researchers, as well as knowledgebases update for EMBL-EBI focuses on data exchanges that integrate and add value to experimental data, with among resources, both within the institute and with many having both functions (1,2). All EMBL-EBI data re- a wider global infrastructure. Within EMBL-EBI, data sources, are open access and freely available to any user resources exchange data through a rich network of worldwide at any time, and EMBL-EBI strongly supports data flows mediated by automated systems. This net- the concept of FAIR data (findable, accessible, interopera- work ensures that users are served with as much ble, and resuable) (3). -
2003 Mulder Nucl Acids Res {22
The InterPro Database, 2003 brings increased coverage and new features Nicola J Mulder, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, et al. To cite this version: Nicola J Mulder, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Daniel Barrell, et al.. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research, Oxford University Press, 2003, 31 (1), pp.315-318. 10.1093/nar/gkg046. hal-01214149 HAL Id: hal-01214149 https://hal.archives-ouvertes.fr/hal-01214149 Submitted on 9 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. # 2003 Oxford University Press Nucleic Acids Research, 2003, Vol. 31, No. 1 315–318 DOI: 10.1093/nar/gkg046 The InterPro Database, 2003 brings increased coverage and new features Nicola J. Mulder1,*, Rolf Apweiler1, Teresa K. Attwood3, Amos Bairoch4, Daniel Barrell1, Alex Bateman2, David Binns1, Margaret Biswas5, Paul Bradley1,3, Peer Bork6, Phillip Bucher7, Richard R. Copley8, Emmanuel Courcelle9, Ujjwal Das1, Richard Durbin2, Laurent Falquet7, Wolfgang Fleischmann1, Sam Griffiths-Jones2, Downloaded from Daniel Haft10, Nicola Harte1, Nicolas Hulo4, Daniel Kahn9, Alexander Kanapin1, Maria Krestyaninova1, Rodrigo Lopez1, Ivica Letunic6, David Lonsdale1, Ville Silventoinen1, Sandra E. -
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. -
MPGM: Scalable and Accurate Multiple Network Alignment
MPGM: Scalable and Accurate Multiple Network Alignment Ehsan Kazemi1 and Matthias Grossglauser2 1Yale Institute for Network Science, Yale University 2School of Computer and Communication Sciences, EPFL Abstract Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applica- tions, such as the prediction of protein function, detection of conserved network motifs, and the reconstruction of species’ phylogenetic relationships. A good multiple-network align- ment (MNA), by considering the data related to several species, provides a deep understand- ing of biological networks and system-level cellular processes. With the massive amounts of available PPI data and the increasing number of known PPI networks, the problem of MNA is gaining more attention in the systems-biology studies. In this paper, we introduce a new scalable and accurate algorithm, called MPGM, for aligning multiple networks. The MPGM algorithm has two main steps: (i) SEEDGENERA- TION and (ii) MULTIPLEPERCOLATION. In the first step, to generate an initial set of seed tuples, the SEEDGENERATION algorithm uses only protein sequence similarities. In the second step, to align remaining unmatched nodes, the MULTIPLEPERCOLATION algorithm uses network structures and the seed tuples generated from the first step. We show that, with respect to different evaluation criteria, MPGM outperforms the other state-of-the-art algo- rithms. In addition, we guarantee the performance of MPGM under certain classes of net- work models. We introduce a sampling-based stochastic model for generating k correlated networks. We prove that for this model if a sufficient number of seed tuples are available, the MULTIPLEPERCOLATION algorithm correctly aligns almost all the nodes. -
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. -
EMBL-EBI-Overview.Pdf
EMBL-EBI Overview EMBL-EBI Overview Welcome Welcome to the European Bioinformatics Institute (EMBL-EBI), a global hub for big data in biology. We promote scientific progress by providing freely available data to the life-science research community, and by conducting exceptional research in computational biology. At EMBL-EBI, we manage public life-science data on a very large scale, offering a rich resource of carefully curated information. We make our data, tools and infrastructure openly available to an increasingly data-driven scientific community, adjusting to the changing needs of our users, researchers, trainees and industry partners. This proactive approach allows us to deliver relevant, up-to-date data and tools to the millions of scientists who depend on our services. We are a founding member of ELIXIR, the European infrastructure for biological information, and are central to global efforts to exchange information, set standards, develop new methods and curate complex information. Our core databases are produced in collaboration with other world leaders including the National Center for Biotechnology Information in the US, the National Institute of Genetics in Japan, SIB Swiss Institute of Bioinformatics and the Wellcome Trust Sanger Institute in the UK. We are also a world leader in computational biology research, and are well integrated with experimental and computational groups on all EMBL sites. Our research programme is highly collaborative and interdisciplinary, regularly producing high-impact works on sequence and structural alignment, genome analysis, basic biological breakthroughs, algorithms and methods of widespread importance. EMBL-EBI is an international treaty organisation, and we serve the global scientific community.