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Database Commons - Ensembl

Ensembl

Citations: 12662

z-index 783.46

Short name Ensembl
Full name Ensembl
Description Ensembl is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms.
URL http://www.ensembl.org
Year founded 1999
Last update & version 2016-12-01    v87.0
Availability Free to all users
University/Institution hosted European Bioinformatics Institute
Address Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
City Cambridge
Province/State Cambridgeshire
Country/Region United Kingdom
Contact name Paul Flicek
Contact email flicek@ebi.ac.uk
Data type(s)
Major organism(s)
Keyword(s)
  • genomic annotation
Publication(s)
  • Ensembl 2017. [PMID: 27899575]

    Bronwen L Aken, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E Hunt, Sophie H Janacek, Thomas Juettemann, Stephen Keenan, Matthew R Laird, Ilias Lavidas, Thomas Maurel, William McLaren, Benjamin Moore, Daniel N Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M Staines, Stephen J Trevanion, Fiona Cunningham, Andrew Yates, Daniel R Zerbino, Paul Flicek
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-17)

    Abstract: Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • Ensembl 2016. [PMID: 26687719]

    Andrew Yates, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E Hunt, Sophie H Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J Martin, Thomas Maurel, William McLaren, Daniel N Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli, Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron Taylor, Anja Thormann, Alessandro Vullo, Steven P Wilder, Amonida Zadissa, Ewan Birney, Jennifer Harrow, Matthieu Muffato, Emily Perry, Magali Ruffier, Giulietta Spudich, Stephen J Trevanion, Fiona Cunningham, Bronwen L Aken, Daniel R Zerbino, Paul Flicek
    Nucleic acids research 2016:44(D1)
    181 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • Ensembl 2015. [PMID: 25352552]

    Fiona Cunningham, M Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E Hunt, Sophie H Janacek, Nathan Johnson, Thomas Juettemann, Andreas K Kähäri, Stephen Keenan, Fergal J Martin, Thomas Maurel, William McLaren, Daniel N Murphy, Rishi Nag, Bert Overduin, Anne Parker, Mateus Patricio, Emily Perry, Miguel Pignatelli, Harpreet Singh Riat, Daniel Sheppard, Kieron Taylor, Anja Thormann, Alessandro Vullo, Steven P Wilder, Amonida Zadissa, Bronwen L Aken, Ewan Birney, Jennifer Harrow, Rhoda Kinsella, Matthieu Muffato, Magali Ruffier, Stephen M J Searle, Giulietta Spudich, Stephen J Trevanion, Andy Yates, Daniel R Zerbino, Paul Flicek
    Nucleic acids research 2015:43(Database issue)
    662 Citations (Google Scholar as of 2017-02-17)

    Abstract: Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • Ensembl 2014. [PMID: 24316576]

    Paul Flicek, M Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Nathan Johnson, Thomas Juettemann, Andreas K Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J Martin, Thomas Maurel, William M McLaren, Daniel N Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet S Riat, Magali Ruffier, Daniel Sheppard, Kieron Taylor, Anja Thormann, Stephen J Trevanion, Alessandro Vullo, Steven P Wilder, Mark Wilson, Amonida Zadissa, Bronwen L Aken, Ewan Birney, Fiona Cunningham, Jennifer Harrow, Javier Herrero, Tim J P Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R Zerbino, Stephen M J Searle
    Nucleic acids research 2014:42(Database issue)
    593 Citations (Google Scholar as of 2016-01-18)

    Abstract: Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.

  • Ensembl 2013. [PMID: 23203987]

    Paul Flicek, Ikhlak Ahmed, M Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Thomas Juettemann, Andreas K Kähäri, Stephen Keenan, Monika Komorowska, Eugene Kulesha, Ian Longden, Thomas Maurel, William M McLaren, Matthieu Muffato, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Graham R S Ritchie, Magali Ruffier, Michael Schuster, Daniel Sheppard, Daniel Sobral, Kieron Taylor, Anja Thormann, Stephen Trevanion, Simon White, Steven P Wilder, Bronwen L Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Jennifer Harrow, Javier Herrero, Tim J P Hubbard, Nathan Johnson, Rhoda Kinsella, Anne Parker, Giulietta Spudich, Andy Yates, Amonida Zadissa, Stephen M J Searle
    Nucleic acids research 2013:41(Database issue)
    1352 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

  • Ensembl 2012. [PMID: 22086963]

    Paul Flicek, M Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas K Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R S Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y Amy Tang, Kieron Taylor, Stephen Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P Wilder, Bronwen L Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M Fernández-Suarez, Jennifer Harrow, Javier Herrero, Tim J P Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M J Searle
    Nucleic acids research 2012:40(Database issue)
    2483 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.

  • Ensembl 2011. [PMID: 21045057]

    Paul Flicek, M Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Pontus Larsson, Ian Longden, William McLaren, Bert Overduin, Bethan Pritchard, Harpreet Singh Riat, Daniel Rios, Graham R S Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Giulietta Spudich, Y Amy Tang, Stephen Trevanion, Jana Vandrovcova, Albert J Vilella, Simon White, Steven P Wilder, Amonida Zadissa, Jorge Zamora, Bronwen L Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M Fernández-Suarez, Javier Herrero, Tim J P Hubbard, Anne Parker, Glenn Proctor, Jan Vogel, Stephen M J Searle
    Nucleic acids research 2011:39(Database issue)
    1455 Citations (Google Scholar as of 2016-01-18)

    Abstract: The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

  • Ensembl's 10th year. [PMID: 19906699]

    Paul Flicek, Bronwen L Aken, Benoit Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y Amy Tang, Stephen Trevanion, Albert Vilella, Jan Vogel, Simon White, Steven P Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M Fernández-Suarez, Javier Herrero, Tim J P Hubbard, Anne Parker, Glenn Proctor, James Smith, Stephen M J Searle
    Nucleic acids research 2010:38(Database issue)
    313 Citations (Google Scholar as of 2017-02-17)

    Abstract: Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.

  • Ensembl 2009. [PMID: 19033362]

    T J P Hubbard, B L Aken, S Ayling, B Ballester, K Beal, E Bragin, S Brent, Y Chen, P Clapham, L Clarke, G Coates, S Fairley, S Fitzgerald, J Fernandez-Banet, L Gordon, S Graf, S Haider, M Hammond, R Holland, K Howe, A Jenkinson, N Johnson, A Kahari, D Keefe, S Keenan, R Kinsella, F Kokocinski, E Kulesha, D Lawson, I Longden, K Megy, P Meidl, B Overduin, A Parker, B Pritchard, D Rios, M Schuster, G Slater, D Smedley, W Spooner, G Spudich, S Trevanion, A Vilella, J Vogel, S White, S Wilder, A Zadissa, E Birney, F Cunningham, V Curwen, R Durbin, X M Fernandez-Suarez, J Herrero, A Kasprzyk, G Proctor, J Smith, S Searle, P Flicek
    Nucleic acids research 2009:37(Database issue)
    853 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

  • Ensembl 2008. [PMID: 18000006]

    P Flicek, B L Aken, K Beal, B Ballester, M Caccamo, Y Chen, L Clarke, G Coates, F Cunningham, T Cutts, T Down, S C Dyer, T Eyre, S Fitzgerald, J Fernandez-Banet, S Gräf, S Haider, M Hammond, R Holland, K L Howe, K Howe, N Johnson, A Jenkinson, A Kähäri, D Keefe, F Kokocinski, E Kulesha, D Lawson, I Longden, K Megy, P Meidl, B Overduin, A Parker, B Pritchard, A Prlic, S Rice, D Rios, M Schuster, I Sealy, G Slater, D Smedley, G Spudich, S Trevanion, A J Vilella, J Vogel, S White, M Wood, E Birney, T Cox, V Curwen, R Durbin, X M Fernandez-Suarez, J Herrero, T J P Hubbard, A Kasprzyk, G Proctor, J Smith, A Ureta-Vidal, S Searle
    Nucleic acids research 2008:36(Database issue)
    1187 Citations (Google Scholar as of 2016-01-18)

    Abstract: The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

  • Ensembl 2007. [PMID: 17148474]

    T J P Hubbard, B L Aken, K Beal, B Ballester, M Caccamo, Y Chen, L Clarke, G Coates, F Cunningham, T Cutts, T Down, S C Dyer, S Fitzgerald, J Fernandez-Banet, S Graf, S Haider, M Hammond, J Herrero, R Holland, K Howe, K Howe, N Johnson, A Kahari, D Keefe, F Kokocinski, E Kulesha, D Lawson, I Longden, C Melsopp, K Megy, P Meidl, B Ouverdin, A Parker, A Prlic, S Rice, D Rios, M Schuster, I Sealy, J Severin, G Slater, D Smedley, G Spudich, S Trevanion, A Vilella, J Vogel, S White, M Wood, T Cox, V Curwen, R Durbin, X M Fernandez-Suarez, P Flicek, A Kasprzyk, G Proctor, S Searle, J Smith, A Ureta-Vidal, E Birney
    Nucleic acids research 2007:35(Database issue)
    888 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of chordate genome sequences. Over the past year the number of genomes available from Ensembl has increased from 15 to 33, with the addition of sites for the mammalian genomes of elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat and european hedgehog; the fish genomes of stickleback and medaka and the second example of the genomes of the sea squirt (Ciona savignyi) and the mosquito (Aedes aegypti). Some of the major features added during the year include the first complete gene sets for genomes with low-sequence coverage, the introduction of new strain variation data and the introduction of new orthology/paralog annotations based on gene trees.

  • Ensembl 2006. [PMID: 16381931]

    E Birney, D Andrews, M Caccamo, Y Chen, L Clarke, G Coates, T Cox, F Cunningham, V Curwen, T Cutts, T Down, R Durbin, X M Fernandez-Suarez, P Flicek, S Gräf, M Hammond, J Herrero, K Howe, V Iyer, K Jekosch, A Kähäri, A Kasprzyk, D Keefe, F Kokocinski, E Kulesha, D London, I Longden, C Melsopp, P Meidl, B Overduin, A Parker, G Proctor, A Prlic, M Rae, D Rios, S Redmond, M Schuster, I Sealy, S Searle, J Severin, G Slater, D Smedley, J Smith, A Stabenau, J Stalker, S Trevanion, A Ureta-Vidal, J Vogel, S White, C Woodwark, T J P Hubbard
    Nucleic acids research 2006:34(Database issue)
    445 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased from 4 to 19, with the addition of the mammalian genomes of Rhesus macaque and Opossum, the chordate genome of Ciona intestinalis and the import and integration of the yeast genome. The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements to the integration of human genome variation data.

  • Ensembl 2005. [PMID: 15608235]

    T Hubbard, D Andrews, M Caccamo, G Cameron, Y Chen, M Clamp, L Clarke, G Coates, T Cox, F Cunningham, V Curwen, T Cutts, T Down, R Durbin, X M Fernandez-Suarez, J Gilbert, M Hammond, J Herrero, H Hotz, K Howe, V Iyer, K Jekosch, A Kahari, A Kasprzyk, D Keefe, S Keenan, F Kokocinsci, D London, I Longden, G McVicker, C Melsopp, P Meidl, S Potter, G Proctor, M Rae, D Rios, M Schuster, S Searle, J Severin, G Slater, D Smedley, J Smith, W Spooner, A Stabenau, J Stalker, R Storey, S Trevanion, A Ureta-Vidal, J Vogel, S White, C Woodwark, E Birney
    Nucleic acids research 2005:33(Database issue)
    545 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences. Over the last year the number of genomes available from the Ensembl site has increased by 7 to 16, with the addition of the six vertebrate genomes of chimpanzee, dog, cow, chicken, tetraodon and frog and the insect genome of honeybee. The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes. With the increased number of vertebrate genomes, the comparative analysis provided to users has been greatly improved, with new website interfaces allowing annotation of different genomes to be directly compared. The Ensembl software system is being increasingly widely reused in different projects showing the benefits of a completely open approach to software development and distribution.

  • Ensembl 2004. [PMID: 14681459]

    E Birney, D Andrews, P Bevan, M Caccamo, G Cameron, Y Chen, L Clarke, G Coates, T Cox, J Cuff, V Curwen, T Cutts, T Down, R Durbin, E Eyras, X M Fernandez-Suarez, P Gane, B Gibbins, J Gilbert, M Hammond, H Hotz, V Iyer, A Kahari, K Jekosch, A Kasprzyk, D Keefe, S Keenan, H Lehvaslaiho, G McVicker, C Melsopp, P Meidl, E Mongin, R Pettett, S Potter, G Proctor, M Rae, S Searle, G Slater, D Smedley, J Smith, W Spooner, A Stabenau, J Stalker, R Storey, A Ureta-Vidal, C Woodwark, M Clamp, T Hubbard
    Nucleic acids research 2004:32(Database issue)
    213 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

  • Ensembl: a genome infrastructure. [PMID: 15338620]

    E Birney, Ensembl Team.
    Cold Spring Harbor symposia on quantitative biology 2003:68
    12 Citations (Google Scholar as of 2017-02-17)

    Abstract:

  • Ensembl 2002: accommodating comparative genomics. [PMID: 12519943]

    M Clamp, D Andrews, D Barker, P Bevan, G Cameron, Y Chen, L Clark, T Cox, J Cuff, V Curwen, T Down, R Durbin, E Eyras, J Gilbert, M Hammond, T Hubbard, A Kasprzyk, D Keefe, H Lehvaslaiho, V Iyer, C Melsopp, E Mongin, R Pettett, S Potter, A Rust, E Schmidt, S Searle, G Slater, J Smith, W Spooner, A Stabenau, J Stalker, E Stupka, A Ureta-Vidal, I Vastrik, E Birney
    Nucleic acids research 2003:31(1)
    257 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

  • The Ensembl genome database project. [PMID: 11752248]

    T Hubbard, D Barker, E Birney, G Cameron, Y Chen, L Clark, T Cox, J Cuff, V Curwen, T Down, R Durbin, E Eyras, J Gilbert, M Hammond, L Huminiecki, A Kasprzyk, H Lehvaslaiho, P Lijnzaad, C Melsopp, E Mongin, R Pettett, M Pocock, S Potter, A Rust, E Schmidt, S Searle, G Slater, J Smith, W Spooner, A Stabenau, J Stalker, E Stupka, A Ureta-Vidal, I Vastrik, M Clamp
    Nucleic acids research 2002:30(1)
    1223 Citations (Google Scholar as of 2017-02-17)

    Abstract: The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

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200 OK2018-11-20
200 OK2018-11-16
200 OK2018-11-13
200 OK2018-11-09
200 OK2018-11-06
200 OK2018-11-02
200 OK2018-10-30
200 OK2018-10-26
200 OK2018-10-23
200 OK2018-10-19
200 OK2018-10-16
200 OK2018-10-12
200 OK2018-10-09
200 OK2018-10-05
200 OK2018-10-02
200 OK2018-09-28
200 OK2018-09-25
200 OK2018-09-21
200 OK2018-09-18
200 OK2018-09-14
200 OK2018-09-11
200 OK2018-09-07
200 OK2018-09-04
200 OK2018-08-31
200 OK2018-08-28
200 OK2018-08-24
200 OK2018-08-21
200 OK2018-08-17
200 OK2018-08-14
200 OK2018-08-10
200 OK2018-08-07
200 OK2018-08-03
200 OK2018-07-31
200 OK2018-07-27
200 OK2018-07-24
200 OK2018-07-20
200 OK2018-07-17
200 OK2018-07-13
200 OK2018-07-10
200 OK2018-07-06
200 OK2018-07-03
200 OK2018-06-29
200 OK2018-06-26
200 OK2018-06-22
200 OK2018-06-19
200 OK2018-06-15
200 OK2018-06-12
200 OK2018-06-08
200 OK2018-06-05
200 OK2018-06-01
200 OK2018-05-29
200 OK2018-05-25
200 OK2018-05-22
200 OK2018-05-18
200 OK2018-05-15
200 OK2018-05-11
200 OK2018-05-08
200 OK2018-05-04
200 OK2018-05-01
200 OK2018-04-27
200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
200 OK2016-12-30
200 OK2016-12-27
200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
-1 Failed2016-11-01
-1 Failed2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
-1 Failed2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
500 Failed2016-08-30
200 OK2016-08-26
200 OK2016-08-23
200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

DNA Protein RNA
Archaea Eukaryota Prokaryote
genomic annotation

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-02-17]
    • Zhang Zhang [2016-05-25]
    • Mengwei Li [2016-02-21]
    • Zhang Zhang [2016-01-18]
    • Lina Ma [2016-01-18]
    • Lin Liu [2016-01-18]
    • Lin Liu [2016-01-12]
    • Zhang Zhang [2015-12-31]
    • Jian Sang [2015-12-11]
    • Jian Sang [2015-06-27]
Stats