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Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephan Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D. McDowall (+9 others)
2011 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes .org) is an integrative resource for genome-scale data from non-vertebrate species.  ...  resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces.  ...  ACKNOWLEDGEMENTS We would also like to acknowledge the contributions of all our collaborators; and of all colleagues working on the Ensembl project at the EBI and the Wellcome Trust Sanger Institute.  ... 
doi:10.1093/nar/gkr895 pmid:22067447 pmcid:PMC3245118 fatcat:eiin7kxbqvgajkocq7yzyw4xsm

Ensembl Genomes 2020-enabling non-vertebrate genomic research

2019 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context  ...  Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across  ...  ACKNOWLEDGEMENTS We would like to acknowledge the following Ensembl developers for developing and maintaining the front-end and back-end software and infrastructure that underpins Ensembl Genomes: Premanand  ... 
doi:10.1093/nar/gkz890 pmid:31598706 pmcid:PMC6943047 fatcat:vj27adwlbnbq3hzxxei5nj55ji

Ensembl Genomes: Extending Ensembl across the taxonomic space

P. J. Kersey, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kähäri, R. J. Kinsella, E. Kulesha (+8 others)
2009 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would like to thank Kim Rutherford for permission to use circular_diagram.pl within EnsemblGenomes.  ...  This paper describes 'Ensembl Genomes', a new resource recently launched by the EBI to complement Ensembl by providing access to genome-scale data from non-vertebrate species through the same user interfaces  ...  With Ensembl Genomes, we aim to provide an integrated portal to reference sequence and annotation from all species of scientific interest; and thereby to complement, and provide convenient access to, data  ... 
doi:10.1093/nar/gkp871 pmid:19884133 pmcid:PMC2808935 fatcat:g6q3xclnp5gzrkmdus5mzspssy

Ensembl Genomes 2016: more genomes, more complexity

Paul Julian Kersey, James E. Allen, Irina Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay Humphrey, Arnaud Kerhornou (+26 others)
2015 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context  ...  23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants.  ...  Vertebrate metazoa are the focus of the Ensembl project (http://www.ensembl.org) (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species.  ... 
doi:10.1093/nar/gkv1209 pmid:26578574 pmcid:PMC4702859 fatcat:n3oewab7gvei5fbg6wfrx2ydaa

Ensembl comparative genomics resources

Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha (+2 others)
2016 Database: The Journal of Biological Databases and Curation  
The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here  ...  The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses.  ...  We also thank the rest of the Ensembl team, especially the members of Ensembl Outreach for supporting the users and helping with the documentation and tutorials.  ... 
doi:10.1093/database/baw053 pmid:27141089 pmcid:PMC4852398 fatcat:sluvrnnct5dpxmd7grm3z76m3y

Ensembl Genomes 2013: scaling up access to genome-wide data

Paul Julian Kersey, James E. Allen, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall (+21 others)
2013 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors would also like to acknowledge the contributions of all our collaborators and of all colleagues working on the Ensembl project.  ...  Vertebrate metazoa are the focus of the Ensembl project (http://www.ensembl.org) (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species.  ...  The overall suite of Ensembl Genomes interfaces mirrors the interfaces provided for vertebrate genomes in Ensembl, and allows users access to genomic data from across the tree of life in a consistent manner  ... 
doi:10.1093/nar/gkt979 pmid:24163254 pmcid:PMC3965094 fatcat:bzydx6qowvdunnkte5sioqgk5y

Ensembl variation resources

Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney (+1 others)
2010 BMC Genomics  
Description: The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes.  ...  The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system.  ...  Additional funding for Ensembl's variation resources comes from EMBL, the European Union Framework 6 STAR project, European Union Framework 7 Programme GEN2PHEN project and the UK Medical Research Council  ... 
doi:10.1186/1471-2164-11-293 pmid:20459805 pmcid:PMC2894800 fatcat:3f65senktbg7tnax5llz4focg4

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Paul Julian Kersey, James E Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu (+34 others)
2017 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl  ...  Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate  ...  Vertebrate metazoa are the focus of the Ensembl project (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species.  ... 
doi:10.1093/nar/gkx1011 pmid:29092050 pmcid:PMC5753204 fatcat:mmgammsp3fcrpdfrwprhsxl4g4

Touring Ensembl: A practical guide to genome browsing

Giulietta M Spudich, Xosé M Fernández-Suárez
2010 BMC Genomics  
This paper offers a practical guide to the integration of gene, comparative genomic, and functional genomics data using the Ensembl website at http://www.ensembl.org.  ...  The number of databases in molecular biological fields has rapidly increased to provide a large-scale resource.  ...  Genome browsers provide an aid to the researcher by importing biological data from various sources and presenting these data in an integrated way.  ... 
doi:10.1186/1471-2164-11-295 pmid:20459808 pmcid:PMC2894802 fatcat:avjtzfwzpzhwlelmfl4nei6ray

Ensembl 2019

Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M Ridwan Amode, Irina M Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla Cummins, Claire Davidson (+56 others)
2018 Nucleic Acids Research  
Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources.  ...  Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.  ...  ACKNOWLEDGEMENTS We thank all our users for their regular questions and feedback and for those external data generators that make prepublication data available to be incorporated into Ensembl.  ... 
doi:10.1093/nar/gky1113 pmid:30407521 fatcat:q2roq24hdjaqrlqc6r52kemvzi

The Ensembl Variant Effect Predictor

William McLaren, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham
2016 Genome Biology  
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions.  ...  It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis.  ...  The data files necessary for annotation in 80 vertebrate species and many invertebrates are distributed by Ensembl and Ensembl Genomes [34] , respectively.  ... 
doi:10.1186/s13059-016-0974-4 pmid:27268795 pmcid:PMC4893825 fatcat:lziduun2xnhpteudwo3utn4nyi

Ensembl 2020

2019 Nucleic Acids Research  
The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource.  ...  The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key  ...  ACKNOWLEDGEMENTS We wish to thank all of our user community and data providers for making their data available for reuse within Ensembl.  ... 
doi:10.1093/nar/gkz966 pmid:31691826 pmcid:PMC7145704 fatcat:i5tdgfqtd5dn7by55qjej2dade

Ensembl 2014

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 (+40 others)
2013 Nucleic Acids Research  
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.  ...  Finally, we provide updated information about our methods for data access and resources for user training.  ...  ACKNOWLEDGEMENTS The authors wish to thank all of their users, the systems teams who maintain their computational infrastructure and those researchers who have provided data to  ... 
doi:10.1093/nar/gkt1196 pmid:24316576 pmcid:PMC3964975 fatcat:knxp7akjtnbvnm7hlxajhvnzra

Ensembl 2018

Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon (+45 others)
2017 Nucleic Acids Research  
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research  ...  Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis.  ...  For their assistance with the Ensembl infrastructure and hardware mi-  ... 
doi:10.1093/nar/gkx1098 pmid:29155950 pmcid:PMC5753206 fatcat:g7pg5j5vpfgilgtr2bflfiqyei

Ensembl 2017

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 (+38 others)
2016 Nucleic Acids Research  
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.  ...  ACKNOWLEDGEMENTS Thank you to the Systems Administration teams at the Wellcome Trust Sanger Institute and at EMBL-EBI for  ... 
doi:10.1093/nar/gkw1104 pmid:27899575 pmcid:PMC5210575 fatcat:hzc4nlutrnfo5obbhqtlljr724
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