The Experts below are selected from a list of 5643 Experts worldwide ranked by ideXlab platform

Paul J Kersey - One of the best experts on this subject based on the ideXlab platform.

  • Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
    Nucleic acids research, 2017
    Co-Authors: Paul J Kersey, James E. Allen, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Alexis Allot, Matthieu Barba, Christoph Grabmueller
    Abstract:

    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 project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. 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 these using automated, scalable methods.

  • Ensembl Genomes 2016: more Genomes, more complexity.
    Nucleic Acids Research, 2015
    Co-Authors: Paul J Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller
    Abstract:

    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 of the Ensembl project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid Genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial Genomes, 400 fungal Genomes and 100 protist Genomes, in addition to 55 Genomes from invertebrate metazoa and 39 Genomes from plants. This dramatic increase in the number of included Genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference Genomes and make it available through the Ensembl user interfaces.

  • Ensembl Genomes 2013: scaling up access to genome-wide data.
    Nucleic acids research, 2013
    Co-Authors: Paul J Kersey, Daniel S T Hughes, Arnaud Kerhornou, James E. Allen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Mikkel Christensen, Jay Humphrey, Julia Khobova
    Abstract:

    Ensembl Genomes (http://www.EnsemblGenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new Genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial Genomes, and now includes the Genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available Genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

  • Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
    Nucleic acids research, 2011
    Co-Authors: 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
    Abstract:

    Ensembl Genomes (http://www.EnsemblGenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of Genomes.

Christoph Grabmueller - One of the best experts on this subject based on the ideXlab platform.

  • Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
    Nucleic acids research, 2017
    Co-Authors: Paul J Kersey, James E. Allen, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Alexis Allot, Matthieu Barba, Christoph Grabmueller
    Abstract:

    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 project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. 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 these using automated, scalable methods.

  • Ensembl Genomes 2016: more Genomes, more complexity.
    Nucleic Acids Research, 2015
    Co-Authors: Paul J Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller
    Abstract:

    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 of the Ensembl project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid Genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial Genomes, 400 fungal Genomes and 100 protist Genomes, in addition to 55 Genomes from invertebrate metazoa and 39 Genomes from plants. This dramatic increase in the number of included Genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference Genomes and make it available through the Ensembl user interfaces.

  • Ensembl Genomes 2013: scaling up access to genome-wide data.
    Nucleic acids research, 2013
    Co-Authors: Paul J Kersey, Daniel S T Hughes, Arnaud Kerhornou, James E. Allen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Mikkel Christensen, Jay Humphrey, Julia Khobova
    Abstract:

    Ensembl Genomes (http://www.EnsemblGenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new Genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial Genomes, and now includes the Genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available Genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

James E. Allen - One of the best experts on this subject based on the ideXlab platform.

  • Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
    Nucleic acids research, 2017
    Co-Authors: Paul J Kersey, James E. Allen, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Alexis Allot, Matthieu Barba, Christoph Grabmueller
    Abstract:

    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 project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. 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 these using automated, scalable methods.

  • Ensembl Genomes 2016: more Genomes, more complexity.
    Nucleic Acids Research, 2015
    Co-Authors: Paul J Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller
    Abstract:

    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 of the Ensembl project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid Genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial Genomes, 400 fungal Genomes and 100 protist Genomes, in addition to 55 Genomes from invertebrate metazoa and 39 Genomes from plants. This dramatic increase in the number of included Genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference Genomes and make it available through the Ensembl user interfaces.

  • Ensembl Genomes 2013: scaling up access to genome-wide data.
    Nucleic acids research, 2013
    Co-Authors: Paul J Kersey, Daniel S T Hughes, Arnaud Kerhornou, James E. Allen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Mikkel Christensen, Jay Humphrey, Julia Khobova
    Abstract:

    Ensembl Genomes (http://www.EnsemblGenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new Genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial Genomes, and now includes the Genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available Genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Paul Davis - One of the best experts on this subject based on the ideXlab platform.

  • Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
    Nucleic acids research, 2017
    Co-Authors: Paul J Kersey, James E. Allen, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Alexis Allot, Matthieu Barba, Christoph Grabmueller
    Abstract:

    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 project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. 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 these using automated, scalable methods.

  • Ensembl Genomes 2016: more Genomes, more complexity.
    Nucleic Acids Research, 2015
    Co-Authors: Paul J Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller
    Abstract:

    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 of the Ensembl project (http://www.Ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid Genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial Genomes, 400 fungal Genomes and 100 protist Genomes, in addition to 55 Genomes from invertebrate metazoa and 39 Genomes from plants. This dramatic increase in the number of included Genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference Genomes and make it available through the Ensembl user interfaces.

  • Ensembl Genomes 2013: scaling up access to genome-wide data.
    Nucleic acids research, 2013
    Co-Authors: Paul J Kersey, Daniel S T Hughes, Arnaud Kerhornou, James E. Allen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Mikkel Christensen, Jay Humphrey, Julia Khobova
    Abstract:

    Ensembl Genomes (http://www.EnsemblGenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new Genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial Genomes, and now includes the Genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available Genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Christophe Combet - One of the best experts on this subject based on the ideXlab platform.

  • BCL2DB: database of BCL-2 family members and BH3-only proteins
    Database : the journal of biological databases and curation, 2014
    Co-Authors: Valentine Rech De Laval, Gilbert Deléage, Abdel Aouacheria, Christophe Combet
    Abstract:

    BCL2DB (http://bcl2db.ibcp.fr) is a database designed to integrate data on BCL-2 family members and BH3-only proteins. These proteins control the mitochondrial apoptotic pathway and probably many other cellular processes as well. This large protein group is formed by a family of pro-apoptotic and anti-apoptotic homologs that have phylogenetic relationships with BCL-2, and by a collection of evolutionarily and structurally unrelated proteins characterized by the presence of a region of local sequence similarity with BCL-2, termed the BH3 motif. BCL2DB is monthly built, thanks to an automated procedure relying on a set of homemade profile HMMs computed from seed reference sequences representative of the various BCL-2 homologs and BH3-only proteins. The BCL2DB entries integrate data from the Ensembl, Ensembl Genomes, European Nucleotide Archive and Protein Data Bank databases and are enriched with specific information like protein classification into orthology groups and distribution of BH motifs along the sequences. The Web interface allows for easy browsing of the site and fast access to data, as well as sequence analysis with generic and specific tools. BCL2DB provides a helpful and powerful tool to both ‘BCL-2-ologists’ and researchers working in the various fields of physiopathology. Database URL: http://bcl2db.ibcp.fr

  • Database tool BCL2DB: database of BCL-2 family members and BH3-only proteins
    2014
    Co-Authors: Valentine Rech De Laval, Abdel Aouacheria, Christophe Combet
    Abstract:

    BCL2DB (http://bcl2db.ibcp.fr) is a database designed to integrate data on BCL-2 family members and BH3-only proteins. These proteins control the mitochondrial apoptotic pathway and probably many other cellular processes as well. This large protein group is formed by a family of pro-apoptotic and anti-apoptotic homologs that have phylogenetic relationships with BCL-2, and by a collection of evolutionarily and structurally unrelated proteins characterized by the presence of a region of local sequence similarity with BCL-2, termed the BH3 motif. BCL2DB is monthly built, thanks to an automated procedure relying on a set of homemade profile HMMs computed from seed reference sequences representative of the various BCL-2 homologs and BH3-only proteins. The BCL2DB entries integrate data from the Ensembl, Ensembl Genomes, European Nucleotide Archive and Protein Data Bank databases and are enriched with specific information like protein classification into orthology groups and distribution of BH motifs along the sequences. The Web interface allows for easy browsing of the site and fast access to data, as well as sequence analysis with generic and specific tools. BCL2DB provides a helpful and powerful tool to both ‘BCL-2-ologists’ and researchers working in the various fields of physiopathology. Database URL: http://bcl2db.ibcp.fr