Ensembl 2008

By Paul Flicek, Bronwen L. Aken, Kathryn M Beal, B. Ballester, M. Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, T. Cutts and 49 more. Nucleic Acids Res., 2007

353 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c44966d4bd8e3e5f84403e1d7ca1007a93a592a4

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Citations in the corpus

Ensembl variation resources (2010, background): “Each year, Ensembl publishes a general update of all the project's resources [11,19,20].”
SMART 6: recent updates and new developments (2008, methodology): “In the initial release, this protein database included 170 genomes, which were available in SWISS-PROT (7) and ENSEMBL (8).”
Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation (2008, background): “In addition, on-line resources, such as the NIAID Bioinformatics Resource Centers (BRCs) (Greene, 2007), CMR (Peterson et al., 2001), IMG (Markowitz et al., 2008), and Ensembl (Flicek et al., 2008), generate and display additional genome annotations.”
Analysing and interpreting DNA methylation data (2012, methodology): “The resulting files are uploaded to a Web‑accessible directory and imported into a Web‑based genome browser for visualization (for exam‑ ple, UCSC Genome Browser 70 , Ensembl 71 or WashU Human Epigenome Browser 72 ).”
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics (2019, methodology): “In this application, we demonstrate SingleCellSignalR mouse data functionality, which is implemented by internally mapping mouse genes to their human orthologs according to Ensembl (48) to exploit LR db .”
BisoGenet: a new tool for gene network building, visualization and analysis (2010, methodology): “Data repositories such as NCBI ’ s Entrez Gene[1] and Ensembl[2] maintain annotation on whole genomes, including sequences, gene location, transcripts, classification and links to several external databases.”