Ensembl 2007

By Tim J. P. Hubbard, Bronwen L. Aken, Kathryn M Beal, B. Ballester, M. Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, T. Cutts and 48 more. Nucleic Acids Res., 2006

531 citations recorded by the source corpus.

The Ensembl () 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f50ad59ed2b38e7290f07a31cf85f041bcfca4f2

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Citations in the corpus

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows (2008, unknown): “Expected benefits from such an endeavour include higher coverage of a proteome, sufficient data density for meaningful statistics and the possibility to contribute extensive observational data back to genome annotation projects. the peptideatlas project thus began as a compendium of peptides observe”
Ensembl variation resources (2010, background): “Each year, Ensembl publishes a general update of all the project's resources [11,19,20].”
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments (2007, methodology): “1) Genomes for 31 organisms, respective namespace mappings, orthology matches, and GO annotations are all retrieved from the Ensembl database (18) via the BioMart (19) interface.”
Integrative regulatory mapping indicates that the RNA-binding protein HuR (ELAVL1) couples pre-mRNA processing and mRNA stability (2011, background): “The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1 (Hubbard et al., 2007).”
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species (2008, background): “• Gene ontology [26] annotations and homology relationships between genes are recovered from Ensembl [27].”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, background): “For the higher eukaryotes from the Ensembl (10) resource, we provide two versions of each genome.”
miRBase: tools for microRNA genomics (2007, methodology): “The miRBase::Targets database uses the miRanda algorithm (7) to predict targets in untranslated regions (UTRs) of 37 animal genomes from Ensembl (18).”
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. (2007, methodology): “To help ameliorate the (presumed minor) effects of such cases, one could incorporate genemodel data from the other species, such as that available from Ensembl (Hubbard et al. 2007).”
Proteinortho: Detection of (Co-)orthologs in large-scale analysis (2011, background): “For protein-coding genes, several well-known databases, including InParanoid [2], OrthoMCL-DB [3], COG [4], Homogene [5], eggNOG [6], OMA Browser [7] and Ensembl Compara [8] compile such information.”