Ensembl 2012

By Paul Flicek, M. Amode, Daniel Barrell, Kathryn M Beal, Simon Brent, D. Carvalho-Silva, P. Clapham, Guy Coates, S. Fairley, Stephen Fitzgerald and 47 more. Nucleic Acids Res., 2011

647 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b645b5f145b31c1ea501d7a307dc3c0ddd3346f3

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In Molecular Biology

Citations in the corpus

eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “For eggNOGv4, selection of these genomes was carried out by ﬁrst down-loading the latest genomes from major sources, which included Ensembl (23), UniProt (24), GiardiaDB (25), JGI (http://genome.jgi-psf.org) and TAIR (26), as in the previous version of eggNOG.”
Removing T-cell epitopes with computational protein design (2014, background): “In the absence of sufficient data on nonbinding peptides for each allele, we assumed that most 15mers in the host genome would not constitute strong MHC binders and generated negative datasets by randomly choosing 1,000 15mers from the human genome (12).”
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features (2013, background): “The computational problem of mapping short sequence reads to a reference genome has received enormous attention in the past few years (Fonseca et al., 2012; Langmead et al., 2009; Li and Durbin, 2009; Liao et al., 2013; Marco-Sola et al., 2012), and the rapid development of fast and reliable…”
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues (2013, methodology): “In contrast, the percentage of Ensembl v. 61 event variations continues to increase roughly linearly with the distance from the ‘anchor’ splice junction.”