Ensembl 2011

By Paul Flicek, M. Amode, Daniel Barrell, Kathryn M Beal, Simon Brent, Yuan Chen, P. Clapham, Guy Coates, S. Fairley, Stephen Fitzgerald and 42 more. Nucleic Acids Res., 2010

480 citations recorded by the source corpus.

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d07369ecb9fc89666273b091486051b727ab851c

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Citations in the corpus

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (2011, background): “The UCSC Genome Browser (14) and ENSEMBL Genome Browser (15,16) both allow genomic regions to be annotated with the results of cutting-edge genomic data, including chromatin state segmentations, ENCODE data, 1000 Genomes variants, evolutionary constraint, LD calculations and NHGRI catalog variants.”
Braveheart, a long non-coding RNA required for cardiovascular lineage commitment (2013, methodology): “5 and E14) (this study) and adult tissues (Mortazavi et al., 2008) were collated using two annotations (Flicek et al., 2011; Guttman et al., 2010) to define a set of murine lncRNAs.”
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? (2015, methodology): “In contrast, the mean Pearson ’ s correlation (±1 SD) between replicates using the count data for four RNA-seq studies from the ReCount project (Frazee et al. 2011) show only (cid:1) R = 0 .”
Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. (2012, methodology): “Reads were filtered for base quality and low complexity, then aligned pairwise to human rRNA and cDNA (Flicek et al. 2011) and genome (hg18) reference sequences using BWA (Li and Durbin 2010), as previously described (Moore et al.”