Ensembl 2014

By Paul Flicek, M. Amode, Daniel Barrell, Kathryn M Beal, Konstantinos Billis, Simon Brent, D. Carvalho-Silva, P. Clapham, Guy Coates, Stephen Fitzgerald and 42 more. Nucleic Acids Res., 2013

908 citations recorded by the source corpus.

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b2278342c6a2b28d40db726d5b5b0486f2690af5

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In Molecular Biology

Citations in the corpus

Developmental regulation of human cortex transcription and its clinical relevance at base resolution (2014, neutral): “We then contrasted these patterns to the clustering of the global transcriptome (based on read counts for all Ensembl-annotated genes, available in Data S1) – here PC1 distinguishes the brain (fetal and post-natal) from non-brain (stem cells and somatic tissues) samples, and PC2 distinguishes develo”
Predicting effective microRNA target sites in mammalian mRNAs (2015, methodology): “Prior to use, our P CT scores were updated to take advantage of improvements in both mouse and human 3 ′ -UTR annotations ( Harrow et al., 2012 ; Flicek et al., 2014 ), the additional sequenced vertebrate genomes aligned to the mouse and human genomes ( Karolchik et al., 2014 ), and our expanded…”
IMGT®, the international ImMunoGeneTics information system® 25 years on (2014, background): “…names are the official international reference and, as such, are entered in IMGT / GENE-DB (8), in Gene (NCBI) (60), in NCBI MapViewer, in En-sembl (61) at the European Bioinformatics Institute and in the Vertebrate Genome Annotation (Vega) Browser (62) at the Wellcome Trust Sanger Institute (UK).”
RNA-Seq workflow: gene-level exploratory analysis and differential expression (2015, neutral): “We will read the gene model from an Ensembl GTF file 8 , using makeTxDbFromGFF from the GenomicFeatures package.”