Ensembl 2017

By Bronwen L. Aken, P. Achuthan, Wasiu A. Akanni, M. Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, D. Carvalho-Silva, Carla A. Cummins, P. Clapham and 40 more. Nucleic Acids Res., 2016

484 citations recorded by the source corpus.

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d3d04809e42ddb17fb0017d052343cdf964c1c1c

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In Molecular Biology

Citations in the corpus

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data (2018, methodology): “To enable gene ID conversion, we downloaded all available gene ID mappings for 220 species from Ensembl [26, 27] (Additional file 1: Table S1), including 98 from Ensembl (vertebrates, release 91), 53 from Ensembl Plants (release 37) [28], and 69 from Ensembl Metazoa (release 37).”
Ensembl 2018 (2017, background): “Genomes are no longer sequenced one by one, rather in batches, and already Ensembl can display clades, as illustrated by our addition in 2016 of a collection of laboratory mouse strains (22).”
How many human proteoforms are there? (2018, background): “How many human proteoforms are there? Nature Chemical Biology, 14(3), 206-214.”