Ensembl 2016

By Andrew D. Yates, Wasiu A. Akanni, M. Amode, Daniel Barrell, Konstantinos Billis, D. Carvalho-Silva, Carla A. Cummins, P. Clapham, Stephen Fitzgerald, Laurent Gil and 37 more. Nucleic Acids Res., 2015

1,132 citations recorded by the source corpus.

The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5a473e808cb1daafbd0832036ec13e696e168395

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Citations in the corpus

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) (2016, methodology): “These pages will link to other data sources, such as Ensembl, to allow views of functional annotation and pathway information.”
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach (2016, methodology): “Region type . this feature value is assigned to each position within the window using one of the 5 types (exon, intron, 5‘UTR, 3‘UTR, CDS) from Ensembl annotation [45], resulting in 101 x 5 = 505 dimensional features.”
A subcellular map of the human proteome (2017, background): “We expect the availability of localization information for the human proteome to complement other systematic efforts on the DNA (25, 26), RNA (27, 28), and proteome (19, 29) levels and aid in the molecular understanding of the human cell and its interactions.”
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (2017, methodology): “For both assemblers, the Ensembl reference transcriptome annotation 25 was provided as the guide.”
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (2016, background): “melanogaster genome assembly BDGP6 and the AaegL2 and CpipJ2 draft genome assemblies available from Ensembl (28, 40).”