Ensembl 2015

By Fiona Cunningham, M. Amode, Daniel Barrell, Kathryn M Beal, Konstantinos Billis, Simon Brent, D. Carvalho-Silva, P. Clapham, Guy Coates, Stephen Fitzgerald and 39 more. Nucleic Acids Res., 2014

825 citations recorded by the source corpus.

Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b42f8a364ea34a402fd6bb5de27f6034e39abc4e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, methodology): “The inference approaches fall into two main categories, namely graph-based (8–15) and tree-based (16–19) methods.”
Tissue-specific mutation accumulation in human adult stem cells during life (2016, neutral): “Finally, exonic sequences were defined as all exonic regions reported in Ensembl v75 (GCRh37) 35 .”
Next-generation diagnostics and disease-gene discovery with the Exomiser (2015, methodology): “Annotation packages, such as ANNOVAR 57 , Ensembl’s Variant Effect Predictor 58 and Jannovar 27 transform the chromosomal coordinates that result from aligning WES reads to the reference genome (e.g., chr14:g.88401213T>C) to the corresponding coordinates for affected transcripts, as well as the…”
gEVAL — a web-based browser for evaluating genome assemblies (2016, background): “Current public genome browsers include many of these types of datasets in their analysis repertoire, but usually focus on gene annotation (Cunningham et al ., 2014, Rosenbloom et al ., 2014).”
Design and Analysis of Single-Cell Sequencing Experiments. (2015, background): “The genomic DNA sequence for most model organisms can be readily obtained from various online databases, such as the UCSC genome browser (Meyer et al., 2013) or www.ensembl. org (Cunningham et al., 2015).”
ChemProt-3.0: a global chemical biology diseases mapping (2016, neutral): “Notably, disease associations are queried through the TCRD (Target Central Ressource Database Application: http://juniper.health.unm.edu/tcrd/) database and the gen-etic variation through the Ensembl database (45).”