Ensembl 2015

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.

Citing Articles

Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection.

Pullen K, Finethy R, Ko S, Reames C, Sassetti C, Lauffenburger D NPJ Syst Biol Appl. 2025; 11(1):19.

PMID: 39955299 PMC: 11830044. DOI: 10.1038/s41540-024-00487-6.

vmrseq: probabilistic modeling of single-cell methylation heterogeneity.

Shen N, Korthauer K Genome Biol. 2024; 25(1):321.

PMID: 39736632 PMC: 11687023. DOI: 10.1186/s13059-024-03457-7.

Long G4-rich enhancers target promoters via a G4 DNA-based mechanism.

DeMeis J, Roberts J, Delcher H, Godang N, Coley A, Brown C Nucleic Acids Res. 2024; 53(2.

PMID: 39658038 PMC: 11754661. DOI: 10.1093/nar/gkae1180.

tRNA, yRNA, and rRNA fragment excisions do not involve canonical microRNA biogenesis machinery.

Godang N, Nguyen A, DeMeis J, Paudel S, Campbell N, Barnes K MicroPubl Biol. 2024; 2024.

PMID: 39634108 PMC: 11615671. DOI: 10.17912/micropub.biology.001332.

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.

Martin R, Gaitan N, Jarlier F, Feuerbach L, de Soyres H, Arbones M Cell Genom. 2024; 4(9):100639.

PMID: 39216474 PMC: 11480849. DOI: 10.1016/j.xgen.2024.100639.

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