Ensembl 2016

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

(2015) Adam Frankish et al.   BMC GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

APPRIS WebServer and WebServices

(2015) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Big data and other challenges in the quest for orthologs

(2014) E. L. L. Sonnhammer et al.   BIOINFORMATICS

The Ensembl REST API: Ensembl Data for Any Language

(2014) Andrew Yates et al.   BIOINFORMATICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

(2014) Mary Shimoyama et al.   NUCLEIC ACIDS RESEARCH

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

(2013) Robert Petryszak et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

(2012) Zhi-Liang Hu et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

eHive: An Artificial Intelligence workflow system for genomic analysis

(2010) Jessica Severin et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH