The Ensembl gene annotation system

Phylogenomic analysis reveals ancient segmental duplications in the human genome

(2016) Madiha Hafeez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ensembl regulation resources

(2016) Daniel R. Zerbino et al.   Database-The Journal of Biological Databases and Curation

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

(2015) Adam Frankish et al.   BMC GENOMICS

A Phase I Trial of BKM120 (Buparlisib) in Combination with Fulvestrant in Postmenopausal Women with Estrogen Receptor-Positive Metastatic Breast Cancer

(2015) C. X. Ma et al.   CLINICAL CANCER RESEARCH

The Avian Transcriptome Response to Malaria Infection

(2015) Elin Videvall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions

(2015) Ariel C. Aspiras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse

(2015) Luis R. Saraiva et al.   Scientific Reports

Stem cells and fluid flow drive cyst formation in an invertebrate excretory organ

(2015) Hanh Thi-Kim Vu et al.   eLife

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

(2014) Emily S. Wong et al.   GENOME RESEARCH

The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease

(2014) Stefanie L. Butland et al.   HUMAN MOLECULAR GENETICS

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

(2014) Xinxia Peng et al.   NATURE BIOTECHNOLOGY

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

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

Analysis of the Skin Transcriptome in Two Oujiang Color Varieties of Common Carp

(2014) Chenghui Wang et al.   PLoS One

The sheep genome illuminates biology of the rumen and lipid metabolism

(2014) Y. Jiang et al.   SCIENCE

The cavefish genome reveals candidate genes for eye loss

(2014) Suzanne E. McGaugh et al.   Nature Communications

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

(2013) Yinhua Huang et al.   NATURE GENETICS

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

GenBank

(2013) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

DDBJ progress report: a new submission system for leading to a correct annotation

(2013) Takehide Kosuge et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

(2012) J. E. Collins et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Facing growth in the European Nucleotide Archive

(2012) Guy Cochrane et al.   NUCLEIC ACIDS RESEARCH

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Genenames.org: the HGNC resources in 2013

(2012) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

De Novo Origin of Protein-Coding Genes in Murine Rodents

(2012) Daniel N. Murphy et al.   PLoS One

Tracking and coordinating an international curation effort for the CCDS Project

(2012) R. A. Harte et al.   Database-The Journal of Biological Databases and Curation

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Modernizing Reference Genome Assemblies

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

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

(2011) Marilyn B Renfree et al.   GENOME BIOLOGY

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH