HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

is-rSNP: a novel technique for in silico regulatory SNP detection

(2010) Geoff Macintyre et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Ensembl variation resources

(2010) Yuan Chen et al.   BMC GENOMICS

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

(2010) N. F. Wasserman et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci

(2010) E. R. Gamazon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus

(2009) Jian-Wen Han et al.   NATURE GENETICS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies

(2009) Zongli Xu et al.   NUCLEIC ACIDS RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Multiple Loci With Different Cancer Specificities Within the 8q24 Gene Desert

(2008) Maya Ghoussaini et al.   JNCI-Journal of the National Cancer Institute

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

(2008) Malin C. Andersen et al.   PLoS Computational Biology