GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets

Epigenomic functional characterization of genetic susceptibility variants in systemic vasculitis

(2016) Amr H. Sawalha et al.   JOURNAL OF AUTOIMMUNITY

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

(2015) Gosia Trynka et al.   AMERICAN JOURNAL OF HUMAN GENETICS

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Populational landscape of INDELs affecting transcription factor-binding sites in humans

(2015) André M. Ribeiro-dos-Santos et al.   BMC GENOMICS

Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes

(2015) Mikhail G Dozmorov   Epigenetics

Multiple sclerosis and susceptibility to celiac disease: An osteopontin gene haplotypes affair?

(2015) Raffaella Mormile   IMMUNOLOGY LETTERS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

dSysMap: exploring the edgetic role of disease mutations

(2015) Roberto Mosca et al.   NATURE METHODS

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Functional characterization of breast cancer using pathway profiles

(2014) Feng Tian et al.   BMC Medical Genomics

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Systematic classification of non-coding RNAs by epigenomic similarity

(2013) Mikhail G Dozmorov et al.   BMC BIOINFORMATICS

Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes

(2013) Mikhail G Dozmorov et al.   Epigenetics

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Impacts of Variation in the Human Genome on Gene Regulation

(2013) Rajini R. Haraksingh et al.   JOURNAL OF MOLECULAR BIOLOGY

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Systematic functional regulatory assessment of disease-associated variants

(2013) Konrad J. Karczewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

ISMB 2012 PROCEEDINGS PAPERS COMMITTEE

(2012)   BIOINFORMATICS

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012)   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

DOSim: An R package for similarity between diseases based on Disease Ontology

(2011) Jiang Li et al.   BMC BIOINFORMATICS

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

(2011) Jason Ernst et al.   NATURE

A New Methodology to Associate SNPs with Human Diseases According to Their Pathway Related Context

(2011) Burcu Bakir-Gungor et al.   PLoS One

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Genetics of human gene expression: mapping DNA variants that influence gene expression

(2009) Vivian G. Cheung et al.   NATURE REVIEWS GENETICS

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

Common and rare variants in multifactorial susceptibility to common diseases

(2008) Walter Bodmer et al.   NATURE GENETICS