Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

QuASAR: quantitative allele-specific analysis of reads

(2014) Chris T. Harvey et al.   BIOINFORMATICS

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data

(2014) Luis G León-Novelo et al.   BMC GENOMICS

Estimating genotype error rates from high-coverage next-generation sequence data

(2014) Jeffrey D. Wall et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

The Transcription Factor CREB Enhances Interleukin-17A Production and Inflammation in a Mouse Model of Atherosclerosis

(2013) S. Kotla et al.   Science Signaling

Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

(2012) Yunyun Ni et al.   BMC GENETICS

MaCH-Admix: Genotype Imputation for Admixed Populations

(2012) Eric Yi Liu et al.   GENETIC EPIDEMIOLOGY

Genotype Imputation of MetabochipSNPs Using a Study-Specific Reference Panel of ∼4,000 Haplotypes in African Americans From the Women's Health Initiative

(2012) Eric Yi Liu et al.   GENETIC EPIDEMIOLOGY

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

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

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

(2012) Jacob F. Degner et al.   NATURE

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

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

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

A new strategy to reduce allelic bias in RNA-Seq readmapping

(2012) Ravi Vijaya Satya et al.   NUCLEIC ACIDS RESEARCH

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A Statistical Framework for eQTL Mapping Using RNA-seq Data

(2011) Wei Sun   BIOMETRICS

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

Implications of gene copy-number variation in health and diseases

(2011) Suhani H Almal et al.   JOURNAL OF HUMAN GENETICS

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

New gene functions in megakaryopoiesis and platelet formation

(2011) Christian Gieger et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

(2010) E. Lalonde et al.   GENOME RESEARCH

Allele-specific and heritable chromatin signatures in humans

(2010) E. Birney et al.   HUMAN MOLECULAR GENETICS

The Role of the Transcription Factor CREB in Immune Function

(2010) A. Y. Wen et al.   JOURNAL OF IMMUNOLOGY

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration

(2010) W. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

(2009) Graham A. Heap et al.   HUMAN MOLECULAR GENETICS

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

Common variants at five new loci associated with early-onset inflammatory bowel disease

(2009) Marcin Imielinski et al.   NATURE GENETICS

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY