Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

The landscape of genomic imprinting across diverse adult human tissues

(2015) Yael Baran et al.   GENOME RESEARCH

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse

(2015) Tomas Babak et al.   NATURE GENETICS

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

(2015) Ricardo Cruz-Herrera del Rosario et al.   NATURE METHODS

Genetic Variation in Human DNA Replication Timing

(2014) Amnon Koren et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Putative cis-regulatory drivers in colorectal cancer

(2014) Halit Ongen et al.   NATURE

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

(2014) Zhihao Ding et al.   PLoS Genetics

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

(2013) Sebastian M. Waszak et al.   BIOINFORMATICS

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

(2013) A. Battle et al.   GENOME RESEARCH

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia

(2013) Sonja I Berndt et al.   NATURE GENETICS

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

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

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

(2012) Jacob F. Degner et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification of allele-specific alternative mRNA processing via transcriptome sequencing

(2012) Gang Li et al.   NUCLEIC ACIDS RESEARCH

Genotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression Data

(2012) Jean Francois Lefebvre et al.   PLoS One

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

(2012) Brian DeVeale et al.   PLoS Genetics

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

A Statistical Framework for eQTL Mapping Using RNA-seq Data

(2011) Wei Sun   BIOMETRICS

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

Sex-Specific Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

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

(2010) R. McDaniell et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li 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

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics