Systematic analysis of binding of transcription factors to noncoding variants

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Antidepressive effects of targeting ELK-1 signal transduction

(2018) Kallia Apazoglou et al.   NATURE MEDICINE

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

(2018) Ekaterina Morgunova et al.   eLife

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Association analyses based on false discovery rate implicate new loci for coronary artery disease

(2017) Christopher P Nelson et al.   NATURE GENETICS

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

LS-GKM: a new gkm-SVM for large-scale datasets

(2016) Dongwon Lee   BIOINFORMATICS

Targeting ApoC-III to Reduce Coronary Disease Risk

(2016) Sumeet A. Khetarpal et al.   Current Atherosclerosis Reports

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

atSNP: transcription factor binding affinity testing for regulatory SNP detection

(2015) Chandler Zuo et al.   BIOINFORMATICS

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

(2015) James Bentham et al.   NATURE GENETICS

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

Associations of Haplotypes Upstream ofIRS1with Insulin Resistance, Type 2 Diabetes, Dyslipidemia, Preclinical Atherosclerosis, and Skeletal MuscleLOC646736mRNA Levels

(2015) Selma M. Soyal et al.   Journal of Diabetes Research

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

(2014) Anubha Mahajan et al.   NATURE GENETICS

Loss-of-Function Mutations in APOC3, Triglycerides, and Coronary Disease

(2014)   NEW ENGLAND JOURNAL OF MEDICINE

Robustly detecting differential expression in RNA sequencing data using observation weights

(2014) Xiaobei Zhou et al.   NUCLEIC ACIDS RESEARCH

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

(2013) Jean-Philippe Lambert et al.   NATURE METHODS

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Insights into the genetic basis of type 2 diabetes

(2013) Norihiro Kato   Journal of Diabetes Investigation

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

(2012) Robert A Scott et al.   NATURE GENETICS

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

(2012) Alisa K Manning et al.   NATURE GENETICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Cross-Talk between PPARγand Insulin Signaling and Modulation of Insulin Sensitivity

(2010) Anna Leonardini et al.   PPAR Research

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

The Transcription Factor TFAP2B Is Associated With Insulin Resistance and Adiposity in Healthy Adolescents

(2009) Niklas Nordquist et al.   Obesity

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

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