Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters

Fine-mapping cis-regulatory variants in diverse human populations

(2019) Ashley Tehranchi et al.   eLife

Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system

(2019) Ludovica Bruno et al.   NATURE IMMUNOLOGY

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

(2019) Carl G. de Boer et al.   NATURE BIOTECHNOLOGY

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2018) Ryan Tewhey et al.   CELL

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants

(2018) Meng Wang et al.   NUCLEIC ACIDS RESEARCH

Sex reversal following deletion of a single distal enhancer ofSox9

(2018) Nitzan Gonen et al.   SCIENCE

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks

(2018) Mun-Kit Choy et al.   Nature Communications

Capture Hi-C identifies putative target genes at 33 breast cancer risk loci

(2018) Joseph S. Baxter et al.   Nature Communications

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants

(2018) Wenqiang Shi et al.   BIOINFORMATICS

Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease

(2017) Giuseppe Gallone et al.   HUMAN MOLECULAR GENETICS

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

(2017) Romina Petersen et al.   Nature Communications

Inherent limitations of probabilistic models for protein-DNA binding specificity

(2017) Shuxiang Ruan et al.   PLoS Computational Biology

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

(2016) Yarui Diao et al.   GENOME RESEARCH

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

(2016) Florian Schmidt et al.   NUCLEIC ACIDS RESEARCH

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

(2016) Sunil Kumar et al.   NUCLEIC ACIDS RESEARCH

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C

(2016) Paul Martin et al.   PLoS One

atSNP: transcription factor binding affinity testing for regulatory SNP detection

(2015) Chandler Zuo et al.   BIOINFORMATICS

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency

(2015) Onkar Joshi et al.   Cell Stem Cell

Transcriptional enhancers: functional insights and role in human disease

(2015) Irene Miguel-Escalada et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Functional genomics bridges the gap between quantitative genetics and molecular biology

(2015) Tuuli Lappalainen   GENOME RESEARCH

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Computational schemes for the prediction and annotation of enhancers from epigenomic assays

(2015) John W. Whitaker et al.   METHODS

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

(2015) Roland Jäger et al.   Nature Communications

Dissection of a Complex Disease Susceptibility Region Using a Bayesian Stochastic Search Approach to Fine Mapping

(2015) Chris Wallace et al.   PLoS Genetics

Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

(2015) Xiaoquan Wen et al.   PLoS Genetics

UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

(2015) Cathie Sudlow et al.   PLOS MEDICINE

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

A significance test for the lasso

(2014) Richard Lockhart et al.   ANNALS OF STATISTICS

Spurious transcription factor binding: Non-functional or genetically redundant?

(2014) Mikhail Spivakov   BIOESSAYS

ASox2distal enhancer cluster regulates embryonic stem cell differentiation potential

(2014) Harry Y. Zhou et al.   GENES & DEVELOPMENT

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

(2014) Nicola H. Dryden et al.   GENOME RESEARCH

Determining causality and consequence of expression quantitative trait loci

(2014) A. Battle et al.   HUMAN GENETICS

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Long-range enhancer activity determinesMycsensitivity to Notch inhibitors in T cell leukemia

(2014) Yumi Yashiro-Ohtani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Zhihao Ding et al.   PLoS Genetics

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Identifying transcriptional cis -regulatory modules in animal genomes

(2014) Kushal Suryamohan et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Methods for population-based eQTL analysis in human genetics

(2014) Lu Tian et al.   TSINGHUA SCIENCE AND TECHNOLOGY

Genetics of human gene expression

(2013) Barbara E Stranger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

(2013) A. I. Ramos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

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

(2012) Jacob F. Degner 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

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

(2012) Matthew T. Maurano et al.   PLoS Genetics

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

(2011) Ivan G Costa et al.   BMC BIOINFORMATICS

Enhancer and promoter interactions—long distance calls

(2011) Ivan Krivega et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Evolutionary Origins of Transcription Factor Binding Site Clusters

(2011) Xin He et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae

(2010) Kevin Chen et al.   Genome Biology and Evolution

An effective model for natural selection in promoters

(2010) M. M. Hoffman et al.   GENOME RESEARCH

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS

Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions

(2008) Thomas Manke et al.   PLoS Computational Biology