Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

(2017) Noah Dukler et al.   GENOME RESEARCH

RTFBSDB: an integrated framework for transcription factor binding site analysis

(2016) Zhong Wang et al.   BIOINFORMATICS

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

(2016) Biola M. Javierre et al.   CELL

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk

(2016) Ashley K. Tehranchi et al.   CELL

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

(2015) Minho Chae et al.   BMC BIOINFORMATICS

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees

(2015) Amy L. Bauernfeind et al.   Genome Biology and Evolution

TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites to Alter the Breast Cancer Cell Transcriptome

(2015) Hector L. Franco et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

(2015) Zeba Wunderlich et al.   Cell Reports

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

(2014) Emily S. Wong et al.   GENOME RESEARCH

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Genome-wide inference of natural selection on human transcription factor binding sites

(2013) Leonardo Arbiza et al.   NATURE GENETICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Enhancer turnover and conserved regulatory function in vertebrate evolution

(2013) S. Domene et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Many human accelerated regions are developmental enhancers

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

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

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

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

(2009) Dara G. Torgerson et al.   PLoS Genetics

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE