Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

Neighboring Genes Show Correlated Evolution in Gene Expression

(2015) Avazeh T. Ghanbarian et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Arttu Jolma et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

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

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

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

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

(2014) Mikhail Spivakov   BIOESSAYS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Allele-specific expression and eQTL analysis in mouse adipose tissue

(2014) Yehudit Hasin-Brumshtein et al.   BMC GENOMICS

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

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

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng 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

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

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis -eQTL Identified Using Genetic Linkage

(2013) Sandrine Lagarrigue et al.   GENETICS

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Global Properties and Functional Complexity of Human Gene Regulatory Variation

(2013) Daniel J. Gaffney   PLoS Genetics

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

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

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Powerful Identification of Cis-regulatory SNPs in Human Primary Monocytes Using Allele-Specific Gene Expression

(2012) Jonas Carlsson Almlöf et al.   PLoS One

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects, and Dominance

(2012) Jonathan D. Gruber et al.   PLoS Genetics

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

(2012) Brian DeVeale et al.   PLoS Genetics

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

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

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

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Natural selection on cis and trans regulation in yeasts

(2010) J. J. Emerson et al.   GENOME RESEARCH

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton 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

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

(2010) D. Schmidt et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Functional Targets of the Monogenic Diabetes Transcription Factors HNF-1  and HNF-4  Are Highly Conserved Between Mice and Humans

(2009) S. F. Boj et al.   DIABETES

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

(2009) I. Tirosh et al.   SCIENCE

Thirty years of Mus spretus: a promising future

(2009) Lien Dejager et al.   TRENDS IN GENETICS

Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes

(2008) ARMANDO GERALDES et al.   MOLECULAR ECOLOGY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression

(2008) B. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE