The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding

(2010) Monique Floer et al.   CELL

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and Gene Regulation

(2010) Zhiming Dai et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse

(2009) Miriam R. Kantorovitz et al.   DEVELOPMENTAL CELL

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

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

CCCTC-Binding Factor and the Transcription Factor T-bet Orchestrate T Helper 1 Cell-Specific Structure and Function at the Interferon-γ Locus

(2009) Masayuki Sekimata et al.   IMMUNITY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

The logic of chromatin architecture and remodelling at promoters

(2009) Bradley R. Cairns   NATURE

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

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

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

(2008) Lucas D. Ward et al.   BIOINFORMATICS

Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription

(2008) Hinrich Boeger et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites

(2008) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources

(2008) Harri Lähdesmäki et al.   PLoS One

Global regulatory logic for specification of an embryonic cell lineage

(2008) P. Oliveri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Nucleosome destabilization in the epigenetic regulation of gene expression

(2007) Steven Henikoff   NATURE REVIEWS GENETICS