DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

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

(2012) Guillaume Junion et al.   CELL

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells

(2011) Hong-Bing Yu et al.   GENOME RESEARCH

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

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

What does biologically meaningful mean? A perspective on gene regulatory network validation

(2011) Albertha JM Walhout   GENOME BIOLOGY

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

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

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

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

How Perfect Can Protein Interactomes Be?

(2009) E. D. Levy et al.   Science Signaling

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

Evidence for a Common Mode of Transcription Factor Interaction with Chromatin as Revealed by Improved Quantitative Fluorescence Recovery after Photobleaching

(2008) Florian Mueller et al.   BIOPHYSICAL JOURNAL

Tools for neuroanatomy and neurogenetics in Drosophila

(2008) B. D. Pfeiffer 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