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

Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination

(2013) Marco Nardini et al.   CELL

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme

(2013) Hashem Koohy et al.   PLoS One

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling

(2012) L. Budry et al.   GENES & DEVELOPMENT

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Wnt signaling specifies and patterns intestinal endoderm

(2011) Richard I. Sherwood et al.   MECHANISMS OF DEVELOPMENT

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

The nucleosome map of the mammalian liver

(2011) Zhaoyu Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

(2011) J. Eddy et al.   NUCLEIC ACIDS RESEARCH

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

(2011) Jason A. Watts et al.   PLoS 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

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data

(2010) Xiaoyu Chen et al.   BIOINFORMATICS

Discovering homotypic binding events at high spatial resolution

(2010) Yuchun Guo et al.   BIOINFORMATICS

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

c-Rel: A pioneer in directing regulatory T-cell lineage commitment?

(2010) Shohei Hori   EUROPEAN JOURNAL OF IMMUNOLOGY

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Early B Cell Factor 1 Regulates B Cell Gene Networks by Activation, Repression, and Transcription- Independent Poising of Chromatin

(2010) Thomas Treiber et al.   IMMUNITY

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

(2010) Roy Joseph et al.   Molecular Systems Biology

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

(2009) J. Xu et al.   GENES & DEVELOPMENT

Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA

(2009) T. Sekiya et al.   GENES & DEVELOPMENT

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

(2009) Jay R Hesselberth et al.   NATURE METHODS

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

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

A Conserved Role for Hox Paralog Group 4 in Regulation of Hematopoietic Progenitors

(2008) Michelina Iacovino et al.   STEM CELLS AND DEVELOPMENT