Transcription factor binding dynamics during human ES cell differentiation

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data

(2013) Yanchun Bao et al.   BMC BIOINFORMATICS

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity

(2013) Siim Pauklin et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Epigenetic programming and reprogramming during development

(2013) Irene Cantone et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

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

(2011) Alan C. Mullen et al.   CELL

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

FGF signalling inhibits neural induction in human embryonic stem cells

(2011) Boris Greber et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

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

Pluripotency factors regulate definitive endoderm specification through eomesodermin

(2011) A. K. K. Teo et al.   GENES & DEVELOPMENT

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes

(2011) J. S. You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Derivation of neural crest cells from human pluripotent stem cells

(2010) Gabsang Lee et al.   Nature Protocols

Mapping the first stages of mesoderm commitment during differentiation of human embryonic stem cells

(2010) D. Evseenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Genetic programming of liver and pancreas progenitors: lessons for stem-cell differentiation

(2008) Kenneth S. Zaret   NATURE REVIEWS GENETICS

Highly efficient differentiation of hESCs to functional hepatic endoderm requires ActivinA and Wnt3a signaling

(2008) D. C. Hay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY