Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

Functions of BET proteins in erythroid gene expression

(2015) Aaron J. Stonestrom et al.   BLOOD

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

(2015) Olgert Denas et al.   BMC GENOMICS

Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence

(2015) T. Org et al.   EMBO JOURNAL

ICOS Coreceptor Signaling Inactivates the Transcription Factor FOXO1 to Promote Tfh Cell Differentiation

(2015) Erica L. Stone et al.   IMMUNITY

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

(2014) Weisheng Wu et al.   GENOME RESEARCH

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

Genome accessibility is widely preserved and locally modulated during mitosis

(2014) Chris C.-S. Hsiung et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Function-based identification of mammalian enhancers using site-specific integration

(2014) Diane E Dickel et al.   NATURE METHODS

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

(2014) Manuel Sánchez-Castillo et al.   NUCLEIC ACIDS RESEARCH

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers

(2013) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Haemogenic endocardium contributes to transient definitive haematopoiesis

(2013) Haruko Nakano et al.   Nature Communications

The role of Tal2 and Tal1 in the differentiation of midbrain GABAergic neuron precursors

(2013) K. Achim et al.   Biology Open

The embryonic origins of erythropoiesis in mammals

(2012) M. H. Baron et al.   BLOOD

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

(2012) Jian Xu et al.   DEVELOPMENTAL CELL

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

(2012) D. U. Gorkin et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

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

Pioneer transcription factors: establishing competence for gene expression

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

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif

(2011) Masato Morikawa et al.   NUCLEIC ACIDS RESEARCH

I B kinase   (IKK ) regulates the balance between type I and type II interferon responses

(2011) S.-L. Ng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The FoxA factors in organogenesis and differentiation

(2010) Klaus H Kaestner   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

(2010) Carmen G Palii et al.   EMBO JOURNAL

The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation

(2010) E. Soler et al.   GENES & DEVELOPMENT

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

(2010) M. T. Kassouf et al.   GENOME RESEARCH

cis-Regulatory Remodeling of the SCL Locus during Vertebrate Evolution

(2010) B. Gottgens et al.   MOLECULAR AND CELLULAR BIOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

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

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

(2010) D. Schmidt et al.   SCIENCE

A Runx1 Intronic Enhancer Marks Hemogenic Endothelial Cells and Hematopoietic Stem Cells

(2010) Cherry Ee Lin Ng et al.   STEM CELLS

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

(2009) Y. Cheng et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

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

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

(2009) Ying Zhang et al.   NUCLEIC ACIDS RESEARCH

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells

(2009) Catia Attanasio et al.   GENOME BIOLOGY

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

SCL and associated proteins distinguish active from repressive GATA transcription factor complexes

(2008) T. Tripic et al.   BLOOD

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

(2008) Rekin's Janky et al.   BMC BIOINFORMATICS

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

(2008) Y. Cheng et al.   GENOME RESEARCH

Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master Regulators of Hematopoiesis

(2008) R. J. Wozniak et al.   MOLECULAR AND CELLULAR BIOLOGY

Of lineage and legacy: the development of mammalian hematopoietic stem cells

(2008) Elaine Dzierzak et al.   NATURE IMMUNOLOGY

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH