Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells

Hematopoietic transcriptional mechanisms: From locus-specific to genome-wide vantage points

(2014) Andrew W. DeVilbiss et al.   EXPERIMENTAL HEMATOLOGY

Direct induction of haematoendothelial programs in human pluripotent stem cells by transcriptional regulators

(2014) Irina Elcheva et al.   Nature Communications

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

(2013) A. Jankowski et al.   GENOME RESEARCH

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Building an ENCODE-style data compendium on a shoestring

(2013) David Ruau et al.   NATURE METHODS

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

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Cell-type specificity of ChIP-predicted transcription factor binding sites

(2012) Tony Håndstad et al.   BMC GENOMICS

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

(2012) Guillaume Junion et al.   CELL

Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

(2012) Graziano Martello et al.   Cell Stem Cell

The transcriptional programme controlled by Runx1 during early embryonic blood development

(2012) Yosuke Tanaka et al.   DEVELOPMENTAL BIOLOGY

RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis

(2012) Monika Lichtinger et al.   EMBO JOURNAL

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

(2012) J. Wang et al.   GENOME RESEARCH

BATF–JUN is critical for IRF4-mediated transcription in T cells

(2012) Peng Li et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang 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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types

(2011) Gang Wei et al.   IMMUNITY

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

GeneProf: analysis of high-throughput sequencing experiments

(2011) Florian Halbritter et al.   NATURE METHODS

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

(2011) Jonathan Göke et al.   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

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

Gfi1 Expression Is Controlled by Five Distinct Regulatory Regions Spread over 100 Kilobases, with Scl/Tal1, Gata2, PU.1, Erg, Meis1, and Runx1 Acting as Upstream Regulators in Early Hematopoietic Cells

(2010) N. K. Wilson et al.   MOLECULAR AND CELLULAR BIOLOGY

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

MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data

(2010) Ravi Gupta et al.   NUCLEIC ACIDS RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Chunlei Wu et al.   GENOME BIOLOGY

Endoglin expression in blood and endothelium is differentially regulated by modular assembly of the Ets/Gata hemangioblast code

(2008) J. E. Pimanda et al.   BLOOD

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY