Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules

Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function

(2012) Jian-Xin Lin et al.   IMMUNITY

The JAK-STAT Pathway at Twenty

(2012) George R. Stark et al.   IMMUNITY

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments

(2012) Mariann Micsinai et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes

(2012) Bing-Mei Zhu et al.   NUCLEIC ACIDS RESEARCH

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

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

(2011) Alan C. Mullen et al.   CELL

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

Dynamic, Sex-Differential STAT5 and BCL6 Binding to Sex-Biased, Growth Hormone-Regulated Genes in Adult Mouse Liver

(2011) Y. Zhang et al.   MOLECULAR AND CELLULAR BIOLOGY

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

(2011) Lena Ho et al.   NATURE CELL BIOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2

(2011) Malay Mandal et al.   NATURE IMMUNOLOGY

Decoding the genome with an integrative analysis tool: Combinatorial CRM Decoder

(2011) Keunsoo Kang 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

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

(2010) B. G. Hoffman et al.   GENOME RESEARCH

Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during T Helper Cell Differentiation

(2010) Lai Wei et al.   IMMUNITY

Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

(2010) G. Ling 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

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

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

(2010) D. Schmidt et al.   SCIENCE

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

(2010) Kenzie D. MacIsaac et al.   PLoS Computational Biology

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

Analysis of Interleukin-21-Induced Prdm1 Gene Regulation Reveals Functional Cooperation of STAT3 and IRF4 Transcription Factors

(2009) Hyokjoon Kwon et al.   IMMUNITY

Foxa1 and Foxa2 regulate bile duct development in mice

(2009) Zhaoyu Li et al.   JOURNAL OF CLINICAL INVESTIGATION

Hepatocyte Nuclear Factor 4  Coordinates a Transcription Factor Network Regulating Hepatic Fatty Acid Metabolism

(2009) C. P. Martinez-Jimenez et al.   MOLECULAR AND CELLULAR BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Interpretation of cytokine signaling through the transcription factors STAT5A and STAT5B

(2008) L. Hennighausen et al.   GENES & DEVELOPMENT

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Priming for T helper type 2 differentiation by interleukin 2–mediated induction of interleukin 4 receptor α-chain expression

(2008) Wei Liao et al.   NATURE IMMUNOLOGY

Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli

(2008) J. Y. Lee et al.   NUCLEIC ACIDS RESEARCH

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY