Genome-wide predictors of NF-κB recruitment and transcriptional activity

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

(2014) Marcin Cieślik et al.   BMC GENOMICS

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver

(2013) Logan J Everett et al.   BMC GENOMICS

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

(2013) Irene Aksoy et al.   EMBO JOURNAL

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

NF-κB Regulates Mesenchymal Transition for the Induction of Non-Small Cell Lung Cancer Initiating Cells

(2013) Manish Kumar et al.   PLoS One

DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases

(2013) M. J. Aryee et al.   Science Translational Medicine

NF‐κB and epigenetic mechanisms as integrative regulators of brain resilience to anoxic stress

(2012) Ilenia Sarnico et al.   BRAIN RESEARCH

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

(2012) Guillaume Junion et al.   CELL

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

(2012) Zhaoyu Li et al.   CELL

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

(2012) Abdenour Soufi et al.   CELL

Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming

(2012) Jieun Lee et al.   CELL

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

Epigenetic obstacles encountered by transcription factors: reprogramming against all odds

(2012) Casey A Gifford et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcriptional regulation in the innate immune system

(2012) Stephen T Smale   CURRENT OPINION IN IMMUNOLOGY

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

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

NF-κB and chromatin: ten years on the path from basic mechanisms to candidate drugs

(2012) Gioacchino Natoli   IMMUNOLOGICAL REVIEWS

Dimer-specific regulatory mechanisms within the NF-κB family of transcription factors

(2012) Stephen T. Smale   IMMUNOLOGICAL REVIEWS

The Stat3/GR Interaction Code: Predictive Value of Direct/Indirect DNA Recruitment for Transcription Outcome

(2012) David Langlais et al.   MOLECULAR CELL

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain

(2012) Rhishikesh Bargaje et al.   NUCLEIC ACIDS RESEARCH

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

(2012) Seth Frietze et al.   GENOME BIOLOGY

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

(2012) Manching Ku et al.   GENOME BIOLOGY

Genomic and Biochemical Insights into the Specificity of ETS Transcription Factors

(2011) Peter C. Hollenhorst et al.   Annual Review of Biochemistry

ACT: aggregation and correlation toolbox for analyses of genome tracks

(2011) J. Jee et al.   BIOINFORMATICS

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida et al.   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC BIOINFORMATICS

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network

(2011) Yen-Sin Ang et al.   CELL

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape

(2011) Bernadett Papp et al.   CELL RESEARCH

Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling

(2011) Richard P. Koche et al.   Cell Stem Cell

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Pioneer transcription factors: establishing competence for gene expression

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

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

(2011) B.-K. Lee et al.   GENOME RESEARCH

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes

(2011) N. A. S. Rao et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

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

Multilineage Priming of Enhancer Repertoires Precedes Commitment to the B and Myeloid Cell Lineages in Hematopoietic Progenitors

(2011) Elinore M. Mercer et al.   IMMUNITY

Transcriptional regulation by STAT6

(2011) Shreevrat Goenka et al.   IMMUNOLOGIC RESEARCH

TGF-β-induced epithelial-mesenchymal transition of A549 lung adenocarcinoma cells is enhanced by pro-inflammatory cytokines derived from RAW 264.7 macrophage cells

(2011) Mikiko Kawata et al.   JOURNAL OF BIOCHEMISTRY

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Crosstalk in NF-κB signaling pathways

(2011) Andrea Oeckinghaus et al.   NATURE IMMUNOLOGY

Inferring transcription factor complexes from ChIP-seq data

(2011) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Modulation of NF- B-dependent gene transcription using programmable DNA minor groove binders

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

PU.1 and C/EBP  synergistically program distinct response to NF- B activation through establishing monocyte specific enhancers

(2011) F. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

(2011) Daniel Wong et al.   GENOME BIOLOGY

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

NF-κB promotes epithelial–mesenchymal transition, migration and invasion of pancreatic carcinoma cells

(2010) Harald J. Maier et al.   CANCER LETTERS

Selective Transcription in Response to an Inflammatory Stimulus

(2010) Stephen T. Smale   CELL

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

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

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

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

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

Synergy between IL-15 and Id2 Promotes the Expansion of Human NK Progenitor Cells, Which Can Be Counteracted by the E Protein HEB Required To Drive T Cell Development

(2010) R. Schotte et al.   JOURNAL OF IMMUNOLOGY

Chromatin Architecture and the Regulation of Nuclear Receptor Inducible Transcription

(2010) S. C. Biddie   JOURNAL OF NEUROENDOCRINOLOGY

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

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Mechanisms Generating Diversity in Glucocorticoid Receptor Signaling

(2009) Javier R. Revollo et al.   Annals of the New York Academy of Sciences

Regulation and Function of NF-κB Transcription Factors in the Immune System

(2009) Sivakumar Vallabhapurapu et al.   Annual Review of Immunology

Persistently Activated Stat3 Maintains Constitutive NF-κB Activity in Tumors

(2009) Heehyoung Lee et al.   CANCER CELL

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

(2009) Sam John et al.   ENDOCRINOLOGY

High expression ofBCL3in human myeloma cells is associated with increased proliferation and inferior prognosis

(2009) Anne-Tove Brenne et al.   EUROPEAN JOURNAL OF HAEMATOLOGY

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

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

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

Foxa1 and Foxa2 regulate bile duct development in mice

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

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

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

(2009) Nathaniel D. Heintzman et al.   NATURE

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Pulsatile Stimulation Determines Timing and Specificity of NF- B-Dependent Transcription

(2009) L. Ashall et al.   SCIENCE

Control of NF- B-dependent Transcriptional Responses by Chromatin Organization

(2009) G. Natoli   Cold Spring Harbor Perspectives in Biology

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

H2AZ Is Enriched at Polycomb Complex Target Genes in ES Cells and Is Necessary for Lineage Commitment

(2008) Menno P. Creyghton et al.   CELL

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

(2008) Effie Apostolou et al.   CELL

Shared Principles in NF-κB Signaling

(2008) Matthew S. Hayden et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

NF-κB and cancer—identifying targets and mechanisms

(2008) Willscott E Naugler et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome-wide profiling of salt fractions maps physical properties of chromatin

(2008) S. Henikoff et al.   GENOME RESEARCH

Bcl-3, a multifaceted modulator of NF-κB-mediated gene transcription

(2008) Scott Palmer et al.   IMMUNOLOGIC RESEARCH

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Multiple facets of junD gene expression are atypical among AP-1 family members

(2008) J M Hernandez et al.   ONCOGENE

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology

Scaling regression inputs by dividing by two standard deviations

(2007) Andrew Gelman   STATISTICS IN MEDICINE