Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Cellular Decision Making by Non-Integrative Processing of TLR Inputs

(2017) Ryan A. Kellogg et al.   Cell Reports

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

(2016) Ge Tan et al.   BIOINFORMATICS

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

Autophagy Proteins ATG5 and ATG7 Are Essential for the Maintenance of Human CD34+Hematopoietic Stem-Progenitor Cells

(2016) Maria Catalina Gomez-Puerto et al.   STEM CELLS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways

(2015) Xiuli Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Network dynamics determine the autocrine and paracrine signaling functions of TNF

(2014) Andrew B. Caldwell et al.   GENES & DEVELOPMENT

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

(2014) Jonathan D. Brown et al.   MOLECULAR CELL

ATM regulates NF-κB-dependent immediate-early genes via RelA Ser 276 phosphorylation coupled to CDK9 promoter recruitment

(2014) Ling Fang et al.   NUCLEIC ACIDS RESEARCH

The NF-κB Genomic Landscape in Lymphoblastoid B Cells

(2014) Bo Zhao et al.   Cell Reports

IRF5:RelA Interaction Targets Inflammatory Genes in Macrophages

(2014) David G. Saliba et al.   Cell Reports

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

NBPF is a potential DNA-binding transcription factor that is directly regulated by NF-κB

(2013) Fei Zhou et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-Seq

(2013) Jun Yang et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Guoliang Li et al.   CELL

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

(2012) Argyris Papantonis et al.   EMBO JOURNAL

Telomerase directly regulates NF-κB-dependent transcription

(2012) Arkasubhra Ghosh et al.   NATURE CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

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

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

The Human Epigenome Browser at Washington University

(2011) Xin Zhou et al.   NATURE METHODS

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma

(2011) Volkhard Seitz et al.   PLoS One

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

Bcl-6 and NF- B cistromes mediate opposing regulation of the innate immune response

(2010) G. D. Barish et al.   GENES & DEVELOPMENT

Single Round of Antigen Receptor Signaling Programs Naive B Cells to Receive T Cell Help

(2010) Bazarragchaa Damdinsuren et al.   IMMUNITY

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

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

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

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

(2009) Shengli Hao et al.   NATURE IMMUNOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

The NF- B Family of Transcription Factors and Its Regulation

(2009) A. Oeckinghaus et al.   Cold Spring Harbor Perspectives in Biology

The Nuclear IκB Protein IκBζ Specifically Binds NF-κB p50 Homodimers and Forms a Ternary Complex on κB DNA

(2008) Dan V. Trinh et al.   JOURNAL OF MOLECULAR BIOLOGY

RelA Ser276 Phosphorylation Is Required for Activation of a Subset of NF- B-Dependent Genes by Recruiting Cyclin-Dependent Kinase 9/Cyclin T1 Complexes

(2008) D. E. Nowak et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY