High-density P300 enhancers control cell state transitions

Super-enhancers delineate disease-associated regulatory nodes in T cells

(2015) Golnaz Vahedi et al.   NATURE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

(2014) Daniel C. Factor et al.   Cell Stem Cell

Small-Molecule RORγt Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms

(2014) Sheng Xiao et al.   IMMUNITY

miR-155 Activates Cytokine Gene Expression in Th17 Cells by Regulating the DNA-Binding Protein Jarid2 to Relieve Polycomb-Mediated Repression

(2014) Thelma M. Escobar et al.   IMMUNITY

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Caspase-11 activation requires lysis of pathogen-containing vacuoles by IFN-induced GTPases

(2014) Etienne Meunier et al.   NATURE

PVT1 dependence in cancer with MYC copy-number increase

(2014) Yuen-Yi Tseng et al.   NATURE

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-γ Locus

(2013) J. Antonio Gomez et al.   CELL

BET bromodomain inhibition suppresses TH17-mediated pathology

(2013) Deanna A. Mele et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Enhanced Atherosclerosis in TIPE2-Deficient Mice Is Associated with Increased Macrophage Responses to Oxidized Low-Density Lipoprotein

(2013) Y. Lou et al.   JOURNAL OF IMMUNOLOGY

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

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

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1

(2013) Chuan Wu et al.   NATURE

Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation

(2013) Gangqing Hu et al.   NATURE IMMUNOLOGY

Predicting enhancer transcription and activity from chromatin modifications

(2013) Yun Zhu et al.   NUCLEIC ACIDS RESEARCH

Mutation in the SLC29A3 Gene: A New Cause of a Monogenic, Autoinflammatory Condition

(2013) I. Melki et al.   PEDIATRICS

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

HIV-1 infection of human macrophages directly induces viperin which inhibits viral production

(2012) N. Nasr et al.   BLOOD

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

(2012) Robert M. Samstein et al.   CELL

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

A Cluster of Interferon-γ-Inducible p65 GTPases Plays a Critical Role in Host Defense against Toxoplasma gondii

(2012) Masahiro Yamamoto et al.   IMMUNITY

KAP1/TRIM28: An inhibitor of IRF5 function in inflammatory macrophages

(2012) H.L. Eames et al.   IMMUNOBIOLOGY

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

GBP5 Promotes NLRP3 Inflammasome Assembly and Immunity in Mammals

(2012) A. R. Shenoy et al.   SCIENCE

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

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

(2011) Gang Wei et al.   IMMUNITY

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Equilibrative Nucleoside Transporter 3 Deficiency Perturbs Lysosome Function and Macrophage Homeostasis

(2011) C.-L. Hsu et al.   SCIENCE

A Family of IFN- -Inducible 65-kD GTPases Protects Against Bacterial Infection

(2011) B.-H. Kim et al.   SCIENCE

RNA-Binding Protein L1TD1 Interacts with LIN28 via RNA and is Required for Human Embryonic Stem Cell Self-Renewal and Cancer Cell Proliferation

(2011) Elisa Närvä et al.   STEM CELLS

Regulation of MicroRNA Expression and Abundance during Lymphopoiesis

(2010) Stefan Kuchen et al.   IMMUNITY

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

(2010) Serena Ghisletti et al.   IMMUNITY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Suppression of inflammation by a synthetic histone mimic

(2010) Edwige Nicodeme et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Genome-wide assessment of differential roles for p300 and CBP in transcription regulation

(2010) Y. F. M. Ramos et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

CCR 7 Ligands Are Required for Development of Experimental Autoimmune Encephalomyelitis through Generating IL-23-Dependent Th17 Cells

(2009) T. Kuwabara et al.   JOURNAL OF IMMUNOLOGY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS

The STAT3 NH2-terminal Domain Stabilizes Enhanceosome Assembly by Interacting with the p300 Bromodomain

(2008) Tieying Hou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY