Charting the cis-regulome of activated B cells by coupling structural and functional genomics

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

TSLP signaling in CD4+T cells programs a pathogenic T helper 2 cell state

(2018) Yrina Rochman et al.   Science Signaling

TSLP signaling in CD4+T cells programs a pathogenic T helper 2 cell state

(2018) Yrina Rochman et al.   Science Signaling

Transcription-factor-mediated supervision of global genome architecture maintains B cell identity

(2018) Timothy M. Johanson et al.   NATURE IMMUNOLOGY

Chromatin Accessibility and Interactions in the Transcriptional Regulation of T Cells

(2018) Peng Li et al.   Frontiers in Immunology

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

(2017) Kyong-Rim Kieffer-Kwon et al.   MOLECULAR CELL

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

(2017) Gang Ren et al.   MOLECULAR CELL

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

Mitotic transcription and waves of gene reactivation during mitotic exit

(2017) Katherine C. Palozola et al.   SCIENCE

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

The aryl hydrocarbon receptor controls cell-fate decisions in B cells

(2016) Bharat Vaidyanathan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Recent advances in functional assays of transcriptional enhancers

(2015) Courtney C. Babbitt et al.   GENOMICS

High throughput technologies for the functional discovery of mammalian enhancers: New approaches for understanding transcriptional regulatory network dynamics

(2015) Lisa Dailey   GENOMICS

Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

(2015) Etienne A. Thévenot et al.   JOURNAL OF PROTEOME RESEARCH

Regulation of bifurcating B cell trajectories by mutual antagonism between transcription factors IRF4 and IRF8

(2015) Heping Xu et al.   NATURE IMMUNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

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

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

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate

(2012) R. Mansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer–promoter communication and transcriptional regulation of Igh

(2011) Ananda L Roy et al.   TRENDS IN IMMUNOLOGY

Memories of lost enhancers

(2010) R. Sen et al.   GENES & DEVELOPMENT

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

Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate

(2010) Ye Zheng et al.   NATURE

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE