Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

The role of T cell receptor signaling thresholds in guiding T cell fate decisions

(2015) Julie Zikherman et al.   CURRENT OPINION IN IMMUNOLOGY

Expanding the role of metabolism in T cells

(2015) D. O'Sullivan et al.   SCIENCE

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Phenotypes of Th lineages generated by the commonly used activation with anti-CD3/CD28 antibodies differ from those generated by the physiological activation with the specific antigen

(2014) Cuiyan Tan et al.   Cellular & Molecular Immunology

Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains

(2014) Sara Mostafavi et al.   JOURNAL OF IMMUNOLOGY

Graded Levels of IRF4 Regulate CD8+ T Cell Differentiation and Expansion, but Not Attrition, in Response to Acute Virus Infection

(2014) R. Nayar et al.   JOURNAL OF IMMUNOLOGY

The clinical development of MEK inhibitors

(2014) Yujie Zhao et al.   Nature Reviews Clinical Oncology

Targeting RAS–ERK signalling in cancer: promises and challenges

(2014) Ahmed A. Samatar et al.   NATURE REVIEWS DRUG DISCOVERY

A sharp T-cell antigen receptor signaling threshold for T-cell proliferation

(2014) B. B. Au-Yeung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antigen affinity, costimulation, and cytokine inputs sum linearly to amplify T cell expansion

(2014) J. M. Marchingo et al.   SCIENCE

High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry

(2014) Filippos Porichis et al.   Nature Communications

The Histone Methyltransferase Activity of MLL1 Is Dispensable for Hematopoiesis and Leukemogenesis

(2014) Bibhu P. Mishra et al.   Cell Reports

MEK Inhibition, Alone or in Combination with BRAF Inhibition, Affects Multiple Functions of Isolated Normal Human Lymphocytes and Dendritic Cells

(2014) L. J. Vella et al.   Cancer Immunology Research

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

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Single Naive CD4+ T Cells from a Diverse Repertoire Produce Different Effector Cell Types during Infection

(2013) Noah J. Tubo et al.   CELL

The Transcription Factor NFAT Exhibits Signal Memory during Serial T Cell Interactions with Antigen-Presenting Cells

(2013) Francesco Marangoni et al.   IMMUNITY

A Single Peptide-Major Histocompatibility Complex Ligand Triggers Digital Cytokine Secretion in CD4+ T Cells

(2013) Jun Huang et al.   IMMUNITY

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

Themis sets the signal threshold for positive and negative selection in T-cell development

(2013) Guo Fu et al.   NATURE

The transcription factor IRF4 is essential for TCR affinity–mediated metabolic programming and clonal expansion of T cells

(2013) Kevin Man et al.   NATURE IMMUNOLOGY

Vespucci: a system for building annotated databases of nascent transcripts

(2013) Karmel A. Allison et al.   NUCLEIC ACIDS RESEARCH

Convergent and divergent effects of costimulatory molecules in conventional and regulatory CD4+ T cells

(2013) E. Wakamatsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quorum sensing allows T cells to discriminate between self and nonself

(2013) T. C. Butler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Translational Control in CD4+ T Cell Subsets

(2013) Eva Bjur et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Limitations and possibilities of low cell number ChIP-seq

(2012) Gregor D Gilfillan et al.   BMC GENOMICS

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

(2012) Abdenour Soufi et al.   CELL

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

(2012) Jingli A. Zhang et al.   CELL

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

TCR-mediated Erk activation does not depend on Sos and Grb2 in peripheral human T cells

(2012) Nicole Warnecke et al.   EMBO REPORTS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Network Analysis Reveals Centrally Connected Genes and Pathways Involved in CD8+ T Cell Exhaustion versus Memory

(2012) Travis A. Doering et al.   IMMUNITY

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

(2012) Manuel Garber et al.   MOLECULAR CELL

Frequency-Modulated Pulses of ERK Activity Transmit Quantitative Proliferation Signals

(2012) John G. Albeck et al.   MOLECULAR CELL

BATF–JUN is critical for IRF4-mediated transcription in T cells

(2012) Peng Li et al.   NATURE

Metabolic checkpoints in activated T cells

(2012) Ruoning Wang et al.   NATURE IMMUNOLOGY

TRIM28 prevents autoinflammatory T cell development in vivo

(2012) Shunsuke Chikuma et al.   NATURE IMMUNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Genomic Regulatory Element That Directs Assembly and Function of Immune-Specific AP-1-IRF Complexes

(2012) E. Glasmacher et al.   SCIENCE

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

(2011) Alan C. Mullen et al.   CELL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

(2011) Lin Wang et al.   PLoS One

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Interplay of transcription factors in T-cell differentiation and function: the role of Runx

(2010) Won Fen Wong et al.   IMMUNOLOGY

Cutting Edge: TCR Ligation Triggers Digital Activation of NF- B

(2010) L. M. Kingeter et al.   JOURNAL OF IMMUNOLOGY

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

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

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

Perspectives for Computer Modeling in the Study of T Cell Activation

(2010) J. Coward et al.   Cold Spring Harbor Perspectives in Biology

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

(2009) Jayajit Das et al.   CELL

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

(2009) Gang Wei et al.   IMMUNITY

Plasticity of CD4+ T Cell Lineage Differentiation

(2009) Liang Zhou et al.   IMMUNITY

Origin of the sharp boundary that discriminates positive and negative selection of thymocytes

(2008) A. Prasad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative challenges in understanding ligand discrimination by αβ T cells

(2007) Ofer Feinerman et al.   MOLECULAR IMMUNOLOGY