The role of chromatin dynamics in immune cell development

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

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

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

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

(2013) D. R. Winter et al.   GENOME RESEARCH

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

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

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells

(2013) Bruno Di Stefano et al.   NATURE

Uniform, optimal signal processing of mapped deep-sequencing data

(2013) Vibhor Kumar et al.   NATURE BIOTECHNOLOGY

Regulatory T cells in nonlymphoid tissues

(2013) Dalia Burzyn et al.   NATURE IMMUNOLOGY

Short-term memory of danger signals and environmental stimuli in immune cells

(2013) Silvia Monticelli et al.   NATURE IMMUNOLOGY

Tissue-resident macrophages

(2013) Luke C Davies et al.   NATURE IMMUNOLOGY

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

Deciphering cis-regulatory control in inflammatory cells

(2013) S. Ghisletti et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

(2013) Leila Taher et al.   GENOME BIOLOGY

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

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

(2012) Jingli A. Zhang et al.   CELL

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Polycomb-group proteins in hematopoietic stem cell regulation and hematopoietic neoplasms

(2012) V Radulović et al.   LEUKEMIA

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

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

(2012) Emmanuel L Gautier et al.   NATURE IMMUNOLOGY

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

Natural Innate and Adaptive Immunity to Cancer

(2011) Matthew D. Vesely et al.   Annual Review of Immunology

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

(2011) G. Hu et al.   GENOME RESEARCH

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu 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

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

(2011) Laure Escoubet-Lozach et al.   PLoS Genetics

Epigenetic Priming of a Pre-B Cell-Specific Enhancer through Binding of Sox2 and Foxd3 at the ESC Stage

(2010) Daniel Liber et al.   Cell Stem Cell

Epigenetic propagation of CD4 expression is established by the Cd4 proximal enhancer in helper T cells

(2010) M. M. W. Chong et al.   GENES & DEVELOPMENT

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

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

Maintaining Cell Identity through Global Control of Genomic Organization

(2010) Gioacchino Natoli   IMMUNITY

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

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

A preoccupied position on nucleosomes

(2010) B Franklin Pugh   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

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

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

(2009) Francesca De Santa et al.   EMBO JOURNAL

Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells

(2009) Yasuto Araki et al.   IMMUNITY

Tumor-associated macrophages (TAM) as major players of the cancer-related inflammation

(2009) G. Solinas et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development

(2009) Duncan M Gascoyne et al.   NATURE IMMUNOLOGY

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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

(2008) Mathieu Lupien et al.   CELL

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

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

(2008) Alan P. Boyle et al.   CELL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY