Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

(2018) Verena M. Link et al.   CELL

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages

(2018) Zsolt Czimmerer et al.   IMMUNITY

The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages

(2018) Bence Daniel et al.   NUCLEIC ACIDS RESEARCH

Unsupervised Learning and Pattern Recognition of Biological Data Structures with Density Functional Theory and Machine Learning

(2018) Chien-Chang Chen et al.   Scientific Reports

The Role of Activator Protein-1 (AP-1) Family Members in CD30-Positive Lymphomas

(2018) Ines Garces de los Fayos Alonso et al.   Cancers

Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF

(2017) Kyuho Kang et al.   IMMUNITY

Toll-Like Receptor Ligands and Interferon-γ Synergize for Induction of Antitumor M1 Macrophages

(2017) Elisabeth Müller et al.   Frontiers in Immunology

OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation

(2016) Zoltan Simandi et al.   MOLECULAR CELL

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

A dualcis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages

(2015) Alessandra Mancino et al.   GENES & DEVELOPMENT

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Modeling the relationship of epigenetic modifications to transcription factor binding

(2015) Liang Liu et al.   NUCLEIC ACIDS RESEARCH

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast

(2015) Zing Tsung-Yeh Tsai et al.   PLoS Computational Biology

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

(2014) B. Daniel et al.   GENES & DEVELOPMENT

JUNB Is a Key Transcriptional Modulator of Macrophage Activation

(2014) Mary F. Fontana et al.   JOURNAL OF IMMUNOLOGY

Ligand Binding Shifts Highly Mobile Retinoid X Receptor to the Chromatin-Bound State in a Coactivator-Dependent Manner, as Revealed by Single-Cell Imaging

(2014) P. Brazda et al.   MOLECULAR AND CELLULAR BIOLOGY

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Peroxisome Proliferator-Activated Receptor   and C/EBP  Synergistically Activate Key Metabolic Adipocyte Genes by Assisted Loading

(2013) M. S. Madsen et al.   MOLECULAR AND CELLULAR 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

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Predicting enhancer transcription and activity from chromatin modifications

(2013) Yun Zhu et al.   NUCLEIC ACIDS RESEARCH

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Genome-Wide Profiling of Peroxisome Proliferator-Activated Receptor   in Primary Epididymal, Inguinal, and Brown Adipocytes Reveals Depot-Selective Binding Correlated with Gene Expression

(2012) M. S. Siersbaek et al.   MOLECULAR AND CELLULAR BIOLOGY

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

(2011) M. Leddin et al.   BLOOD

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Live-cell fluorescence correlation spectroscopy dissects the role of coregulator exchange and chromatin binding in retinoic acid receptor mobility

(2011) P. Brazda et al.   JOURNAL OF CELL SCIENCE

Multilevel support vector regression analysis to identify condition-specific regulatory networks

(2010) Li Chen et al.   BIOINFORMATICS

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

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

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

(2010) Serena Ghisletti et al.   IMMUNITY

Alternative Activation of Macrophages: Mechanism and Functions

(2010) Siamon Gordon et al.   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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

PU.1 and C/EBP /  convert fibroblasts into macrophage-like cells

(2008) R. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA