Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs

Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity

(2019) Nicholas N. Jarjour et al.   NATURE IMMUNOLOGY

Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells

(2019) Federico Comoglio et al.   GENES & DEVELOPMENT

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

Myeloid cell recruitment versus local proliferation differentiates susceptibility from resistance to filarial infection

(2018) Sharon M Campbell et al.   eLife

The Nuclear Receptor PPARγ Controls Progressive Macrophage Polarization as a Ligand-Insensitive Epigenomic Ratchet of Transcriptional Memory

(2018) Bence Daniel et al.   IMMUNITY

TFClass: expanding the classification of human transcription factors to their mammalian orthologs

(2017) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Zinc Induces Dendritic Cell Tolerogenic Phenotype and Skews Regulatory T Cell–Th17 Balance

(2016) Mariam Mathew George et al.   JOURNAL OF IMMUNOLOGY

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Deconvolving the Recognition of DNA Shape from Sequence

(2015) Namiko Abe et al.   CELL

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data

(2014) Michael T. McCarthy et al.   BIOINFORMATICS

Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct

(2014) U. M. Gundra et al.   BLOOD

RGMb is a novel binding partner for PD-L2 and its engagement with PD-L2 promotes respiratory tolerance

(2014) Yanping Xiao et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2014) Iros Barozzi et al.   MOLECULAR CELL

Neutrophils prime a long-lived effector macrophage phenotype that mediates accelerated helminth expulsion

(2014) Fei Chen et al.   NATURE IMMUNOLOGY

The Transcription Factor Gata6 Links Tissue Macrophage Phenotype and Proliferative Renewal

(2014) M. Rosas et al.   SCIENCE

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

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

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

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

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

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

An essential role for TH2-type responses in limiting acute tissue damage during experimental helminth infection

(2012) Fei Chen et al.   NATURE MEDICINE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The genomic landscapes of inflammation

(2011) G. Natoli et al.   GENES & DEVELOPMENT

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

Local Macrophage Proliferation, Rather than Recruitment from the Blood, Is a Signature of TH2 Inflammation

(2011) S. J. Jenkins et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Serena Ghisletti 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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH