Related references
Note: Only part of the references are listed.Deep neural networks identify sequence context features predictive of transcription factor binding
An Zheng et al.
NATURE MACHINE INTELLIGENCE (2021)
Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis
Jason S. Seidman et al.
IMMUNITY (2020)
MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function
Zeyang Shen et al.
BIOINFORMATICS (2020)
Global reference mapping of human transcription factor footprints
Jeff Vierstra et al.
NATURE (2020)
The transcription factor EGR2 is the molecular linchpin connecting STAT6 activation to the late, stable epigenomic program of alternative macrophage polarization
Bence Daniel et al.
GENES & DEVELOPMENT (2020)
Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells
Joris van der Veeken et al.
IMMUNITY (2019)
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Ivan Juric et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes
Judith F. Kribelbauer et al.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 35 (2019)
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
Yingyao Zhou et al.
NATURE COMMUNICATIONS (2019)
Brain cell type-specific enhancer-promoter interactome maps and disease-risk association
Alexi Nott et al.
SCIENCE (2019)
Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function
Verena M. Link et al.
CELL (2018)
The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages
Zsolt Czimmerer et al.
IMMUNITY (2018)
Genetic determinants of co-accessible chromatin regions in activated T cells across humans
Rachel E. Gate et al.
NATURE GENETICS (2018)
Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses
Olivier B. Bakker et al.
NATURE IMMUNOLOGY (2018)
MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements
Verena M. Link et al.
NUCLEIC ACIDS RESEARCH (2018)
Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility
Vivek Behera et al.
NATURE COMMUNICATIONS (2018)
The Nuclear Receptor PPARγ Controls Progressive Macrophage Polarization as a Ligand-Insensitive Epigenomic Ratchet of Transcriptional Memory
Bence Daniel et al.
IMMUNITY (2018)
Type 2 immunity in tissue repair and fibrosis
Richard L. Gieseck et al.
NATURE REVIEWS IMMUNOLOGY (2018)
Systematic dissection of genomic features determining transcription factor binding and enhancer function
Sharon R. Grossman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
NRF1 Is an ER Membrane Sensor that Is Central to Cholesterol Homeostasis
Scott B. Widenmaier et al.
CELL (2017)
The Genetics of Transcription Factor DNA Binding Variation
Bart Deplancke et al.
CELL (2016)
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
Maxwell R. Mumbach et al.
NATURE METHODS (2016)
Nrf2 suppresses macrophage inflammatory response by blocking proinflammatory cytokine transcription
Eri H. Kobayashi et al.
NATURE COMMUNICATIONS (2016)
Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages
Dawn Z. Eichenfield et al.
ELIFE (2016)
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions
Fabian Grubert et al.
CELL (2015)
Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo
Raymond E. Soccio et al.
CELL (2015)
Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness
Justin Crocker et al.
CELL (2015)
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans
Sebastian M. Waszak et al.
CELL (2015)
Predicting effects of noncoding variants with deep learning-based sequence model
Jian Zhou et al.
NATURE METHODS (2015)
limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie et al.
NUCLEIC ACIDS RESEARCH (2015)
Suboptimization of developmental enhancers
Emma K. Farley et al.
SCIENCE (2015)
Genetic and epigenetic fine mapping of causal autoimmune disease variants
Kyle Kai-How Farh et al.
NATURE (2015)
EGR2 is critical for peripheral naive T-cell differentiation and the T-cell response to influenza
Ning Du et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression
Benjamin P. Fairfax et al.
SCIENCE (2014)
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law et al.
GENOME BIOLOGY (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin et al.
BIOINFORMATICS (2013)
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Warren A. Whyte et al.
CELL (2013)
Latent Enhancers Activated by Stimulation in Differentiated Cells
Renato Ostuni et al.
CELL (2013)
Effect of natural genetic variation on enhancer selection and function
S. Heinz et al.
NATURE (2013)
Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription
Helena Kilpinen et al.
SCIENCE (2013)
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
Stefan Bonn et al.
NATURE GENETICS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS
Qunhua Li et al.
ANNALS OF APPLIED STATISTICS (2011)
Transcriptional regulation by STAT6
Shreevrat Goenka et al.
IMMUNOLOGIC RESEARCH (2011)
Kruppel-like factor 4 regulates macrophage polarization
Xudong Liao et al.
JOURNAL OF CLINICAL INVESTIGATION (2011)
Mouse genomic variation and its effect on phenotypes and gene regulation
Thomas M. Keane et al.
NATURE (2011)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
Alternative Activation of Macrophages: Mechanism and Functions
Siamon Gordon et al.
IMMUNITY (2010)
Interleukin-4 induced interferon regulatory factor (Irf) 4 participates in the regulation of alternative macrophage priming
Carol El Chartouni et al.
IMMUNOBIOLOGY (2010)
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz et al.
MOLECULAR CELL (2010)
The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection
Takashi Satoh et al.
NATURE IMMUNOLOGY (2010)
Histone H3K27ac separates active from poised enhancers and predicts developmental state
Menno P. Creyghton et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
WGCNA: an R package for weighted correlation network analysis
Peter Langfelder et al.
BMC BIOINFORMATICS (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
Quantifying similarity between motifs
Shobhit Gupta et al.
GENOME BIOLOGY (2007)