Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Multi-study inference of regulatory networks for more accurate models of gene regulation

(2019) Dayanne M. Castro et al.   PLoS Computational Biology

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

(2018) Jianhong Ou et al.   BMC GENOMICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

A cellular and molecular view of T helper 17 cell plasticity in autoimmunity

(2018) Ralph Stadhouders et al.   JOURNAL OF AUTOIMMUNITY

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

(2018) Konstantine Tchourine et al.   Cell Reports

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility

(2017) Xi Chen et al.   NUCLEIC ACIDS RESEARCH

Modeling gene regulation from paired expression and chromatin accessibility data

(2017) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility

(2017) David Lamparter et al.   PLoS Computational Biology

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation

(2017) Ricardo N. Ramirez et al.   Cell Systems

The obesity-related pathology and Th17 cells

(2016) Yusuke Endo et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Biophysically Motivated Regulatory Network Inference: Progress and Prospects

(2016) Tarmo Äijö et al.   HUMAN HEREDITY

A prior-based integrative framework for functional transcriptional regulatory network inference

(2016) Alireza F. Siahpirani et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

The maternal interleukin-17a pathway in mice promotes autism-like phenotypes in offspring

(2016) G. B. Choi et al.   SCIENCE

Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks

(2016) André F. Rendeiro et al.   Nature Communications

The role of neutrophils in the pathogenesis of systemic lupus erythematosus

(2015) Carolyne K. Smith et al.   CURRENT OPINION IN RHEUMATOLOGY

Th17 Cell Pathway in Human Immunity: Lessons from Genetics and Therapeutic Interventions

(2015) Dhavalkumar D. Patel et al.   IMMUNITY

STAT3-Activating Cytokines: A Therapeutic Opportunity for Inflammatory Bowel Disease?

(2015) Paul M. Nguyen et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

(2015) M. L. Arrieta-Ortiz et al.   Molecular Systems Biology

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

(2015) Charles Blatti et al.   NUCLEIC ACIDS RESEARCH

A validated gene regulatory network and GWAS identifies early regulators of T cell–associated diseases

(2015) Mika Gustafsson et al.   Science Translational Medicine

TRRUST: a reference database of human transcriptional regulatory interactions

(2015) Heonjong Han et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Metformin Ameliorates Inflammatory Bowel Disease by Suppression of the STAT3 Signaling Pathway and Regulation of the between Th17/Treg Balance

(2015) Seon-Yeong Lee et al.   PLoS One

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

(2014) Michael T. McCarthy et al.   BIOINFORMATICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Functional association networks as priors for gene regulatory network inference

(2014) Matthew E. Studham et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A review on the computational approaches for gene regulatory network construction

(2014) Lian En Chai et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Inhibiting RORγt/Th17 axis for autoimmune disorders

(2014) Fujio Isono et al.   DRUG DISCOVERY TODAY

Complex interactions of transcription factors in mediating cytokine biology in T cells

(2014) Peng Li et al.   IMMUNOLOGICAL REVIEWS

Novel NFKB2 Mutation in Early-Onset CVID

(2014) Yiwen Liu et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Combined Immune Deficiency in a Patient with a Novel NFKB2 Mutation

(2014) Andrew W. Lindsley et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods

(2014) Jing Qin et al.   METHODS

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

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

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

TFClass: a classification of human transcription factors and their rodent orthologs

(2014) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

Th17 Pathway-Mediated Immunopathogenesis of Schizophrenia: Mechanisms and Implications

(2014) M. Debnath et al.   SCHIZOPHRENIA BULLETIN

Targeting Th17 cells in autoimmune diseases

(2014) Jianfei Yang et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Germline Mutations in NFKB2 Implicate the Noncanonical NF-κB Pathway in the Pathogenesis of Common Variable Immunodeficiency

(2013) Karin Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

IL-17 signaling accelerates the progression of nonalcoholic fatty liver disease in mice

(2013) Isaac T.W. Harley et al.   HEPATOLOGY

Dynamic regulatory network controlling TH17 cell differentiation

(2013) Nir Yosef 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

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Deleterious Mutations in LRBA Are Associated with a Syndrome of Immune Deficiency and Autoimmunity

(2012) Gabriela Lopez-Herrera et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Validated Regulatory Network for Th17 Cell Specification

(2012) Maria Ciofani et al.   CELL

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The dual nature of Ets-1: Focus to the pathogenesis of systemic lupus erythematosus

(2011) Rui-Xue Leng et al.   AUTOIMMUNITY REVIEWS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

(2011) Yao Fu et al.   BMC BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Th17 and Regulatory T Cells in Mediating and Restraining Inflammation

(2010) Dan R. Littman et al.   CELL

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma 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

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Th17 cells at the crossroads of innate and adaptive immunity against infectious diseases at the mucosa

(2009) S A Khader et al.   Mucosal Immunology

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

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

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

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

(2008) Alan P. Boyle et al.   CELL

Autoimmune Manifestations in Common Variable Immunodeficiency

(2008) C. Cunningham-Rundles   JOURNAL OF CLINICAL IMMUNOLOGY

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

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

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY