GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks

CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia

(2022) Lixiazi He et al.   EMBO Molecular Medicine

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

(2022) Jacob W. Freimer et al.   NATURE GENETICS

Inferring and perturbing cell fate regulomes in human brain organoids

(2022) Jonas Simon Fleck et al.   NATURE

MBD2 serves as a viable target against pulmonary fibrosis by inhibiting macrophage M2 program

(2021) Yi Wang et al.   Science Advances

Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

(2021) Gloriia Novikova et al.   Nature Communications

IRF8 Is an AML-Specific Susceptibility Factor That Regulates Signaling Pathways and Proliferation of AML Cells

(2021) Franziska Liss et al.   Cancers

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

MBD2 acts as a repressor to maintain the homeostasis of the Th1 program in type 1 diabetes by regulating the STAT1-IFN-γ axis

(2021) Tiantian Yue et al.   CELL DEATH AND DIFFERENTIATION

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

(2021) Urmo Võsa et al.   NATURE GENETICS

ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination

(2021) Quan Xu et al.   NUCLEIC ACIDS RESEARCH

Transcription factors: Bridge between cell signaling and gene regulation

(2021) Paula Weidemüller et al.   PROTEOMICS

Enhancers in disease: molecular basis and emerging treatment strategies

(2021) Annique Claringbould et al.   TRENDS IN MOLECULAR MEDICINE

The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection

(2021) Wanhai Qin et al.   Frontiers in Immunology

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

(2021) Fayrouz Hammal et al.   NUCLEIC ACIDS RESEARCH

Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors

(2021) Lizhi He et al.   Cell Reports

Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of NFKB1 Knockout THP1 Cells

(2021) Domenico Somma et al.   Frontiers in Immunology

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions

(2020) Ignacio L. Ibarra et al.   Nature Communications

The Methyl-CpG-Binding Protein Mbd2 Regulates Susceptibility to Experimental Colitis via Control of CD11c+ Cells and Colonic Epithelium

(2020) Gareth-Rhys Jones et al.   Frontiers in Immunology

Targeted Perturb-seq enables genome-scale genetic screens in single cells

(2020) Daniel Schraivogel et al.   NATURE METHODS

Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension

(2020) Armando Reyes-Palomares et al.   Nature Communications

The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection

(2020) Alexandre Giraud-Gatineau et al.   eLife

Predictive features of gene expression variation reveal mechanistic link with differential expression

(2020) Olga M Sigalova et al.   Molecular Systems Biology

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons

(2020) Daria Bunina et al.   Cell Systems

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Emerging Evasion Mechanisms of Macrophage Defenses by Pathogenic Bacteria

(2020) Clarisse Leseigneur et al.   Frontiers in Cellular and Infection Microbiology

Communications Between Bone Marrow Macrophages and Bone Cells in Bone Remodeling

(2020) Kaixuan Chen et al.   Frontiers in Cell and Developmental Biology

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

(2019) Luca Cassetta et al.   CANCER CELL

Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML.

(2019) Swati Garg et al.   BLOOD

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

(2019) Alexandra B Keenan et al.   NUCLEIC ACIDS RESEARCH

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Macrophage Polarization: Different Gene Signatures in M1(LPS+) vs. Classically and M2(LPS–) vs. Alternatively Activated Macrophages

(2019) Marco Orecchioni et al.   Frontiers in Immunology

Transfer of regulatory knowledge from human to mouse for functional genomic analysis

(2019) Christian H. Holland et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

The contribution of macrophages to systemic lupus erythematosus

(2019) Chunyan Ma et al.   CLINICAL IMMUNOLOGY

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

TRIM59 expression is regulated by Sp1 and Nrf1 in LPS-activated macrophages through JNK signaling pathway

(2019) Yanying An et al.   CELLULAR SIGNALLING

Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

(2019) Ivan Berest et al.   Cell Reports

Emerging role of lncRNAs in systemic lupus erythematosus

(2018) Chan-Na Zhao et al.   BIOMEDICINE & PHARMACOTHERAPY

Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data

(2018) Shuonan Chen et al.   BMC BIOINFORMATICS

Enhancers: bridging the gap between gene control and human disease

(2018) Jaret M Karnuta et al.   HUMAN MOLECULAR GENETICS

The impact of interferon-regulatory factors to macrophage differentiation and polarization into M1 and M2

(2018) Dimitry A. Chistiakov et al.   IMMUNOBIOLOGY

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

(2018) Kaur Alasoo et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data

(2018) Vân Anh Huynh-Thu et al.   Scientific Reports

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

(2018) Wilberforce Zachary Ouma et al.   PLoS Computational Biology

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression

(2017) Yanxia Guo et al.   JOURNAL OF IMMUNOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation

(2016) David Langlais et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Macrophages: An Inflammatory Link Between Angiogenesis and Lymphangiogenesis

(2016) Bruce A. Corliss et al.   MICROCIRCULATION

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

Macrophage heterogeneity in the context of rheumatoid arthritis

(2016) Irina A. Udalova et al.   Nature Reviews Rheumatology

Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection

(2016) Athma A. Pai et al.   PLoS Genetics

Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha

(2016) Janine Weber et al.   eLife

DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells

(2016) Sarah J Hainer et al.   eLife

Role of Cathepsins in Mycobacterium tuberculosis Survival in Human Macrophages

(2016) David Pires et al.   Scientific Reports

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

Excessive Production of IFN-  in Patients with Systemic Lupus Erythematosus and Its Contribution to Induction of B Lymphocyte Stimulator/B Cell-Activating Factor/TNF Ligand Superfamily-13B

(2014) M. Harigai et al.   JOURNAL OF IMMUNOLOGY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Role of p38 MAPK and STAT3 in lipopolysaccharide-stimulated mouse alveolar macrophages

(2014) AIHONG MENG et al.   Experimental and Therapeutic Medicine

Metal ions in macrophage antimicrobial pathways: emerging roles for zinc and copper

(2013) Sian L. Stafford et al.   BIOSCIENCE REPORTS

Mapping functional transcription factor networks from gene expression data

(2013) B. C. Haynes et al.   GENOME RESEARCH

Tumor Necrosis Factor-α Signaling in Macrophages

(2012) Narayanan Parameswaran et al.   CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION

Copper at the Front Line of the Host-Pathogen Battle

(2012) Richard A. Festa et al.   PLoS Pathogens

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Fra-1 negatively regulates lipopolysaccharide-mediated inflammatory responses

(2009) H. Morishita et al.   INTERNATIONAL IMMUNOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT