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

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

Dynamic ADP-Ribosylome, Phosphoproteome, and Interactome in LPS-Activated Macrophages

(2020) Casey M. Daniels et al.   JOURNAL OF PROTEOME RESEARCH

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Integrated Functional Analysis of the Nuclear Proteome of Classically and Alternatively Activated Macrophages

(2019) John E. Wiktorowicz et al.   MEDIATORS OF INFLAMMATION

Divergent Dynamics and Functions of ERK MAP Kinase Signaling in Development, Homeostasis and Cancer: Lessons from Fluorescent Bioimaging

(2019) Yu Muta et al.   Cancers

The Metabolic Signature of Macrophage Responses

(2019) Antonella Viola et al.   Frontiers in Immunology

Manipulating macrophage polarization and function using classical HDAC inhibitors: Implications for autoimmunity and inflammation

(2018) Asadollah Mohammadi et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

The metabolic axis of macrophage and immune cell polarization

(2018) Spencer A. Hobson-Gutierrez et al.   Disease Models & Mechanisms

PPARγ is a nexus controlling alternative activation of macrophages via glutamine metabolism

(2018) Victoria L. Nelson et al.   GENES & DEVELOPMENT

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

Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

(2018) Jesse Lyons et al.   Science Signaling

Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

(2018) Jesse Lyons et al.   Science Signaling

TLR7/8-agonist-loaded nanoparticles promote the polarization of tumour-associated macrophages to enhance cancer immunotherapy

(2018) Christopher B. Rodell et al.   Nature Biomedical Engineering

A curated resource for phosphosite-specific signature analysis

(2018) Karsten Krug et al.   MOLECULAR & CELLULAR PROTEOMICS

Akt Signaling Pathway in Macrophage Activation and M1/M2 Polarization

(2017) Eleni Vergadi et al.   JOURNAL OF IMMUNOLOGY

Proteomic Signature Reveals Modulation of Human Macrophage Polarization and Functions Under Differing Environmental Oxygen Conditions

(2017) Magali Court et al.   MOLECULAR & CELLULAR PROTEOMICS

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities

(2017) John D Lapek et al.   NATURE BIOTECHNOLOGY

Post-transcriptional regulation across human tissues

(2017) Alexander Franks et al.   PLoS Computational Biology

All-Trans Retinoic Acid Promotes an M1- to M2-Phenotype Shift and Inhibits Macrophage-Mediated Immunity to Leishmania major

(2017) Natália S. Vellozo et al.   Frontiers in Immunology

Targeting Platelet-Derived Growth Factor Receptor β + Scaffold Formation Inhibits Choroidal Neovascularization

(2016) Karin Strittmatter et al.   AMERICAN JOURNAL OF PATHOLOGY

Spatial and Temporal Regulation of Receptor Tyrosine Kinase Activation and Intracellular Signal Transduction

(2016) John J.M. Bergeron et al.   Annual Review of Biochemistry

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Macrophages in Tissue Repair, Regeneration, and Fibrosis

(2016) Thomas A. Wynn et al.   IMMUNITY

The TORC1-activated Proteins, p70S6K and GRB10, Regulate IL-4 Signaling and M2 Macrophage Polarization by Modulating Phosphorylation of Insulin Receptor Substrate-2

(2016) Kristi J. Warren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MEK1/2 Inhibition Promotes Macrophage Reparative Properties

(2016) Matthew E. Long et al.   JOURNAL OF IMMUNOLOGY

Synergistic activation ofArg1gene by retinoic acid and IL-4 involves chromatin remodeling for transcription initiation and elongation coupling

(2016) Bomi Lee et al.   NUCLEIC ACIDS RESEARCH

Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation

(2016) Anthony J Covarrubias et al.   eLife

All Trans Retinoic Acid, Transforming Growth Factor β and Prostaglandin E2 in Mouse Plasma Synergize with Basophil-Secreted Interleukin-4 to M2 Polarize Murine Macrophages

(2016) Victor W. Ho et al.   PLoS One

Macrophage polarization in experimental and clinical choroidal neovascularization

(2016) Yu Yang et al.   Scientific Reports

Perivascular M2 Macrophages Stimulate Tumor Relapse after Chemotherapy

(2015) R. Hughes et al.   CANCER RESEARCH

Abundance of infiltrating CD163+ cells in the retina of postmortem eyes with dry and neovascular age-related macular degeneration

(2015) Eleonora M. Lad et al.   GRAEFES ARCHIVE FOR CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY

Quantitative proteomics analyses of activation states of human THP-1 macrophages

(2015) Kees Meijer et al.   Journal of Proteomics

Retinoic Acid Signaling Coordinates Macrophage-Dependent Injury and Repair after AKI

(2015) T. Chiba et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Myeloid expression of the AP-1 transcription factor JUNB modulates outcomes of type 1 and type 2 parasitic infections

(2015) M. F. Fontana et al.   PARASITE IMMUNOLOGY

Control of macrophage metabolism and activation by mTOR and Akt signaling

(2015) Anthony J. Covarrubias et al.   SEMINARS IN IMMUNOLOGY

ROCK-Isoform-Specific Polarization of Macrophages Associated with Age-Related Macular Degeneration

(2015) Souska Zandi et al.   Cell Reports

Regulation of EGFR signal transduction by analogue-to-digital conversion in endosomes

(2015) Roberto Villaseñor et al.   eLife

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

Macrophage Activation and Polarization: Nomenclature and Experimental Guidelines

(2014) Peter J. Murray et al.   IMMUNITY

Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation

(2014) Jia Xue et al.   IMMUNITY

Doxycycline Inhibits Polarization of Macrophages to the Proangiogenic M2-type and Subsequent Neovascularization

(2014) Lizhi He et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

JUNB Is a Key Transcriptional Modulator of Macrophage Activation

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

Phosphoproteome Profiling of the Macrophage Response to Different Toll-Like Receptor Ligands Identifies Differences in Global Phosphorylation Dynamics

(2014) Virginie Sjoelund et al.   JOURNAL OF PROTEOME RESEARCH

Macrophages Are Essential for the Early Wound Healing Response and the Formation of a Fibrovascular Scar

(2013) Lizhi He et al.   AMERICAN JOURNAL OF PATHOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Genetic programs expressed in resting and IL-4 alternatively activated mouse and human macrophages: similarities and differences

(2013) F. O. Martinez et al.   BLOOD

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

IL-4 and Retinoic Acid Synergistically Induce Regulatory Dendritic Cells Expressing Aldh1a2

(2013) B. Zhu et al.   JOURNAL OF IMMUNOLOGY

RDH10, RALDH2, and CRABP2 are required components of PPARγ-directed ATRA synthesis and signaling in human dendritic cells

(2013) Adrienn Gyöngyösi et al.   JOURNAL OF LIPID RESEARCH

CSF-1R inhibition alters macrophage polarization and blocks glioma progression

(2013) Stephanie M Pyonteck et al.   NATURE MEDICINE

NLRP3 Inflammasome Blockade Inhibits VEGF-A-Induced Age-Related Macular Degeneration

(2013) Alexander G. Marneros   Cell Reports

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses

(2012) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Macrophage plasticity and polarization: in vivo veritas

(2012) Antonio Sica et al.   JOURNAL OF CLINICAL INVESTIGATION

Macrophage plasticity and polarization in tissue repair and remodelling

(2012) Alberto Mantovani et al.   JOURNAL OF PATHOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Role of c-MYC in alternative activation of human macrophages and tumor-associated macrophage biology

(2011) O. M. Pello et al.   BLOOD

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Kinase-Dead BRAF and Oncogenic RAS Cooperate to Drive Tumor Progression through CRAF

(2010) Sonja J. Heidorn et al.   CELL

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

(2010) Edward L. Huttlin et al.   CELL

Control of Macrophage Activation and Function by PPARs

(2010) Ajay Chawla   CIRCULATION RESEARCH

Macrophages, innate immunity and cancer: balance, tolerance, and diversity

(2010) Alberto Mantovani et al.   CURRENT OPINION IN IMMUNOLOGY

Quantitative Analysis of Kinase-Proximal Signaling in Lipopolysaccharide-Induced Innate Immune Response

(2010) Kirti Sharma et al.   JOURNAL OF PROTEOME RESEARCH

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 phosphoproteome of toll-like receptor-activated macrophages

(2010) Gabriele Weintz et al.   Molecular Systems Biology

RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth

(2010) Georgia Hatzivassiliou et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Antitumor Efficacy of the Novel RAF Inhibitor GDC-0879 Is Predicted by BRAFV600E Mutational Status and Sustained Extracellular Signal-Regulated Kinase/Mitogen-Activated Protein Kinase Pathway Suppression

(2009) K. P. Hoeflich et al.   CANCER RESEARCH

Dynamics of macrophage polarization reveal new mechanism to inhibit IL-1β release through pyrophosphates

(2009) Pablo Pelegrin et al.   EMBO JOURNAL

“Re-educating” tumor-associated macrophages by targeting NF-κB

(2008) Thorsten Hagemann et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Type I IL-4Rs Selectively Activate IRS-2 to Induce Target Gene Expression in Macrophages

(2008) N. M. Heller et al.   Science Signaling

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY