Functional heterogeneity of alveolar macrophage population based on expression of CXCL2

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Dectin-1 Binding to Annexins on Apoptotic Cells Induces Peripheral Immune Tolerance via NADPH Oxidase-2

(2019) Kevin Bode et al.   Cell Reports

Macrophage phenotype and bioenergetics are controlled by oxidized phospholipids identified in lean and obese adipose tissue

(2018) Vlad Serbulea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

(2018) Charlotte L. Scott et al.   IMMUNITY

Rim Pathway-Mediated Alterations in the Fungal Cell Wall Influence Immune Recognition and Inflammation

(2017) Kyla S. Ost et al.   mBio

MafB is a critical regulator of complement component C1q

(2017) Mai Thi Nhu Tran et al.   Nature Communications

Precision-cut Mouse Lung Slices to Visualize Live Pulmonary Dendritic Cells

(2017) Miranda R. Lyons-Cohen et al.   Jove-Journal of Visualized Experiments

Tissue-Resident Macrophages in Fungal Infections

(2017) Shengjie Xu et al.   Frontiers in Immunology

DUSP5 functions as a feedback regulator of TNFα-induced ERK1/2 dephosphorylation and inflammatory gene expression in adipocytes

(2017) Justine S. Habibian et al.   Scientific Reports

Yolk Sac Macrophages, Fetal Liver, and Adult Monocytes Can Colonize an Empty Niche and Develop into Functional Tissue-Resident Macrophages

(2016) Lianne van de Laar et al.   IMMUNITY

A Protocol for the Comprehensive Flow Cytometric Analysis of Immune Cells in Normal and Inflamed Murine Non-Lymphoid Tissues

(2016) Yen-Rei A. Yu et al.   PLoS One

MerTK cleavage limits proresolving mediator biosynthesis and exacerbates tissue inflammation

(2016) Bishuang Cai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line

(2015) Lauren A Solomon et al.   BMC GENOMICS

SOD2 targeted gene editing by CRISPR/Cas9 yields Human cells devoid of MnSOD

(2015) Kimberly Cramer-Morales et al.   FREE RADICAL BIOLOGY AND MEDICINE

C-Myb+ Erythro-Myeloid Progenitor-Derived Fetal Monocytes Give Rise to Adult Tissue-Resident Macrophages

(2015) Guillaume Hoeffel et al.   IMMUNITY

C1q Deficiency Promotes Pulmonary Vascular Inflammation and Enhances the Susceptibility of the Lung Endothelium to Injury

(2015) Dilip Shah et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

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

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

Autophagy enhances NFκB activity in specific tissue macrophages by sequestering A20 to boost antifungal immunity

(2015) Masashi Kanayama et al.   Nature Communications

Compartment-Specific and Sequential Role of MyD88 and CARD9 in Chemokine Induction and Innate Defense during Respiratory Fungal Infection

(2015) Anupam Jhingran et al.   PLoS Pathogens

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

(2015) Malika Charrad et al.   Journal of Statistical Software

Novel Markers to Delineate Murine M1 and M2 Macrophages

(2015) Kyle A. Jablonski et al.   PLoS One

Embryonic and Adult-Derived Resident Cardiac Macrophages Are Maintained through Distinct Mechanisms at Steady State and during Inflammation

(2014) Slava Epelman et al.   IMMUNITY

Complement protein C1q promotes macrophage anti-inflammatory M2-like polarization during the clearance of atherogenic lipoproteins

(2014) Weston Spivia et al.   INFLAMMATION RESEARCH

Pulmonary macrophage transplantation therapy

(2014) Takuji Suzuki et al.   NATURE

Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors

(2014) Elisa Gomez Perdiguero et al.   NATURE

Cell-intrinsic lysosomal lipolysis is essential for alternative activation of macrophages

(2014) Stanley Ching-Cheng Huang et al.   NATURE IMMUNOLOGY

Regulation of O2 consumption by the PI3K and mTOR pathways contributes to tumor hypoxia

(2014) Catherine J. Kelly et al.   RADIOTHERAPY AND ONCOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Tissue-Resident Macrophages Self-Maintain Locally throughout Adult Life with Minimal Contribution from Circulating Monocytes

(2013) Daigo Hashimoto et al.   IMMUNITY

Macrophage M1/M2 Polarization Dynamically Adapts to Changes in Cytokine Microenvironments in Cryptococcus neoformans Infection

(2013) M. J. Davis et al.   mBio

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Inhibiting Mer receptor tyrosine kinase suppresses STAT1, SOCS1/3, and NF-κB activation and enhances inflammatory responses in lipopolysaccharide-induced acute lung injury

(2012) Ye-Ji Lee et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Hidden Killers: Human Fungal Infections

(2012) G. D. Brown et al.   Science Translational Medicine

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Molecular Mechanisms for Synchronized Transcription of Three Complement C1q Subunit Genes in Dendritic Cells and Macrophages

(2011) Guobao Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Paradoxical roles of alveolar macrophages in the host response to Cryptococcus neoformans

(2011) Travis J. McQuiston et al.   JOURNAL OF INFECTION AND CHEMOTHERAPY

Targeted PPARγ deficiency in alveolar macrophages disrupts surfactant catabolism

(2010) Anna D. Baker et al.   JOURNAL OF LIPID RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Role of Dendritic Cells and Alveolar Macrophages in Regulating Early Host Defense against Pulmonary Infection with Cryptococcus neoformans

(2009) J. J. Osterholzer et al.   INFECTION AND IMMUNITY

Arginase in Parasitic Infections: Macrophage Activation, Immunosuppression, and Intracellular Signals

(2009) Cinthia C. Stempin et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Enhanced Innate Immune Responsiveness to Pulmonary Cryptococcus neoformans Infection Is Associated with Resistance to Progressive Infection

(2008) L. Guillot et al.   INFECTION AND IMMUNITY