Identification of a broadly fibrogenic macrophage subset induced by type 3 inflammation

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

(2022) Martin Guilliams et al.   CELL

TREM-2 plays a protective role in cholestasis by acting as a negative regulator of inflammation

(2022) Ibone Labiano et al.   JOURNAL OF HEPATOLOGY

Soluble TREM2 levels reflect the recruitment and expansion of TREM2+ macrophages that localize to fibrotic areas and limit NASH

(2022) Tim Hendrikx et al.   JOURNAL OF HEPATOLOGY

Nebulosa recovers single-cell gene expression signals by kernel density estimation

(2021) Jose Alquicira-Hernandez et al.   BIOINFORMATICS

Dynamic Shifts in the Composition of Resident and Recruited Macrophages Influence Tissue Remodeling in NASH

(2021) Sabine Daemen et al.   Cell Reports

TREM2 sustains macrophage-hepatocyte metabolic coordination in nonalcoholic fatty liver disease and sepsis

(2021) Jinchao Hou et al.   JOURNAL OF CLINICAL INVESTIGATION

TREM2 Regulates Microglial Cholesterol Metabolism upon Chronic Phagocytic Challenge

(2020) Alicia A. Nugent et al.   NEURON

Establishment and Maintenance of the Macrophage Niche

(2020) Martin Guilliams et al.   IMMUNITY

Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis

(2020) Jason S. Seidman et al.   IMMUNITY

Variability in the analysis of a single neuroimaging dataset by many teams

(2020) Rotem Botvinik-Nezer et al.   NATURE

Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis

(2020) Tatsuya Tsukui et al.   Nature Communications

Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human

(2020) Juanjuan Zhao et al.   Cell Discovery

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

(2020) Taylor S. Adams et al.   Science Advances

Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

(2020) Arun C. Habermann et al.   Science Advances

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma

(2020) Ankur Sharma et al.   CELL

TREM-2 defends the liver against hepatocellular carcinoma through multifactorial protective mechanisms

(2020) Aitor Esparza-Baquer et al.   GUT

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver

(2020) Anneleen Remmerie et al.   IMMUNITY

The Genetic Architecture of Carbon Tetrachloride-Induced Liver Fibrosis in Mice

(2020) Iina Tuominen et al.   Cellular and Molecular Gastroenterology and Hepatology

Fibrosis: from mechanisms to medicines

(2020) Neil C. Henderson et al.   NATURE

Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

(2019) Diego Adhemar Jaitin et al.   CELL

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

(2019) Christina Morse et al.   EUROPEAN RESPIRATORY JOURNAL

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease

(2019) Eleanor Valenzi et al.   ANNALS OF THE RHEUMATIC DISEASES

Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis

(2019) Xuelian Xiong et al.   MOLECULAR CELL

A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signaling in monocyte-derived alveolar macrophages

(2019) Nikita Joshi et al.   EUROPEAN RESPIRATORY JOURNAL

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine AtherosclerosisNovelty and Significance

(2018) Clément Cochain et al.   CIRCULATION RESEARCH

Non-parenchymal TREM-2 protects the liver from immune-mediated hepatocellular damage

(2018) Maria J Perugorria et al.   GUT

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

(2017) Alexander V. Misharin et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Pathology of non-alcoholic fatty liver disease

(2017) Pierre Bedossa   LIVER INTERNATIONAL

Mechanisms of hepatic stellate cell activation

(2017) Takuma Tsuchida et al.   Nature Reviews Gastroenterology & Hepatology

Inflammation and metabolism in tissue repair and regeneration

(2017) Sabine A. Eming et al.   SCIENCE

Type 2 immunity is protective in metabolic disease but exacerbates NAFLD collaboratively with TGF-β

(2017) Kevin M. Hart et al.   Science Translational Medicine

Macrophages in Tissue Repair, Regeneration, and Fibrosis

(2016) Thomas A. Wynn et al.   IMMUNITY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

TIMP-1 mediates TGF-β-dependent crosstalk between hepatic stellate and cancer cells via FAK signaling

(2015) Sang-A Park et al.   Scientific Reports

Glycoprotein Nonmetastatic Melanoma B (Gpnmb)-Positive Macrophages Contribute to the Balance between Fibrosis and Fibrolysis during the Repair of Acute Liver Injury in Mice

(2015) Kotaro Kumagai et al.   PLoS One

Matrix metalloproteinase-9 activates TGF-β and stimulates fibroblast contraction of collagen gels

(2014) Tetsu Kobayashi et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Cigarette Smoke Induction of Osteopontin (SPP1) Mediates TH17 Inflammation in Human and Experimental Emphysema

(2012) M. Shan et al.   Science Translational Medicine

Scraping fibrosis: Expressway to the core of fibrosis

(2011) Wajahat Z Mehal et al.   NATURE MEDICINE

Regulation of Th17 Differentiation by Epidermal Fatty Acid-Binding Protein

(2009) B. Li et al.   JOURNAL OF IMMUNOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY