Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

[1]  Y. Saeys,et al.  Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches , 2021, bioRxiv.

[2]  F. Ginhoux,et al.  A subset of Kupffer cells regulates metabolism through the expression of CD36. , 2021, Immunity.

[3]  F. Ginhoux,et al.  Identification of a Kupffer cell subset capable of reverting the T cell dysfunction induced by hepatocellular priming , 2021, Immunity.

[4]  Agnès Desroches-Castan,et al.  BMP9 and BMP10: Two close vascular quiescence partners that stand out , 2021, Developmental dynamics : an official publication of the American Association of Anatomists.

[5]  F. Ginhoux,et al.  Genetic fate-mapping reveals surface accumulation but not deep organ invasion of pleural and peritoneal cavity macrophages following injury , 2021, Nature Communications.

[6]  A. Regev,et al.  Towards a Human Cell Atlas: Taking Notes from the Past. , 2021, Trends in genetics : TIG.

[7]  S. Klein,et al.  Dynamic Shifts in the Composition of Resident and Recruited Macrophages Influence Tissue Remodeling in NASH , 2021, Cell reports.

[8]  Aaron M. Streets,et al.  Joint probabilistic modeling of single-cell multi-omic data with totalVI , 2021, Nature Methods.

[9]  Andrea J. Radtke,et al.  Commensal-driven immune zonation of the liver promotes host defence , 2020, Nature.

[10]  Justine Jia Wen Seow,et al.  Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma , 2020, Cell.

[11]  Y. Saeys,et al.  Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver , 2020, Immunity.

[12]  Amit A. Patel,et al.  Longevity and replenishment of human liver-resident memory T cells and mononuclear phagocytes , 2020, The Journal of experimental medicine.

[13]  Lin Cheng,et al.  Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19 , 2020, Nature Medicine.

[14]  A. Saliba,et al.  Single-cell transcriptomic profiling maps monocyte/macrophage transitions after myocardial infarction in mice , 2020, bioRxiv.

[15]  M. Bajénoff,et al.  Establishment and Maintenance of the Macrophage Niche. , 2020, Immunity.

[16]  Y. Saeys,et al.  NicheNet: modeling intercellular communication by linking ligands to target genes , 2019, Nature Methods.

[17]  Natalia Gimelshein,et al.  PyTorch: An Imperative Style, High-Performance Deep Learning Library , 2019, NeurIPS.

[18]  Astrid Gall,et al.  Ensembl 2020 , 2019, Nucleic Acids Res..

[19]  C. Ponting,et al.  Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis , 2019, Cell reports.

[20]  Y. Saeys,et al.  Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche , 2019, Immunity.

[21]  C. Glass,et al.  Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity. , 2019, Immunity.

[22]  Fred A. Hamprecht,et al.  ilastik: interactive machine learning for (bio)image analysis , 2019, Nature Methods.

[23]  Kamil Slowikowski,et al.  Fast, sensitive, and accurate integration of single cell data with Harmony , 2019, Nature Methods.

[24]  C. Ponting,et al.  Resolving the fibrotic niche of human liver cirrhosis at single cell level , 2019, Nature.

[25]  I. Amit,et al.  Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner , 2019, Cell.

[26]  Dominic Grün,et al.  A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors , 2019, Nature.

[27]  S. Fleury,et al.  Transcriptional network analysis implicates altered hepatic immune function in NASH development and resolution , 2019, Nature Metabolism.

[28]  Jing Wang,et al.  WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs , 2019, Nucleic Acids Res..

[29]  M. Tosolini,et al.  Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets , 2019, bioRxiv.

[30]  Paul J. Hoffman,et al.  Comprehensive Integration of Single-Cell Data , 2018, Cell.

[31]  Michael I. Jordan,et al.  Deep Generative Modeling for Single-cell Transcriptomics , 2018, Nature Methods.

[32]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[33]  Y. Saeys,et al.  The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages , 2018, Immunity.

[34]  Uri Alon,et al.  Circuit Design Features of a Stable Two-Cell System , 2018, Cell.

[35]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[36]  Alfonso Valencia,et al.  APPRIS 2017: principal isoforms for multiple gene sets , 2017, Nucleic Acids Res..

[37]  William Ritchie,et al.  A Liver Capsular Network of Monocyte‐Derived Macrophages Restricts Hepatic Dissemination of Intraperitoneal Bacteria by Neutrophil Recruitment , 2017, Immunity.

[38]  H. Swerdlow,et al.  Large-scale simultaneous measurement of epitopes and transcriptomes in single cells , 2017, Nature Methods.

[39]  I. Amit,et al.  A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease , 2017, Cell.

[40]  M. Guilliams,et al.  Does niche competition determine the origin of tissue-resident macrophages? , 2017, Nature Reviews Immunology.

[41]  Aaron T. L. Lun,et al.  Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R , 2017, Bioinform..

[42]  I. Amit,et al.  Single-cell spatial reconstruction reveals global division of labor in the mammalian liver , 2016, Nature.

[43]  John C Marioni,et al.  A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor , 2016, F1000Research.

[44]  Cynthia C. Hession,et al.  Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons , 2016, Science.

[45]  Andrew D. Rouillard,et al.  Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..

[46]  D. Kleiner,et al.  Histology of Nonalcoholic Fatty Liver Disease and Nonalcoholic Steatohepatitis in Adults and Children. , 2016, Clinics in liver disease.

[47]  Y. Saeys,et al.  Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells , 2016, Nature Communications.

[48]  V. Lukacs-Kornek,et al.  The Complex Myeloid Network of the Liver with Diverse Functional Capacity at Steady State and in Inflammation , 2015, Front. Immunol..

[49]  Roland Eils,et al.  circlize implements and enhances circular visualization in R , 2014, Bioinform..

[50]  Sean Gerrish,et al.  Black Box Variational Inference , 2013, AISTATS.

[51]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[52]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[53]  A. Andrianopoulos,et al.  mpeg1 promoter transgenes direct macrophage-lineage expression in zebrafish. , 2011, Blood.

[54]  D. Stainier,et al.  Hematopoietic stem cells derive directly from aortic endothelium during development , 2009, Nature.

[55]  B. Ruffell,et al.  CD44 and its role in inflammation and inflammatory diseases. , 2009, Inflammation & allergy drug targets.

[56]  Jason D. Gans,et al.  Improved assay-dependent searching of nucleic acid sequence databases , 2008, Nucleic acids research.

[57]  O. Cummings,et al.  Relationship of steatosis grade and zonal location to histological features of steatohepatitis in adult patients with non-alcoholic fatty liver disease. , 2008, Journal of hepatology.

[58]  V. Kaartinen,et al.  ALK5- and TGFBR2-independent role of ALK1 in the pathogenesis of hereditary hemorrhagic telangiectasia type 2. , 2008, Blood.

[59]  Jonas Larsson,et al.  Activin receptor-like kinase (ALK)1 is an antagonistic mediator of lateral TGFbeta/ALK5 signaling. , 2003, Molecular cell.

[60]  A. Gerbes,et al.  The role of graft-resident Kupffer cells and lymphocytes of donor type during the time course after liver transplantation—a clinico-pathological study , 2003, Virchows Archiv.

[61]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[62]  D. Vivien,et al.  Chimeric extracellular domain type II transforming growth factor (TGF)-beta receptor fused to the Fc region of human immunoglobulin as a TGF-beta antagonist. , 1998, European journal of biochemistry.

[63]  M. Furie,et al.  The adhesion molecules used by monocytes for migration across endothelium include CD11a/CD18, CD11b/CD18, and VLA-4 on monocytes and ICAM-1, VCAM-1, and other ligands on endothelium. , 1995, Journal of immunology.

[64]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .