Cross-tissue organization of the fibroblast lineage

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Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

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Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

Neutrophils Follow Stromal Omens to Limit Peritoneal Inflammation

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Visualizing and interpreting cancer genomics data via the Xena platform

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Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth

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Reticular Fibroblasts Expressing the Transcription Factor WT1 Define a Stromal Niche that Maintains and Replenishes Splenic Red Pulp Macrophages

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

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Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

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Type I interferon signaling in fibroblastic reticular cells prevents exhaustive activation of antiviral CD8+ T cells

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ClusterMap: Compare multiple Single Cell RNA-Seq datasets across different experimental conditions

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Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes

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Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds

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Adventitial Stromal Cells Define Group 2 Innate Lymphoid Cell Tissue Niches

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Defining the Activated Fibroblast Population in Lung Fibrosis Using Single Cell Sequencing

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A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

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Distinct fibroblast subsets drive inflammation and damage in arthritis

(2019) Adam P. Croft et al.   NATURE

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

(2019) Fan Zhang et al.   NATURE IMMUNOLOGY

Identification of a mesenchymal progenitor cell hierarchy in adipose tissue

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Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp

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Comprehensive Integration of Single-Cell Data

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Correction: Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions (doi: 10.1242/dev.174177)

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A Stromal Niche Defined by Expression of the Transcription Factor WT1 Mediates Programming and Homeostasis of Cavity-Resident Macrophages

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Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

(2019) Ela Elyada et al.   Cancer Discovery

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

(2019) Xuelian Xiong et al.   MOLECULAR CELL

Adventitial Cuffs: Regional Hubs for Tissue Immunity

(2019) Madelene W. Dahlgren et al.   TRENDS IN IMMUNOLOGY

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy

(2019) Claudia X Dominguez et al.   Cancer Discovery

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis

(2019) Ross Dobie et al.   Cell Reports

Hic1 Defines Quiescent Mesenchymal Progenitor Subpopulations with Distinct Functions and Fates in Skeletal Muscle Regeneration

(2019) R. Wilder Scott et al.   Cell Stem Cell

Evasion of apoptosis by myofibroblasts: a hallmark of fibrotic diseases

(2019) Boris Hinz et al.   Nature Reviews Rheumatology

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

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Circuit Design Features of a Stable Two-Cell System

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Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling

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Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

A short field guide to fibroblast function in immunity

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Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis

(2018) Ting Xie et al.   Cell Reports

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

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A stromal cell population that inhibits adipogenesis in mammalian fat depots

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Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice

(2018) Chelsea Hepler et al.   eLife

Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer

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Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

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Context-Dependent Development of Lymphoid Stroma from Adult CD34+ Adventitial Progenitors

(2016) Katarzyna M. Sitnik et al.   Cell Reports

Efficient conditional knockout targeting vector construction using co-selection BAC recombineering (CoSBR)

(2015) Robert J. Newman et al.   NUCLEIC ACIDS RESEARCH

Identification and isolation of a dermal lineage with intrinsic fibrogenic potential

(2015) Y. Rinkevich et al.   SCIENCE

MatchIt: Nonparametric Preprocessing for Parametric Causal Inference

(2015) Daniel E. Ho et al.   Journal of Statistical Software

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

B cell homeostasis and follicle confines are governed by fibroblastic reticular cells

(2014) Viviana Cremasco et al.   NATURE IMMUNOLOGY

Maturation of Lymph Node Fibroblastic Reticular Cells from Myofibroblastic Precursors Is Critical for Antiviral Immunity

(2013) Qian Chai et al.   IMMUNITY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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(2013) Su Wang et al.   Nature Protocols

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

(2012) Emmanuel L Gautier et al.   NATURE IMMUNOLOGY

Transcriptomes of the B and T Lineages Compared by Multiplatform Microarray Profiling

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(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Genomic phenotype of non-cultured pulmonary fibroblasts in idiopathic pulmonary fibrosis

(2010) Margaret C. Emblom-Callahan et al.   GENOMICS

Efficient Generation of Germ Line Transmitting Chimeras from C57BL/6N ES Cells by Aggregation with Outbred Host Embryos

(2010) Marina Gertsenstein et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY