Inference and analysis of cell-cell communication using CellChat
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Lihua Zhang | Maksim V. Plikus | Qing Nie | Suoqin Jin | Christian F. Guerrero-Juarez | Ivan Chang | Peggy Myung | Q. Nie | Suoqin Jin | M. Plikus | Raul Ramos | C. Guerrero-Juarez | Lihua Zhang | P. Myung | Chen-Hsiang Kuan | Ivan Chang
[1] Leland McInnes,et al. UMAP: Uniform Manifold Approximation and Projection , 2018, J. Open Source Softw..
[2] Long Cai,et al. Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data , 2019, bioRxiv.
[3] A. Danchin. The specification of the immune response revisited , 1982, Survey of immunologic research.
[4] Mauro J. Muraro,et al. Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. , 2019, Developmental cell.
[5] David van Dijk,et al. Manifold learning-based methods for analyzing single-cell RNA-sequencing data , 2018 .
[6] C. Dickson,et al. A crucial role for Fgfr2-IIIb signalling in epidermal development and hair follicle patterning , 2003, Development.
[7] Ulrike von Luxburg,et al. A tutorial on spectral clustering , 2007, Stat. Comput..
[8] Qing Nie,et al. Inferring spatial and signaling relationships between cells from single cell transcriptomic data , 2020, Nature Communications.
[9] Jean-Michel Marin,et al. Confidence bands for Brownian motion and applications to Monte Carlo simulation , 2007, Stat. Comput..
[10] J. Bernhagen,et al. MIF: a key player in cutaneous biology and wound healing , 2011, Experimental dermatology.
[11] Bonnie Berger,et al. Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape. , 2019, Cell systems.
[12] D. D. Cros. Fibroblast growth factor and epidermal growth factor in hair development. , 1993 .
[13] Jean-Loup Guillaume,et al. Fast unfolding of communities in large networks , 2008, 0803.0476.
[14] Kan Liu,et al. Giotto, a toolbox for integrative analysis and visualization of spatial expression data , 2020 .
[15] T. Doetschman,et al. The TGF-beta2 isoform is both a required and sufficient inducer of murine hair follicle morphogenesis. , 1999, Developmental biology.
[16] Y. Kluger,et al. Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis. , 2019, Developmental cell.
[17] T. Koh,et al. Blocking Interleukin-1β Induces a Healing-Associated Wound Macrophage Phenotype and Improves Healing in Type 2 Diabetes , 2013, Diabetes.
[18] Altuna Akalin,et al. netSmooth: Network-smoothing based imputation for single cell RNA-seq , 2017, bioRxiv.
[19] Amos Tanay,et al. Dissecting cellular crosstalk by sequencing physically interacting cells , 2020, Nature Biotechnology.
[20] Mirjana Efremova,et al. CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes , 2020, Nature Protocols.
[21] W. Border,et al. Transforming Growth Factor β in Tissue Fibrosis , 1994 .
[22] Panos M. Pardalos,et al. Quantification of network structural dissimilarities , 2017, Nature Communications.
[23] Shihua Zhang,et al. A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration , 2020, IEEE Transactions on Fuzzy Systems.
[24] B. Hinz,et al. Wound‐healing defect of CD18−/− mice due to a decrease in TGF‐β1 and myofibroblast differentiation , 2005, The EMBO journal.
[25] Darren J. Burgess,et al. Spatial transcriptomics coming of age , 2019, Nature Reviews Genetics.
[26] Benjamin J. Raphael,et al. Network propagation: a universal amplifier of genetic associations , 2017, Nature Reviews Genetics.
[27] N. Kaminski,et al. WNT5A is a regulator of fibroblast proliferation and resistance to apoptosis. , 2009, American journal of respiratory cell and molecular biology.
[28] G. Christensen,et al. Wnt5a is elevated in heart failure and affects cardiac fibroblast function , 2017, Journal of Molecular Medicine.
[29] R. Atit,et al. Dermal β-catenin activity in response to epidermal Wnt ligands is required for fibroblast proliferation and hair follicle initiation , 2012, Development.
[30] Michael J. T. Stubbington,et al. Single-cell transcriptomics to explore the immune system in health and disease , 2017, Science.
[31] A. Rezza,et al. Wnt/β-catenin signaling in dermal condensates is required for hair follicle formation. , 2014, Developmental biology.
[32] Benjamin D. Yu,et al. Negative regulation of Shh levels by Kras and Fgfr2 during hair follicle development. , 2013, Developmental biology.
[33] R. Galiano,et al. Macrophage colony-stimulating factor accelerates wound healing and upregulates TGF-beta1 mRNA levels through tissue macrophages. , 1997, The Journal of surgical research.
[34] J. Albina,et al. Disruption of interleukin-1 signaling improves the quality of wound healing. , 2009, The American journal of pathology.
[35] W. Hsu,et al. Epidermal Wnt controls hair follicle induction by orchestrating dynamic signaling crosstalk between the epidermis and dermis , 2012, The Journal of investigative dermatology.
[36] J. Weiss,et al. Osteopontin and the skin: multiple emerging roles in cutaneous biology and pathology , 2009, Experimental dermatology.
[37] Angela M. Christiano,et al. KGF and EGF signalling block hair follicle induction and promote interfollicular epidermal fate in developing mouse skin , 2009, Development.
[38] Kerstin B. Meyer,et al. Single-cell reconstruction of the early maternal–fetal interface in humans , 2018, Nature.
[39] M J Banda,et al. Wound macrophages express TGF-alpha and other growth factors in vivo: analysis by mRNA phenotyping. , 1988, Science.
[40] S. Millar,et al. WNT signals are required for the initiation of hair follicle development. , 2002, Developmental cell.
[41] Matthew J Ford,et al. Hierarchical patterning modes orchestrate hair follicle morphogenesis , 2017, PLoS biology.
[42] Douglas A. Lauffenburger,et al. Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics , 2018, Cell reports.
[43] Q. Nie,et al. scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles , 2020, Genome Biology.
[44] M. Mikkola,et al. Fgf20 governs formation of primary and secondary dermal condensations in developing hair follicles. , 2013, Genes & development.
[45] T. Shaw,et al. Molecular mechanisms linking wound inflammation and fibrosis: knockdown of osteopontin leads to rapid repair and reduced scarring , 2008, The Journal of experimental medicine.
[46] M. Mikkola,et al. Hair follicle dermal condensation forms via Fgf20 primed cell cycle exit, cell motility, and aggregation , 2018, eLife.
[47] Andrea Landherr,et al. A Critical Review of Centrality Measures in Social Networks , 2010, Bus. Inf. Syst. Eng..
[48] Jacques Colinge,et al. SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics , 2020, Nucleic acids research.
[49] Qing Nie,et al. Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds , 2019, Nature Communications.
[50] Y. Saeys,et al. NicheNet: modeling intercellular communication by linking ligands to target genes , 2019, Nature Methods.
[51] R. Satija,et al. Integrative single-cell analysis , 2019, Nature Reviews Genetics.
[52] Randy L. Johnson,et al. The signaling protein Wnt5a promotes TGFβ1-mediated macrophage polarization and kidney fibrosis by inducing the transcriptional regulators Yap/Taz , 2018, The Journal of Biological Chemistry.
[53] Xianwen Ren,et al. Reconstruction of cell spatial organization based on ligand-receptor mediated self-assembly , 2020, bioRxiv.
[54] E. Birney,et al. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.
[55] M. Horan,et al. Estrogen modulates cutaneous wound healing by downregulating macrophage migration inhibitory factor. , 2003, The Journal of clinical investigation.
[56] P. Murphy,et al. Chemokine Receptor CX3CR1 Mediates Skin Wound Healing by Promoting Macrophage and Fibroblast Accumulation and Function1 , 2008, The Journal of Immunology.
[57] Elaine Fuchs,et al. A Signaling Pathway Involving TGF-β2 and Snail in Hair Follicle Morphogenesis , 2004, PLoS biology.
[58] D. Foreman,et al. Neutralising antibody to TGF-beta 1,2 reduces cutaneous scarring in adult rodents. , 1994, Journal of cell science.
[59] Carter T. Butts,et al. Social Network Analysis with sna , 2008 .
[60] W. Ge,et al. Single-cell Transcriptome Profiling reveals Dermal and Epithelial cell fate decisions during Embryonic Hair Follicle Development , 2019, bioRxiv.
[61] H. Bazzi,et al. Transcriptional profiling of developing mouse epidermis reveals novel patterns of coordinated gene expression , 2007, Developmental dynamics : an official publication of the American Association of Anatomists.
[62] Ka-Wai Mok,et al. An updated classification of hair follicle morphogenesis , 2019, Experimental dermatology.
[63] J. Ajani,et al. iTALK: an R Package to Characterize and Illustrate Intercellular Communication , 2019, bioRxiv.
[64] Damian Szklarczyk,et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..
[65] R. Derynck,et al. Specificity, versatility, and control of TGF-β family signaling , 2019, Science Signaling.
[66] B. Hogan,et al. Altered wound healing in mice lacking a functional osteopontin gene (spp1). , 1998, The Journal of clinical investigation.
[67] M. Elowitz,et al. Challenges and emerging directions in single-cell analysis , 2017, Genome Biology.
[68] Tao Peng,et al. scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data , 2018, Bioinform..
[69] Y. Kluger,et al. Single-cell connectomic analysis of adult mammalian lungs , 2019, Science Advances.
[70] E. Fuchs,et al. Programming gene expression in developing epidermis. , 1994, Development.
[71] F. Watt,et al. Skin Cell Heterogeneity in Development, Wound Healing, and Cancer , 2018, Trends in cell biology.
[72] Minoru Kanehisa,et al. KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..
[73] Qing Nie,et al. Cell lineage and communication network inference via optimization for single-cell transcriptomics , 2019, Nucleic acids research.
[74] H. Sebastian Seung,et al. Learning the parts of objects by non-negative matrix factorization , 1999, Nature.
[75] Leland McInnes,et al. UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction , 2018, ArXiv.
[76] C. Chuong,et al. STAT3 signalling pathway is implicated in keloid pathogenesis by preliminary transcriptome and open chromatin analyses , 2019, Experimental dermatology.
[77] W. Eaglstein,et al. Interleukin-1 enhances epidermal wound healing. , 1990, Lymphokine research.