Inference and analysis of cell-cell communication using CellChat

Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis

(2020) Helen He et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Dissecting cellular crosstalk by sequencing physically interacting cells

(2020) Amir Giladi et al.   NATURE BIOTECHNOLOGY

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

(2020) Zixuan Cang et al.   Nature Communications

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

(2020) Xin Shao et al.   Protein & Cell

Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly

(2020) Xianwen Ren et al.   CELL RESEARCH

Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing

(2020) Sepideh Abbasi et al.   Cell Stem Cell

AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion protein network

(2020) Afnan Abu-Thuraia et al.   Nature Communications

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

(2019) Christian F. Guerrero-Juarez et al.   Nature Communications

Specificity, versatility, and control of TGF-β family signaling

(2019) Rik Derynck et al.   Science Signaling

Cell lineage and communication network inference via optimization for single-cell transcriptomics

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

STAT 3 Signaling Pathway is Implicated in Keloid Pathogenesis by Preliminary Transcriptome and Open Chromatin Analyses

(2019) Yun‐Shain Lee et al.   EXPERIMENTAL DERMATOLOGY

An Updated Classification of Hair Follicle Morphogenesis

(2019) Nivedita Saxena et al.   EXPERIMENTAL DERMATOLOGY

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization

(2019) Lihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape

(2019) Brian Hie et al.   Cell Systems

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Single-cell connectomic analysis of adult mammalian lungs

(2019) Micha Sam Brickman Raredon et al.   Science Advances

A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration

(2019) Lihua Zhang et al.   IEEE TRANSACTIONS ON FUZZY SYSTEMS

scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data

(2018) Suoqin Jin et al.   BIOINFORMATICS

Skin Cell Heterogeneity in Development, Wound Healing, and Cancer

(2018) Emanuel Rognoni et al.   TRENDS IN CELL BIOLOGY

Hair follicle dermal condensation forms via Fgf20 primed cell cycle exit, cell motility, and aggregation

(2018) Leah C Biggs et al.   eLife

Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent

(2018) Ka-Wai Mok et al.   DEVELOPMENTAL CELL

Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis

(2018) Khusali Gupta et al.   DEVELOPMENTAL CELL

The signaling protein Wnt5a promotes TGFβ1-mediated macrophage polarization and kidney fibrosis by inducing the transcriptional regulators Yap/Taz

(2018) Ye Feng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

Tumor Initiation Capacity and Therapy Resistance Are Differential Features of EMT-Related Subpopulations in the NSCLC Cell Line A549

(2018) Colin Charles Tièche et al.   NEOPLASIA

Wnt5a is elevated in heart failure and affects cardiac fibroblast function

(2017) Aurelija Abraityte et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

Single-cell transcriptomics to explore the immune system in health and disease

(2017) Michael J. T. Stubbington et al.   SCIENCE

Quantification of network structural dissimilarities

(2017) Tiago A. Schieber et al.   Nature Communications

Hierarchical patterning modes orchestrate hair follicle morphogenesis

(2017) James D. Glover et al.   PLOS BIOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Multiple roles of CD90 in cancer

(2016) Atul Kumar et al.   TUMOR BIOLOGY

Agonists and Antagonists of TGF-β Family Ligands

(2016) Chenbei Chang   Cold Spring Harbor Perspectives in Biology

Exploring the role of sphingolipid machinery during the epithelial to mesenchymal transition program using an integrative approach

(2016) Anastasia Meshcheryakova et al.   Oncotarget

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Wnt/β-catenin signaling in dermal condensates is required for hair follicle formation

(2013) Su-Yi Tsai et al.   DEVELOPMENTAL BIOLOGY

Blocking Interleukin-1  Induces a Healing-Associated Wound Macrophage Phenotype and Improves Healing in Type 2 Diabetes

(2013) R. E. Mirza et al.   DIABETES

Fgf20 governs formation of primary and secondary dermal condensations in developing hair follicles

(2013) S.-H. Huh et al.   GENES & DEVELOPMENT

Dermal  -catenin activity in response to epidermal Wnt ligands is required for fibroblast proliferation and hair follicle initiation

(2012) D. Chen et al.   DEVELOPMENT

Negative regulation of Shh levels by Kras and Fgfr2 during hair follicle development

(2012) Anandaroop Mukhopadhyay et al.   DEVELOPMENTAL BIOLOGY

Epidermal Wnt Controls Hair Follicle Induction by Orchestrating Dynamic Signaling Crosstalk between the Epidermis and Dermis

(2012) Jiang Fu et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

A Critical Review of Centrality Measures in Social Networks

(2010) Andrea Landherr et al.   Business & Information Systems Engineering

MIF: a key player in cutaneous biology and wound healing

(2010) Stephen C. Gilliver et al.   EXPERIMENTAL DERMATOLOGY

Disruption of Interleukin-1 Signaling Improves the Quality of Wound Healing

(2009) Alan A. Thomay et al.   AMERICAN JOURNAL OF PATHOLOGY

WNT5A Is a Regulator of Fibroblast Proliferation and Resistance to Apoptosis

(2009) Louis J. Vuga et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

KGF and EGF signalling block hair follicle induction and promote interfollicular epidermal fate in developing mouse skin

(2009) G. D. Richardson et al.   DEVELOPMENT

Osteopontin and the skin: multiple emerging roles in cutaneous biology and pathology

(2009) Franziska Buback et al.   EXPERIMENTAL DERMATOLOGY

Survival and Migration of Human Dendritic Cells Are Regulated by an IFN- -Inducible Axl/Gas6 Pathway

(2009) S. Scutera 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

Molecular mechanisms linking wound inflammation and fibrosis: knockdown of osteopontin leads to rapid repair and reduced scarring

(2008) Ryoichi Mori et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Endothelin 3 Induces Skin Pigmentation in a Keratin-Driven Inducible Mouse Model

(2007) Roman J. Garcia et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY