CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Dissection of intercellular communication using the transcriptome-based framework ICELLNET

(2021) Floriane Noël et al.   Nature Communications

Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer

(2020) Anthony R. Cillo et al.   IMMUNITY

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

(2020) Mirjana Efremova et al.   Nature Protocols

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

(2020) Simon Cabello-Aguilar et al.   NUCLEIC ACIDS RESEARCH

Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis

(2020) Adrienne Niederriter Shami et al.   DEVELOPMENTAL CELL

BMPR1A is necessary for chondrogenesis and osteogenesis while BMPR1B prevents hypertrophic differentiation

(2020) Tanja Mang et al.   JOURNAL OF CELL SCIENCE

A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions

(2020) Woj M. Wojtowicz et al.   CELL

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

(2020) Ankur Sharma et al.   CELL

Predicting cell-to-cell communication networks using NATMI

(2020) Rui Hou et al.   Nature Communications

Fibroblast Growth Factor 1 Promotes Rat Stem Leydig Cell Development

(2019) Lanlan Chen et al.   Frontiers in Endocrinology

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

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

Multiple signaling pathways in Sertoli cells: recent findings in spermatogenesis

(2019) Fei-Da Ni et al.   Cell Death & Disease

Crosstalk between cancer and immune cells: Role of tumor-associated macrophages in the tumor microenvironment

(2019) Jing Wang et al.   Cancer Medicine

Manipulation of spermatogonial stem cells in livestock species

(2019) Filipp Savvulidi et al.   Journal of Animal Science and Biotechnology

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

(2019) Xuelian Xiong et al.   MOLECULAR CELL

Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization

(2019) Chiara Baccin et al.   NATURE CELL BIOLOGY

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Basis of PD1/PD-L1 Therapies

(2019) Barbara Seliger   Journal of Clinical Medicine

The M2 triangle: gp130 binding cytokines drive macrophages to promote tumor growth

(2018) Dominik Rückerl et al.   IMMUNOLOGY AND CELL BIOLOGY

NF-κB RelA renders tumor-associated macrophages resistant to and capable of directly suppressing CD8+ T cells for tumor promotion

(2018) Liwen Li et al.   OncoImmunology

Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis

(2018) Mei Wang et al.   Cell Stem Cell

Compartments with predominant ephrin-B1 and EphB2/B4 expression are present alternately along the excurrent duct system in the adult mouse testis and epididymis

(2018) M. R. Gofur et al.   Andrology

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

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

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Periodic production of retinoic acid by meiotic and somatic cells coordinates four transitions in mouse spermatogenesis

(2017) Tsutomu Endo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BMP8A sustains spermatogenesis by activating both SMAD1/5/8 and SMAD2/3 in spermatogonia

(2017) Fang-Ju Wu et al.   Science Signaling

The NOTCH Ligand JAG1 Regulates GDNF Expression in Sertoli Cells

(2017) Thomas X. Garcia et al.   STEM CELLS AND DEVELOPMENT

BMP8A sustains spermatogenesis by activating both SMAD1/5/8 and SMAD2/3 in spermatogonia

(2017) Fang-Ju Wu et al.   Science Signaling

Reprogramming of Tumor-Associated Macrophages with Anticancer Therapies: Radiotherapy versus Chemo- and Immunotherapies

(2017) Géraldine Genard et al.   Frontiers in Immunology

Activins in reproductive biology and beyond

(2016) R. Wijayarathna et al.   HUMAN REPRODUCTION UPDATE

Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks

(2016) L. Naomi Handly et al.   JOURNAL OF MOLECULAR BIOLOGY

Metastatic colonization by circulating tumour cells

(2016) Joan Massagué et al.   NATURE

Genetic Dissection of the Host Tropism of Human-Tropic Pathogens

(2015) Florian Douam et al.   Annual Review of Genetics

Biglycan is a novel binding partner of fibroblast growth factor receptor 3c (FGFR3c) in the human testis

(2015) S.B. Winge et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

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

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

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

TRRUST: a reference database of human transcriptional regulatory interactions

(2015) Heonjong Han et al.   Scientific Reports

TNF Counterbalances the Emergence of M2 Tumor Macrophages

(2015) Franz Kratochvill et al.   Cell Reports

BMP4/Smad Signaling Pathway Induces the Differentiation of Mouse Spermatogonial Stem Cells via Upregulation of Sohlh2

(2014) Yi Li et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

Nice Neighborhood: Emerging Concepts of the Stem Cell Niche

(2014) David T. Scadden   CELL

Cell-Cell Communication in the Tumor Microenvironment, Carcinogenesis, and Anticancer Treatment

(2014) Björn L.D.M. Brücher et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

RBPJ in mouse Sertoli cells is required for proper regulation of the testis stem cell niche

(2014) T. X. Garcia et al.   DEVELOPMENT

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

ViRBase: a resource for virus–host ncRNA-associated interactions

(2014) Yanhui Li et al.   NUCLEIC ACIDS RESEARCH

Intercellular adhesion molecules (ICAMs) and spermatogenesis

(2013) Xiang Xiao et al.   HUMAN REPRODUCTION UPDATE

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

Fibroblast growth factor receptor 3 is highly expressed in rarely dividing human type A spermatogonia

(2012) Kathrein Kopylow et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Foxo1 is required in mouse spermatogonial stem cells for their maintenance and the initiation of spermatogenesis

(2011) Meredith J. Goertz et al.   JOURNAL OF CLINICAL INVESTIGATION

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

MotifMap: a human genome-wide map of candidate regulatory motif sites

(2008) Xiaohui Xie et al.   BIOINFORMATICS