CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data

The many flavors of monocyte/macrophage--endothelial cell interactions

(2020) Gloria E. Hernandez et al.   CURRENT OPINION IN HEMATOLOGY

Interferon-Induced Transmembrane Protein 3 Genetic Variant rs12252-C Associated With Disease Severity in Coronavirus Disease 2019

(2020) Yonghong Zhang et al.   JOURNAL OF INFECTIOUS DISEASES

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19

(2020) Irani Thevarajan et al.   NATURE MEDICINE

MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses

(2020) Anna Bruchez et al.   SCIENCE

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

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

Microglia-derived TNF-α mediates endothelial necroptosis aggravating blood brain–barrier disruption after ischemic stroke

(2019) An-Qi Chen et al.   Cell Death & Disease

Tissue-specific genes as an underutilized resource in drug discovery

(2019) Maria Ryaboshapkina et al.   Scientific Reports

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Neurovascular Interactions in the Nervous System

(2019) Marta Segarra et al.   Annual Review of Cell and Developmental Biology

The reactome pathway knowledgebase

(2019) Bijay Jassal et al.   NUCLEIC ACIDS RESEARCH

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

New Insights into Microglia–Neuron Interactions: A Neuron’s Perspective

(2018) Balázs Pósfai et al.   NEUROSCIENCE

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

(2018) Daniel A. Skelly et al.   Cell Reports

Widespread Rewiring of Genetic Networks upon Cancer Signaling Pathway Activation

(2018) Maximilian Billmann et al.   Cell Systems

Fibrinogen-like Protein 1 Is a Major Immune Inhibitory Ligand of LAG-3

(2018) Jun Wang et al.   CELL

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

(2018) Merav Cohen et al.   CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

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

(2018) Roser Vento-Tormo et al.   NATURE

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

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

Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons

(2018) Burak Tepe et al.   Cell Reports

Astrocytic neuroligins control astrocyte morphogenesis and synaptogenesis

(2017) Jeff A. Stogsdill et al.   NATURE

Interaction of endothelial cells with macrophages—linking molecular and metabolic signaling

(2017) Joanna Kalucka et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Recombinant Slit2 Reduces Surgical Brain Injury Induced Blood Brain Barrier Disruption via Robo4 Dependent Rac1 Activation in a Rodent Model

(2017) Prativa Sherchan et al.   Scientific Reports

Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes

(2017) Joseph X. Zhou et al.   Scientific Reports

Coinhibitory Pathways in Immunotherapy for Cancer

(2016) Susanne H. Baumeister et al.   Annual Review of Immunology

A benchmark of gene expression tissue-specificity metrics

(2016) Nadezda Kryuchkova-Mostacci et al.   BRIEFINGS IN BIOINFORMATICS

Lag-3, Tim-3, and TIGIT: Co-inhibitory Receptors with Specialized Functions in Immune Regulation

(2016) Ana C. Anderson et al.   IMMUNITY

Coinhibitory Pathways in the B7-CD28 Ligand-Receptor Family

(2016) Frank A. Schildberg et al.   IMMUNITY

Constitutively Expressed IFITM3 Protein in Human Endothelial Cells Poses an Early Infection Block to Human Influenza Viruses

(2016) Xiangjie Sun et al.   JOURNAL OF VIROLOGY

Revealing disease-associated pathways by network integration of untargeted metabolomics

(2016) Leila Pirhaji et al.   NATURE METHODS

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Autocrine Signaling and Quorum Sensing: Extreme Ends of a Common Spectrum

(2016) Berkalp A. Doğaner et al.   TRENDS IN CELL BIOLOGY

Functions of Fibroblast Growth Factor Receptors in cancer defined by novel translocations and mutations

(2015) Leandro H. Gallo et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Wiring the Vascular Network with Neural Cues: A CNS Perspective

(2015) Thomas Wälchli et al.   NEURON

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

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

FGF ligands of the postnatal mammary stroma regulate distinct aspects of epithelial morphogenesis

(2014) X. Zhang et al.   DEVELOPMENT

Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data

(2014) Andrew E. Teschendorff et al.   METHODS

Emerging interactions between skin stem cells and their niches

(2014) Ya-Chieh Hsu et al.   NATURE MEDICINE

Modulating neurotoxicity through CX3CL1/CX3CR1 signaling

(2014) Cristina Limatola et al.   Frontiers in Cellular Neuroscience

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

(2013) Nurcan Tuncbag et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Astrocyte-derived VEGF-A drives blood-brain barrier disruption in CNS inflammatory disease

(2012) Azeb Tadesse Argaw et al.   JOURNAL OF CLINICAL INVESTIGATION

parmigene—a parallel R package for mutual information estimation and gene network reconstruction

(2011) Gabriele Sales et al.   BIOINFORMATICS

Brain Energy Metabolism: Focus on Astrocyte-Neuron Metabolic Cooperation

(2011) Mireille Bélanger et al.   Cell Metabolism

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The Role of the Microenvironment in Mammary Gland Development and Cancer

(2010) K. Polyak et al.   Cold Spring Harbor Perspectives in Biology