Context-aware deconvolution of cell–cell communication with Tensor-cell2cell

Characterization of cell-cell communication in autistic brains with single-cell transcriptomes

(2022) Maider Astorkia et al.   Journal of Neurodevelopmental Disorders

CorrIndex: A permutation invariant performance index

(2022) Elaheh Sobhani et al.   SIGNAL PROCESSING

Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

(2022) Daniel Dimitrov et al.   Nature Communications

Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

(2021) Rogan A. Grant et al.   NATURE

Normalization of single-cell RNA-seq counts by log(x + 1)* or log(1 + x)*

(2021) A Sina Booeshaghi et al.   BIOINFORMATICS

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Dissection of intercellular communication using the transcriptome-based framework ICELLNET

(2021) Floriane Noël et al.   Nature Communications

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation

(2021) Fan Zhang et al.   Genome Medicine

Context-aware synthetic biology by controller design: Engineering the mammalian cell

(2021) Nika Shakiba et al.   Cell Systems

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

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

The role of MIF in chronic lung diseases: looking beyond inflammation

(2020) Laura Florez-Sampedro et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

(2020) Mingfeng Liao et al.   NATURE MEDICINE

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

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

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

Circulating immune cell phenotype dynamics reflect the strength of tumor–immune cell interactions in patients during immunotherapy

(2020) Jason I. Griffiths et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of MIF Cytokine/CD74 Receptor Pathway in Protecting Against Injury and Promoting Repair

(2020) Laura Farr et al.   Frontiers in Immunology

An aberrant STAT pathway is central to COVID-19

(2020) Toshifumi Matsuyama et al.   CELL DEATH AND DIFFERENTIATION

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

(2020) Cameron Martino et al.   NATURE BIOTECHNOLOGY

Monocyte activation in systemic Covid-19 infection: Assay and rationale

(2020) Fernando O. Martinez et al.   EBioMedicine

Physiology of Midkine and Its Potential Pathophysiological Role in COVID-19

(2020) Giulia Sanino et al.   Frontiers in Physiology

Enhanced expression of immune checkpoint receptors during SARS-CoV-2 viral infection

(2020) Narjes Saheb Sharif-Askari et al.   Molecular Therapy-Methods & Clinical Development

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

(2019) Shuxiong Wang et al.   NUCLEIC ACIDS RESEARCH

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

A perturbed gene network containing PI3K–AKT, RAS–ERK and WNT–β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity

(2019) Vahid H. Gazestani et al.   NATURE NEUROSCIENCE

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

Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis

(2018) Alex H. Williams et al.   NEURON

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

CD99 at the crossroads of physiology and pathology

(2018) Michela Pasello et al.   Journal of Cell Communication and Signaling

Enter the Matrix: Factorization Uncovers Knowledge from Omics

(2018) Genevieve L. Stein-O’Brien et al.   TRENDS IN GENETICS

Neuregulin1 types mRNA level changes in autism spectrum disorder, and is associated with deficit in executive functions

(2018) Samane Abbasy et al.   EBioMedicine

Quantification of network structural dissimilarities

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

Monocyte infiltration into obese and fibrilized tissues is regulated by PILRα

(2016) Masako Kohyama et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Advancing the understanding of autism disease mechanisms through genetics

(2016) Luis de la Torre-Ubieta et al.   NATURE MEDICINE

TIM-3 Regulates Distinct Functions in Macrophages

(2016) Ranferi Ocaña-Guzman et al.   Frontiers in Immunology

Semaphorin-Plexin Signaling Controls Mitotic Spindle Orientation during Epithelial Morphogenesis and Repair

(2015) Jingjing Xia et al.   DEVELOPMENTAL CELL

Serum Syndecan-4 as a Possible Biomarker in Patients With Acute Pneumonia

(2015) Takefumi Nikaido et al.   JOURNAL OF INFECTIOUS DISEASES

Amyloid Precursor Protein Mediated Changes in Intestinal Epithelial Phenotype In Vitro

(2015) Kendra L. Puig et al.   PLoS One

The Gini Index and Measures of Inequality

(2014) Frank A. Farris   AMERICAN MATHEMATICAL MONTHLY

Context-dependent transcriptional regulations between signal transduction pathways

(2011) Sohyun Hwang et al.   BMC BIOINFORMATICS

Transcription and translation of human F11R gene are required for an initial step of atherogenesis induced by inflammatory cytokines

(2011) Bani M Azari et al.   Journal of Translational Medicine

Feedback regulation of EGFR signalling: decision making by early and delayed loops

(2011) Roi Avraham et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Midkine in Inflammation

(2011) Ludwig T. Weckbach et al.   TheScientificWorldJOURNAL

Transepithelial Migration of Neutrophils

(2008) Rachel L. Zemans et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Computing non-negative tensor factorizations

(2008) Michael P. Friedlander et al.   OPTIMIZATION METHODS & SOFTWARE