The diversification of methods for studying cell–cell interactions and communication

E Armingol, HM Baghdassarian, NE Lewis - Nature Reviews Genetics, 2024 - nature.com
No cell lives in a vacuum, and the molecular interactions between cells define most
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …

Cell–cell communication: new insights and clinical implications

J Su, Y Song, Z Zhu, X Huang, J Fan, J Qiao… - Signal Transduction and …, 2024 - nature.com
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …

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

D Dimitrov, D Türei, M Garrido-Rodriguez… - Nature …, 2022 - nature.com
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

Z Cang, Y Zhao, AA Almet, A Stabell, R Ramos… - Nature …, 2023 - nature.com
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing
datasets provide unprecedented opportunities to dissect cell–cell communication (CCC) …

High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer

S Salcher, G Sturm, L Horvath, G Untergasser… - Cancer cell, 2022 - cell.com
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …

Squidpy: a scalable framework for spatial omics analysis

G Palla, H Spitzer, M Klein, D Fischer, AC Schaar… - Nature …, 2022 - nature.com
Spatial omics data are advancing the study of tissue organization and cellular
communication at an unprecedented scale. Flexible tools are required to store, integrate and …

[HTML][HTML] Spatial multi-omic map of human myocardial infarction

C Kuppe, RO Ramirez Flores, Z Li, S Hayat… - Nature, 2022 - nature.com
Myocardial infarction is a leading cause of death worldwide. Although advances have been
made in acute treatment, an incomplete understanding of remodelling processes has limited …

decoupleR: ensemble of computational methods to infer biological activities from omics data

P Badia-i-Mompel, J Vélez Santiago… - Bioinformatics …, 2022 - academic.oup.com
Many methods allow us to extract biological activities from omics data using information from
prior knowledge resources, reducing the dimensionality for increased statistical power and …

[HTML][HTML] Fibrin drives thromboinflammation and neuropathology in COVID-19

JK Ryu, Z Yan, M Montano, EG Sozmen, K Dixit… - Nature, 2024 - nature.com
Life-threatening thrombotic events and neurological symptoms are prevalent in COVID-19
and are persistent in patients with long COVID experiencing post-acute sequelae of SARS …

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

Y Zhang, T Liu, X Hu, M Wang, J Wang… - Nucleic acids …, 2021 - academic.oup.com
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies,
the systematic decoding of cell-cell communication has received great research interest. To …