Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

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 …

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) …

The landscape of cell–cell communication through single-cell transcriptomics

AA Almet, Z Cang, S Jin, Q Nie - Current opinion in systems biology, 2021 - Elsevier
Cell–cell communication is a fundamental process that shapes biological tissue. Historically,
studies of cell–cell communication have been feasible for one or two cell types and a few …

Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network

W Yang, P Wang, S Xu, T Wang, M Luo, Y Cai… - Nature …, 2024 - nature.com
The inference of cell–cell communication (CCC) is crucial for a better understanding of
complex cellular dynamics and regulatory mechanisms in biological systems. However …

Integrated intra‐and intercellular signaling knowledge for multicellular omics analysis

D Türei, A Valdeolivas, L Gul… - Molecular systems …, 2021 - embopress.org
Molecular knowledge of biological processes is a cornerstone in omics data analysis.
Applied to single‐cell data, such analyses provide mechanistic insights into individual cells …

Cell–cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies

L Peng, F Wang, Z Wang, J Tan, L Huang… - Briefings in …, 2022 - academic.oup.com
Carcinomas are complex ecosystems composed of cancer, stromal and immune cells.
Communication between these cells and their microenvironments induces cancer …

Whole-body gene expression atlas of an adult metazoan

A Ghaddar, E Armingol, C Huynh, L Gevirtzman… - Science …, 2023 - science.org
Gene activity defines cell identity, drives intercellular communication, and underlies the
functioning of multicellular organisms. We present the single-cell resolution atlas of gene …

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

E Armingol, HM Baghdassarian, C Martino… - Nature …, 2022 - nature.com
Cell interactions determine phenotypes, and intercellular communication is shaped by
cellular contexts such as disease state, organismal life stage, and tissue microenvironment …