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 …

[HTML][HTML] Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

M Cheng, Y Jiang, J Xu, AFA Mentis, S Wang… - Journal of Genetics and …, 2023 - Elsevier
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in
technology, from the invention of the microscope 350 years ago to the recent emergence of …

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 …

Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial information

Z Liu, D Sun, C Wang - Genome Biology, 2022 - Springer
Background Cell-cell interactions are important for information exchange between different
cells, which are the fundamental basis of many biological processes. Recent advances in …

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk

X Shao, C Li, H Yang, X Lu, J Liao, J Qian… - Nature …, 2022 - nature.com
Spatially resolved transcriptomics provides genetic information in space toward elucidation
of the spatial architecture in intact organs and the spatially resolved cell-cell …

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 …

A first computational frame for recognizing heparin-binding protein

W Zhu, SS Yuan, J Li, CB Huang, H Lin, B Liao - Diagnostics, 2023 - mdpi.com
Heparin-binding protein (HBP) is a cationic antibacterial protein derived from multinuclear
neutrophils and an important biomarker of infectious diseases. The correct identification of …

Single-cell RNA-sequencing reveals radiochemotherapy-induced innate immune activation and MHC-II upregulation in cervical cancer

C Liu, X Li, Q Huang, M Zhang, T Lei, F Wang… - … and Targeted Therapy, 2023 - nature.com
Radiochemotherapy (RCT) is a powerful treatment for cervical cancer, which affects not only
malignant cells but also the immune and stromal compartments of the tumor. Understanding …

MetaboliteCOVID: A manually curated database of metabolite markers for COVID-19

L Ren, L Ning, Y Yang, T Yang, X Li, S Tan, P Ge… - Computers in Biology …, 2023 - Elsevier
In the realm of unraveling COVID-19's intricacies, numerous metabolomic investigations
have been conducted to discern the unique metabolic traits exhibited within infected …

Deciphering ligand–receptor-mediated intercellular communication based on ensemble deep learning and the joint scoring strategy from single-cell transcriptomic …

L Peng, J Tan, W Xiong, L Zhang, Z Wang… - Computers in Biology …, 2023 - Elsevier
Background: Cell–cell communication in a tumor microenvironment is vital to tumorigenesis,
tumor progression and therapy. Intercellular communication inference helps understand …