[HTML][HTML] The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth
KE De Visser, JA Joyce - Cancer cell, 2023 - cell.com
Cancers represent complex ecosystems comprising tumor cells and a multitude of non-
cancerous cells, embedded in an altered extracellular matrix. The tumor microenvironment …
cancerous cells, embedded in an altered extracellular matrix. The tumor microenvironment …
Spatial components of molecular tissue biology
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 …
evolving, making it possible to comprehensively characterize cells and tissues in health and …
[HTML][HTML] Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …
increased interest in the inference of cell-cell communication. Many computational tools …
[HTML][HTML] Screening cell–cell communication in spatial transcriptomics via collective optimal transport
Spatial transcriptomic technologies and spatially annotated single-cell RNA sequencing
datasets provide unprecedented opportunities to dissect cell–cell communication (CCC) …
datasets provide unprecedented opportunities to dissect cell–cell communication (CCC) …
[HTML][HTML] Molecularly defined and spatially resolved cell atlas of the whole mouse brain
In mammalian brains, millions to billions of cells form complex interaction networks to enable
a wide range of functions. The enormous diversity and intricate organization of cells have …
a wide range of functions. The enormous diversity and intricate organization of cells have …
Single-cell atlases: shared and tissue-specific cell types across human organs
R Elmentaite, C Domínguez Conde, L Yang… - Nature Reviews …, 2022 - nature.com
The development of single-cell and spatial transcriptomics methods was instrumental in the
conception of the Human Cell Atlas initiative, which aims to generate an integrated map of …
conception of the Human Cell Atlas initiative, which aims to generate an integrated map of …
[HTML][HTML] Statistical and machine learning methods for spatially resolved transcriptomics data analysis
The recent advancement in spatial transcriptomics technology has enabled multiplexed
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …
[HTML][HTML] 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 …
cells, which are the fundamental basis of many biological processes. Recent advances in …
The diversification of methods for studying cell–cell interactions and communication
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 …
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
[HTML][HTML] Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk
Spatially resolved transcriptomics provides genetic information in space toward elucidation
of the spatial architecture in intact organs and the spatially resolved cell-cell …
of the spatial architecture in intact organs and the spatially resolved cell-cell …