Redefining tumor-associated macrophage subpopulations and functions in the tumor microenvironment

K Wu, K Lin, X Li, X Yuan, P Xu, P Ni, D Xu - Frontiers in immunology, 2020 - frontiersin.org
The immunosuppressive status of the tumor microenvironment (TME) remains poorly
defined due to a lack of understanding regarding the function of tumor-associated …

Computational approaches and challenges in spatial transcriptomics

S Fang, B Chen, Y Zhang, H Sun, L Liu… - Genomics …, 2023 - academic.oup.com
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …

Giotto: a toolbox for integrative analysis and visualization of spatial expression data

R Dries, Q Zhu, R Dong, CHL Eng, H Li, K Liu, Y Fu… - Genome biology, 2021 - Springer
Spatial transcriptomic and proteomic technologies have provided new opportunities to
investigate cells in their native microenvironment. Here we present Giotto, a comprehensive …

Spatially resolved transcriptomics provide a new method for cancer research

B Zheng, L Fang - Journal of Experimental & Clinical Cancer Research, 2022 - Springer
A major feature of cancer is the heterogeneity, both intratumoral and intertumoral. Traditional
single-cell techniques have given us a comprehensive understanding of the biological …

Spatially resolved transcriptomics technology facilitates cancer research

Q Wang, Y Zhi, M Zi, Y Mo, Y Wang, Q Liao… - Advanced …, 2023 - Wiley Online Library
Single cell RNA sequencing (scRNA‐seq) provides a great convenience for studying tumor
occurrence and development for its ability to study gene expression at the individual cell …

Spatial transcriptomics: molecular maps of the mammalian brain

C Ortiz, M Carlén, K Meletis - Annual review of neuroscience, 2021 - annualreviews.org
Maps of the nervous system inspire experiments and theories in neuroscience. Advances in
molecular biology over the past decades have revolutionized the definition of cell and tissue …

Unravelling prostate cancer heterogeneity using spatial approaches to lipidomics and transcriptomics

SM Mutuku, X Spotbeen, PJ Trim, MF Snel, LM Butler… - Cancers, 2022 - mdpi.com
Simple Summary Prostate cancer is a heterogenous disease in terms of disease
aggressiveness and therapy response, leading to dilemmas in treatment decisions. This …

Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer

J Moehlin, B Mollet, BM Colombo, MA Mendoza-Parra - Cell Systems, 2021 - cell.com
Spatially resolved transcriptomics (SrT) can investigate organ or tissue architecture from the
angle of gene programs that define their molecular complexity. However, computational …

Inferring spatially transient gene expression pattern from spatial transcriptomic studies

J Kueckelhaus, J von Ehr, VM Ravi, P Will, K Joseph… - BioRxiv, 2020 - biorxiv.org
Spatial transcriptomic is a technology to provide deep transcriptomic profiling by preserving
the spatial organization. Here, we present a framework for SPAtial Transcriptomic Analysis …

Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones

M Marklund, N Schultz, S Friedrich, E Berglund… - Nature …, 2022 - nature.com
The molecular mechanisms underlying lethal castration-resistant prostate cancer remain
poorly understood, with intratumoral heterogeneity a likely contributing factor. To examine …