Nature Search

Spatial genomics maps the structure, nature and evolution of cancer clones

A workflow centred around base-specific in situ sequencing generates detailed maps of, and can phenotypically characterize, the unique set of subclones of cancers.

Artem Lomakin
Jessica Svedlund
Lucy R. Yates
ResearchOpen Access09 Nov 2022
Nature

Volume: 611, P: 594-602
Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships

A method integrates perturbation mapping with 10X Visium spatial transcriptomics to map tumour genetic complexity and heterogeneity.

Marco Breinig
Artem Lomakin
Darjus F. Tschaharganeh
ResearchOpen Access28 Jul 2025
Nature Biomedical Engineering

Volume: 10, P: 125-143
Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors

Application of a nanopore sequencing workflow for real-time analysis of brain tumors results in molecular classification within a 30-minute intraoperative window, followed by comprehensive profiling within 24 hours.

Areeba Patel
Kirsten Göbel
Felix Sahm
ResearchOpen Access25 Mar 2025
Nature Medicine

Volume: 31, P: 1567-1577
Cell2location maps fine-grained cell types in spatial transcriptomics

A Bayesian model maps the location of cell types in tissues with higher sensitivity.

Vitalii Kleshchevnikov
Artem Shmatko
Omer Ali Bayraktar
Research13 Jan 2022
Nature Biotechnology

Volume: 40, P: 661-671
Teacher-student collaborated multiple instance learning for pan-cancer PDL1 expression prediction from histopathology slides

PDL1 expression is a common biomarker for immunotherapy response in cancer, and it is usually quantified using immunohistochemistry. Here, the authors develop a weakly supervised learning approach combining multiple instance learning and a teacher-student framework to predict PDL1 expression from histopathological imaging.

Darui Jin
Shangying Liang
Xiangzhi Bai
ResearchOpen Access09 Apr 2024
Nature Communications

Volume: 15, P: 1-14
Spatial biology of cancer evolution

In this Review, the authors discuss our latest understanding of the spatial aspects of cancer evolution, including the roles of cancer subclonal structure, tissue architecture, and interactions between cancer cells and diverse cell types of the microenvironment at local and distant sites.

Zaira Seferbekova
Artem Lomakin
Moritz Gerstung
Reviews09 Dec 2022
Nature Reviews Genetics

Volume: 24, P: 295-313

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Spatial genomics maps the structure, nature and evolution of cancer clones

Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships

Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors

Cell2location maps fine-grained cell types in spatial transcriptomics

Teacher-student collaborated multiple instance learning for pan-cancer PDL1 expression prediction from histopathology slides

Spatial biology of cancer evolution

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Spatial genomics maps the structure, nature and evolution of cancer clones

Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships

Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors

Cell2location maps fine-grained cell types in spatial transcriptomics

Teacher-student collaborated multiple instance learning for pan-cancer PDL1 expression prediction from histopathology slides

Spatial biology of cancer evolution

Search

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