Challenges and Opportunities in the Clinical Translation of High-Resolution Spatial Transcriptomics

TM Pentimalli, N Karaiskos… - Annual Review of …, 2024 - annualreviews.org
Pathology has always been fueled by technological advances. Histology powered the study
of tissue architecture at single-cell resolution and remains a cornerstone of clinical …

[HTML][HTML] Clonal expansion of cancer driver gene mutants investigated using advanced sequencing technologies

BL Parsons - Mutation Research-Reviews in Mutation Research, 2024 - Elsevier
Advanced sequencing technologies (ASTs) have revolutionized the quantitation of cancer
driver mutations (CDMs) as rare events, which has utility in clinical oncology, cancer …

scTML: a pan-cancer single-cell landscape of multiple mutation types<? mode longmeta?>

H Li, T Ma, Z Zhao, Y Chen, X Xi, X Zhao… - Nucleic acids …, 2025 - academic.oup.com
Investigating mutations, including single nucleotide variations (SNVs), gene fusions,
alternative splicing and copy number variations (CNVs), is fundamental to cancer study …

stSNV: a comprehensive resource of SNVs in spatial transcriptome

C Yang, Y Liu, X Wang, Q Jia, Y Fan, Z Lu… - Nucleic Acids …, 2025 - academic.oup.com
Single nucleotide variants (SNVs), as important components of genetic variation, affect gene
expression, function and phenotype. Mining and summarizing the spatial distribution of …

SIngle cell level Genotyping Using scRna Data (SIGURD)

M Grasshoff, M Kalmer, N Chatain… - Briefings in …, 2024 - academic.oup.com
Motivation: By accounting for variants within measured transcripts, it is possible to evaluate
the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to …

Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma

B Tandukar, D Deivendran, L Chen, N Cruz-Pacheco… - …, 2024 - pmc.ncbi.nlm.nih.gov
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic
keratoses, and squamous cell carcinomas to understand the molecular transitions during …

STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics

J Chen, M Zhou, W Wu, J Zhang, Y Li, D Li - arXiv preprint arXiv …, 2024 - arxiv.org
Recent advances in multi-modal algorithms have driven and been driven by the increasing
availability of large image-text datasets, leading to significant strides in various fields …

Current computational methods for spatial transcriptomics in cancer biology

J Mo, J Bae, J Saqib, D Hwang, Y Jin… - … in cancer research, 2024 - pubmed.ncbi.nlm.nih.gov
Cells in multicellular organisms constitute a self-organizing society by interacting with their
neighbors. Cancer originates from malfunction of cellular behavior in the context of such a …