Article

AI-based separation of malignant cell- and microenvironment-specific gene expression from bulk RNA sequencing enhances biomarker interpretation

2026-04-30

Abstract excerpt

<h4>ABSTRACT</h4> Bulk RNA sequencing (RNA-seq)-based gene expression analysis is a promising tool for personalized cancer diagnostics, disease monitoring, and treatment decision-making. However, its clinical utility is limited by interference from non-malignant tumor microenvironment cells, which can dominate transcript data in low-purity tumors. While cell deconvolution methods like Kassandra can predict digita...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: ea3aa19b-15b0-51ad-9608-35f6bd10cf56
DOI: 10.64898/2026.04.28.721082

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

AI-based separation of malignant cell- and microenvironment-specific gene expression from bulk RNA sequencing enhances biomarker interpretationDOI 10.64898/2026.04.28.721082Read

Resolving malignant cell heterogeneity from bulk tumor RNA-seq data with CDStateSemantic proximity Read

DeSide: A unified deep learning approach for cellular decomposition of bulk tumors based on limited scRNA-seq dataSemantic proximity Read

Applications of single-cell and bulk RNA sequencing in onco-immunologySemantic proximity Read

Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancerSemantic proximity Read

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression dataSemantic proximity Read

Leveraging single-cell sequencing to classify and characterize tumor subgroups in bulk RNA-sequencing dataSemantic proximity Read

Routine FFPE sections support clinically compatible single-nucleus transcriptomics across six human cancer typesSemantic proximity Read

Estimation of immune cell content in tumor using single-cell RNA-seq reference dataSemantic proximity Read

PUREE: accurate pan-cancer tumor purity estimation from gene expression dataSemantic proximity Read

Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-seq Data with Single-cell AtlasSemantic proximity Read

Single-cell RNA sequencing in cancer: Applications, advances, and emerging challengesSemantic proximity Read