A matched-sample pan-cancer benchmark of three major copy number signature compendia is established, showing that compendium choice is an analytical decision rather than an interchangeable preprocessing step and provides a reproducible framework for selecting and interpreting copy number signature representations in pan-cancer studies.
Summary Single-sample transcriptomic analysis can provide gene-level views of how individual tumors deviate from matched reference states, complementing cohort-level differential expression. Here, we present HopRatio, a rank-based framework that quantifies, for each gene in each sample, the fraction of stable reference...
Yue Zhao, Bo Gao, Rui-Zhong Chen· iScience· 0 citations
This work evaluated which layers of evidence reproduce across independent datasets and whether discovery-derived panels retain locked tumor-versus-non-tumor classification performance, and introduced REDE-2Fold, which provides a seven-level quantitative framework for matching transcriptomic claims to the evidence actua...
An interpretable three-stage machine learning framework integrating mRNA, microRNA, DNA methylation, copy number variation, and protein expression data from The Cancer Genome Atlas that couples improved prognostic estimation with biological interpretability supporting multi-omics biomarker discovery in ovarian cancer.
LGR5 expression defines a colorectal cancer subset that is pharmacologically tractable despite the absence of genetic dependency, including condensate-directed modulation of NKD1 as a route to targets inaccessible by antibody- or pocket-based approaches.
Lucía Paniagua-Herranz, A. Feito, Cristian Privat et al.· bioRxiv· 0 citations
This work establishes persistent homology as a transformative paradigm for transcriptomic biomarker discovery, offering a principled, structure-aware foundation for precision oncology and next-generation cancer diagnostics.
Sudarshana Gogoi, S. Bandyopadhyay, S. Bera et al.· Computational biology and ch...· 0 citations
These findings support cautious reporting of patient-enriched microbial DNA and ARG signals rather than inference of a resident blood microbiome or clinical resistance phenotype, and identify a subset of microbial DNA and ARG signals that remained detectable under increasingly stringent control criteria while distingui...
Ming Zhang, Lan He, Hua-Ping Xin et al.· Frontiers in Microbiology· 0 citations
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