Biology subjects

YU, J.

Publications and source records attributed to YU, J..

3 recordsLinked to original sources

bioRxiv2026

CNVSIM: an interpretable copy-number reference atlas for cancer subtyping

Background: Genome-wide copy-number variation (CNV) profiles provide a structural representation of cancer genomes, but interpreting new profiles within a reusable reference remains challenging. Results: We developed CNVSIM, which organizes CNV profiles into cancer root-specific reference spaces and defines reference subtypes annotated with chromosome-scale and gene-level signatures. Applied to the Progenetix dataset, CNVSIM established 112 CNV-defined subtypes across 19 cancer roots, supported by 155,881 analyses from neoplastic samples. Within each cancer root, samples sharing a broad diagnosis separated into distinct CNV subtypes, whereas individual subtypes spanned multiple diagnostic labels. All subtypes included analyses from multiple assay platforms and data sources, and core subtypes remained reproducible after systematic reduction of reference analyses. Calibrated projection assigned 85.7% of held-out CNV profiles while maintaining high accuracy for supported assignments. Projection of 4,605 cell-line CNV profiles identified cell lines representative for 90/112 cancer subtypes while highlighting gaps in cell line representation. Conclusions: CNVSIM provides a reusable and interpretable CNV reference that complements diagnostic classification for profile comparison, projection, and cell line selection.

genomics↗

bioRxiv2026

Structured cross-omics interaction discovery with a triple-graph model

Multi-omics analyses often yield fragmented pairwise associations that obscure coordinated relationships among molecular features. We developed TriGer, a triple-graph framework that identifies many-to-many cross-omics modules by combining cross-layer associations with dependency structures within each layer. In simulations with sparse or nested signals, TriGer recovered planted modules while balancing sensitivity and specificity. In inflammatory bowel disease, it identified subtype-associated metabolite--transcript modules; in colorectal cancer, it identified genus--metabolite modules whose organization was attenuated in cancer. TriGer provides an interpretable approach for studying coordinated cross-omics structure in high-dimensional molecular data.

bioinformatics↗

bioRxiv2026

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

The outbreak frequency and geographic distribution of viral pathogens are continuously expanding, making enhanced genomic surveillance an urgent global public health need. Parallel library preparation combining next-generation sequencing (NGS) and third-generation sequencing (TGS) can substantially improve the coverage and resolution of genomic surveillance, representing a key strategy for strengthening surveillance. Here we developed a complete sample-to-result system integrating a programmable active-matrix digital microfluidic (AM-DMF) chip with a bioinformatics analysis pipeline. Compared with conventional manual protocols used in public health laboratories, our system reduces reagent consumption by 72%, shortens library preparation time by 45% and decreases the inter-batch coefficient of variation (CV) by 20%. In 20 RT-qPCR-confirmed clinical samples, the system achieved complete concordance for viral identification and assigned serotypes/genotypes consistent with sequencing-based phylogenetic analysis. This system is field-deployable and enables rapid virus serotyping as well as in-depth genomic surveillance. TeaserA digital microfluidic platform integrating short- and long-read sequencing enables rapid comprehensive viral genome analysis.

bioengineering↗