Author

X. Zhou

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Open access Sep 2026

A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection

Abstract Motivation Accurate detection of genetic variants, including single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), and structural variants (SVs), is essential for comprehensive genomic analysis. While short-read sequencing performs well for SNP and INDEL detection, it remains limited...

Can Luo, Y. Liu, Han Liu et al. · Bioinformatics Advances · 0 citations

Open access Aug 2026

Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states

A comprehensive, context-specific guide to current annotation strategies for spatial transcriptomics is presented and open-set recognition of reference-absent cell states, adaptive incorporation of spatial context, and improved resolution of rare and transitional cell identities are identified as central priorities for...

Yu-Ling Zhu, Yunfei Hu, M. Xie et al. · Research Square · 0 citations

Open access Jul 2026

CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes

Single-cell DNA sequencing (scDNA-seq) resolves copy number variation (CNV) at single-cell resolution, revealing tumor heterogeneity and subclonal structure. Most existing methods, however, infer only total copy number. Haplotype-resolved copy number, which captures allelic imbalance and clonal evolution, remains far l...

Weiman Yuan, Can Luo, Yunfei Hu et al. · bioRxiv · 0 citations