LongPhase-TO co-phases germline and somatic alleles in a unified graph instead of mapping somatic variants onto germline haplotypes, and resolves LOH and tumor DNA fraction internally from heterozygosity depletion and haplotype imbalance without a copy-number and ploidy model.
Zhen-Yu Chen, Zhen-Xian Zheng, Rui-Bang Luo et al.· bioRxiv· 0 citations
Although long‐read sequencing enables comprehensive genomic analysis, its potential is hindered by its reliance on the incomplete GRCh38 reference genome. GRCh38’s unresolved bases, structural errors, and haplotype mosaics introduce reference biases, leading to missed variants and false‐positive calls. This limitatio...
This Primer outlines the computational foundations of long-read whole-genome analysis in human genomics, spanning read processing, mapping, de novo assembly, multi-class variant detection, haplotype phasing, repeat analysis and epigenetic profiling, and highlights key analytical trade-offs between mapping-based and ass...
Xin-Chang Zheng, P. Sanio, Rui-Bang Luo et al.· Nature Reviews Methods Prime...· 0 citations
Large-scale genomic language models (gLMs) hold promise for modeling gene regulation, yet their ability to capture personal gene expression variations remains unresolved. We developed xDecoder, a unified decoding framework that utilizes gLMs and sequence-to-function (S2F) embeddings to learn how personal genetic variat...
