Ruibang Luo

Telomere-to-telomere CHM13 reference reveals missing truth variants and improves deep learning-based variant calling in long-read sequencing data

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...

Bioinformatics for human long-read whole-genome sequencing

xDecoder unlocks the potential of genomic foundation models for few-shot personal gene expression prediction.

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...