Y Liu

HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues

HOMED improves DNA methylation deconvolution by integrating cell-lineage hierarchies and single-cell data, achieving higher accuracy across tissues.

Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors

The paper identifies regeneration-associated transitional progenitors (RATPs) in Cldn18 knockout mice, showing they are less fibrogenic and contribute to lung repair rather than fibrosis.

CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data

CNVeil improves tumor subclone identification and copy number estimation in single-cell DNA sequencing by addressing noise and bias through novel computational methods.

BiATNovo: An Attention-based Bidirectional De Novo Sequencing Framework for Data-Independent-Acquisition Mass Spectrometry

BiATNovo improves de novo peptide sequencing from DIA mass spectrometry data by using attention-based bidirectional models and post-processing, achieving better accuracy for long peptides and amino acid-level predictions.