Kai Li

CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo

CasanovoGUI provides a user-friendly desktop interface for Casanovo, a deep learning model for de novo peptide sequencing, simplifying setup and result interpretation.

Comparative genomic and transcriptomic analyses of Strongylus vulgaris reveal developmental and evolutionary deployment of parasitism in a migratory equine nematode

This paper presents a genomic and transcriptomic analysis of Strongylus vulgaris, revealing developmental and evolutionary aspects of its parasitic lifestyle and identifying key genes and isoforms involved in its biology.

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data by generating pseudo-MS/MS spectra for direct peptide identification and quantification.

Patient-Derived Xenograft-Guided Prediction of Chemotherapy Response in Triple-Negative Breast Cancer

This paper develops chemotherapy-specific predictors for triple-negative breast cancer using patient-derived xenografts and multi-omic data, achieving high AUROC scores for response prediction.

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

MSFragger-Labile improves the analysis of labile post-translational modifications by incorporating modification-specific fragment ions into mass spectrometry searches.

Quantitative profiling of pseudouridylation landscape in the human transcriptome

The paper develops a method to quantitatively profile pseudouridylation sites in the human transcriptome and identifies modification targets of pseudouridine synthases.

Modeling human TBX5 haploinsufficiency predicts regulatory networks for congenital heart disease

The paper models TBX5 haploinsufficiency in iPSC-derived cardiomyocytes to identify gene regulatory network imbalances linked to congenital heart disease.