Tzong-Yi Lee

Geometry-enhanced protein language modeling enables discovery of novel antibiotic resistance genes

GeoARG improves detection of distant antibiotic resistance genes using structural features and protein language models, uncovering 1,485 novel candidates.

Impact of Peptide Initial Configuration and Membrane Composition on Melittin's Pore-Forming Ability under Unbiased All-Atom Molecular Dynamics Simulations

This study uses molecular dynamics simulations to show that melittin's pore-forming ability depends on initial configuration and membrane composition, with lysine-7 playing a key role in pore formation.

Enhanced spatially resolved transcriptomics analysis by matching between expression profiles and spatial topology

This paper introduces STForte, a method for spatially resolved transcriptomics analysis that matches expression profiles with spatial topology, improving downstream analysis and spatial enhancement.

Guided Diffusion for molecular generation with interaction prompt

This paper introduces InterDiff, a diffusion model guided by atomic interactions to generate molecules with desired ligand-protein interactions, showing improved or comparable binding modes to known drugs.

KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites

KinasePhos 3.0 improves phosphorylation site prediction by expanding kinase classification and building 771 models, achieving average accuracy of 87.2%.

Clinically applicable rapid susceptibility testing of multi-drug resistant Staphylococcus aureus by mass spectrometry and extreme gradient boosting machine

This study uses mass spectrometry and machine learning to predict antibiotic susceptibility of Staphylococcus aureus, enabling faster and more accurate treatment decisions.