Ying Chi

The paper shows that ensemble tests can overstate evidence of learned dynamics in protein conformational generators by demonstrating that agreement with equilibrium ensembles does not ensure accurate dynamics.

The paper provides a resource of 1,079 post-translationally modified protein systems with molecular dynamics simulations and descriptors for research and method evaluation.

LNGCN improves PPI prioritization by using a distance-aware continuous-time graph framework, achieving high precision on imbalanced datasets and preserving residue-level representation diversity.

TRAIT compiles nearly 8 million experimentally validated TCR-antigen pairs to provide a comprehensive resource for T-cell receptor interactions, aiding immunotherapy and vaccine design.

TSNAdb v2.0 updates the tumor-specific neoantigen database with stricter identification criteria, predicted neoantigens from three mutation types, and experimentally validated neoantigens classified by evidence.

scSpace reconstructs a pseudo-space from single-cell RNA-seq data to identify spatially variable cell subclusters and their biological relevance.

This paper presents a data-driven drug repositioning framework that identifies CVL218, a PARP1 inhibitor, as a potential therapeutic for COVID-19 through in silico and experimental validation.