Shuqing Chen

TRAIT: A Comprehensive Database for T-cell Receptor-Antigen Interactions

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.

DeepTAP: an RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens

DeepTAP predicts TAP-binding peptides using an RNN, outperforming existing methods on benchmark datasets.

Spanve: A Statistical Method for Detecting Downstream-Friendly Spatially Variable Genes in Large-Scale Spatial Transcriptomic Data

Spanve is a nonparametric statistical method that identifies spatially variable genes in spatial transcriptomic data with fewer false positives, enabling better downstream analysis.

TSNAdb v2.0: the updated version of tumor-specific neoantigen database

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.

Defining the Sensitivity Landscape of 74,389 EGFR Variants to Tyrosine Kinase Inhibitors

The paper systematically studies the sensitivity of 74,389 EGFR variants to five tyrosine kinase inhibitors using cytotoxicity assays and presents a comprehensive reference for treatment responses.

COVIEdb: A database for potential immune epitopes of coronaviruses

The paper predicts potential B/T-cell epitopes for multiple coronaviruses and stores the results in a database for vaccine development.

Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2)

This paper designs multi-epitope peptide vaccines against SARS-CoV-2 using immunoinformatics, showing they elicit strong humoral and cellular immune responses in mice.