Dong Q, Shen D, Ye J, Chen J, Li J*. PhosCancer: A comprehensive database for investigating protein phosphorylation in human cancer. iScience. 27(11):111060, 2024. 

Dong Q, Tan M, Zhou Y, Zhang Y*, Li J*.Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies. Molecular & Cellular Proteomics. 24(3): 100905, 2025.

Yi X, Zhao H, Hu S, Dong L, Dou Y, Li J*, Qiang Gao Q*, Bing Zhang*. Tumor-associated antigen prediction using a single-sample gene expression state inference algorithm. Cell Reports Methods. 4:100906,2024.

Dong B, Xu JY, Huang Y, Guo J, Dong Q, ... , Li J*, Xue W*, Tan M*, Qin J*. Integrative proteogenomic profiling of high-risk prostate cancer samples from Chinese patients indicates metabolic vulnerabilities and diagnostic biomarkers. Nature Cancer. 5 :1427–1447, 2024.

Tian G, Hou C, Li J*, J Wu*. Three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development. Clinical and Translational Medicine. 12(6):e927, 2022.

Xu JY, Zhang C, Wang X, Zhai L, Ma Y, ..., Qian X, Wang Y*, Li J*, He F8, Xiao T*, Tan M*. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell. 2020 Jul 9;182(1):245-261.e17.

Yang X, Zhao L, Wei F, Li J*. DeepNetBim: deep learning model for predicting HLA‑epitope interactions based on network analysis by harnessing binding and immunogenicity information. BMC Bioinformatics. 22:231, 2021.

Cheng X, Qian L, Wang B, Tan M*, Li J*. SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models. Genomics Proteomics Bioinformatics. 2021 Aug;19(4):522-533. 

Chang Y, Fan Q, Hou J, Zhang Y, Li J*. A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota. Briefings in Bioinformatics. 2021 Sep 2;22(5):bbab052.

Lei M, Xu J, Huang L, Wang L, Li J*. Network Module-Based Model in the Differen-tial Expression Analysis for RNA-seq. Bioinformatics. 33(17):2699-2705, 2017.