Hong X, Li N, Lv J, Zhang Y, Li J, Zhang J, Chen HF. PTMint database of experimentally verified PTM regulation on protein-protein interaction. Bioinformatics. 2023 Jan 1;39(1):btac823.

Cheng X, Zhao W, Zhu M, Wang B, Wang X, Yang X, Huang Y, Tan M, Li J. Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network. Cancer Biol Med. 2021 Apr 24;19(1):74–89.

Tian GG, Zhao X, Hou C, Xie W, Li X, Wang Y, Wang L, Li H, Zhao X, Li J, Wu J. Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells. Cell Mol Life Sci. 2022 Jan 3;79(1):22. 

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

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. 

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

Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B, Li Y, Li J. CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. J Proteome Res. 2017 Feb 3;16(2):421-432.

Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B. A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics. 2011 May;10(5):M110.006536.

Li J, Zimmerman LJ, Park BH, Tabb DL, Liebler DC, Zhang B. Network-assisted protein identification and data interpretation in shotgun proteomics. Mol Syst Biol. 2009;5:303.

Li J, Liu ZJ, Pan YC, Liu Q, Fu X, Cooper NG, Li Y, Qiu M, Shi T. Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain. Genome Biol. 2007;8(11):R244.