Bio:

Zhiwei Liu received his PhD in Pharmacology from the Shanghai Institute of Materia Medica, Chinese Academy of Sciences. His research focuses on Artificial Intelligence (AI) and omics data analysis. As first author, he developed a novel computational strategy to identify drug combination therapies, uncovering potential precision treatments for KRAS-mutant cancers using bioinformatics and machine learning. This work was published in Molecular Cell (2021, 81: 1–15) and selected as a “Featured Article” by the journal. Additionally, he is the co-first author of a study on colon multi-omics analysis published in Advanced Science (2025, 6:e11744). He also co-authored two studies on precision therapy published in Cell (2020, 182: 245–261; 2018, 175(1): 186–199.e19). In perturbation proteomics, he applied drug perturbation data to uncover drug mechanisms, targets, and off-targets, publishing these findings as first author in Journal of Pharmaceutical Analysis (2024, 14: 128–139).

More recently, as the first author, he co-developed DIA-BERT, a deep learning-based tool for DIA proteomics analysis, achieving 51% more protein and 22% more peptide precursor identifications. DIA-BERT is the first to leverage simulated DIA datasets for low-cost, large-scale model training and was published in Nature Communications (2025, 16: 3530). He is currently involved in developing a new DIA-MS dataset and companion software to advance precision medicine through proteomics.

Representative publications

[Note: #, co-first author]

Proteomics Methodology & Artificial Intelligence

Zhiwei Liu #, Pu Liu #, Yingying Sun #, Zongxiang Nie, Xiaofan Zhang, Yuqi Zhang, Yi Chen*, Tiannan Guo*. DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis. Nature Communications. 2025, 16: 3530.

Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Perez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann*, Bing Zhang*, Tiannan Guo*. Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. Preprint at arXiv. 2025, https://doi.org/10.48550/arXiv.2502.15867.

Pharmacological Perturbation Proteomics

Zhiwei Liu, Shangwen Jiang, Bingbing Hao, Shuyu Xie, Yingluo Liu, Yuqi Huang, Heng Xu, Cheng Luo, Min Huang, Minjia Tan, Jun-Yu Xu*. A proteomic landscape of pharmacologic perturbations for functional relevance. Journal of Pharmaceutical Analysis. 2024, 14: 128-139.

Wensi Zhao#, Lei Zhao#, Yannan Lian#, Zhiwei Liu#, Yaqi Li#, Xuege Wang#, Mingya Zhang, Ni Li, Jingli Guo, Danqing Shen, Shaobo Mo, Jiahao Li, Linhui Zhai, Jiahui Ni, Sangkyu Lee, Bin Liu, Jing Li, Fei Wang, Junjie Peng,* Jun Qin,* and Minjia Tan*. A proteomic landscape of pharmacologic perturbations for functional relevance. Advanced Science. 2025, 6:e11744.

Cancer Proteomics & Precision Medicine

Zhiwei Liu #, Yingluo Liu #, Lili Qian, Shangwen Jiang, Xiameng Gai, Shu Ye, Yuehong Chen, Xiaomin Wang, Linhui Zhai, Jun Xu, Congying Pu, Jing Li, Fuchu He, Min Huang*, Minjia Tan*. A proteomic and phosphoproteomic landscape of KRAS mutant cancers identifies combination therapies. Molecular cell. 2021, 81: 1-15.

JunYu Xu #, Chunchao Zhang #, Xiang Wang #, Linhui Zhai #, Yiming Ma #, Yousheng Mao, Kun Qian, Changqing Sun, Zhiwei Liu, Shangwen Jiang, Minghui Wang, Lin Feng,Lei Zhao, Ping Liu, Bo Wang, Xin Zhao, Hui Xie, Xiaoyun Yang, Liyuan Zhao, Yafei Chang, Jingya Jia, Xijun Wang, Yimin Zhang, Yaru Wang, Yikun Yang, Zhixiang Wu, Longhai Yang, Bin Liu, Teng Zhao, Shengguo Ren, Aihua Sun, Yang Zhao, Wantao Ying, Fei Wang, Guangshun Wang, Yi Zhang, Shujun Cheng, Jun Qin, Xiaohong Qian, Yi Wang*, Jing Li*, Fuchu He*, Ting Xiao*, Minjia Tan*. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell. 2020, 182: 245–261.

Phosphoproteomics, Ubiquitination & Signaling Mechanisms

Ping Liu #, Xiaoji Cong #, Shengjie Liao #, Xinglong Jia #, Xiaomin Wang, Wei Dai, Linhui Zhai, Lei Zhao, Jing Ji, Duan Ni, Zhiwei Liu, Yulu Chen, Lulu Pan, Wei Liu, Jian Zhang, Min Huang, Bin Liu*, Minjia Tan*. Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. Cell Death & Differentiation. 2022; 29:1–13.

Epigenetics & Targeted Cancer Therapy

Xun Huang #, Juan Yan #, Min Zhang #, Yafang Wang #, Yi Chen, Xuhong Fu , Rongrui Wei , Xing-Ling Zheng, Zhiwei Liu, Xiong Zhang , Hong Yang , Bingbing Hao, Yan-Yan Shen, Yi Su, Xiaoji Cong, Min Huang, Minjia Tan*, Jian Ding*, Meiyu Geng*. Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors. Cell. 2018;175(1):186-99 e19.

Foundation

National Natural Science Foundation of China (Young Scientist Fund): Exploring the proteomics BERT model for enhancing the depth of phosphorylation modification identification and quantitative accuracy (Grant No. 32501341 to Dr Zhiwei Liu) 2026.01-2028.12

Patent

CN116699043A

A pressure-based method for detecting intermolecular protein affinity

Inventors: Tiannan Guo, Zhiwei Liu, Fangfei Zhang.

Honor

Pioneer Scholar award (2023.7)

HUPO (Human Proteome Organization World Congress) Travel Award (2024.10)

Presentations

2024.10 Poster presentation for the HUPO 2024 (Dresden, Germany)

2025.05 Oral presentation for the NCCBB 2025 (Jinan, China)

2025.08 Oral presentation for the CNCP 2025 (Hangzhou, China)

2025.10 Poster presentation for the AOHUPO/CNHUPO 2025 (Guangzhou, China)