Grow AI Virtual Cells: Three Data Pillars and Closed-Loop Learning
Liujia Qian, Zhen Dong, Tiannan Guo*.
Cell Research. Accepted in principle.
Mass-spectrometry-based proteomics: from single cells to clinical applications
Tiannan Guo*, Judith A. Steen*, Matthias Mann*.
Nature. 2025 Feb;638(8052):901-911. doi: 10.1038/s41586-025-08584-0. Epub 2025 Feb 26. PMID: 40011722.
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence
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*.
arXiv preprint. 21 Feb 2025. https://doi.org/10.48550/arXiv.2502.15867
Spatial distribution of the proteome in human body and cancers
Liang Yue#, Wenhao Jiang#, Sainan Li#, Meng Luo#, Ning Fan, Xiaolu Zhan, Kexin Chen, Tian Lu, Fang Guo, Dongwei Li, Weigang Ge, Zongxiang Nie, Mengge Lyu, Jun A, Yingrui Wang, Yingdan Chen, Zhenhai Fu, Nan Xiang, Lu Li, Fengchao Yu, Guo Ci Teo, Alexy I Nesvizhskii, Meng Wang, Michael P. Snyder, Ben Collins, Ruedi Aebersold, Fei Xu, Yi Zhu*, Tong Liu*, Yan Li*, Tiannan Guo*.
bioRxiv preprint. 18 Feb, 2025. https://doi.org/10.1101/2025.02.14.638212
A perturbation proteomics-based foundation model for virtual cell construction
Rui Sun#, Liujia Qian#, Yongge Li#, Honghan Cheng, Zhangzhi Xue, Xuedong Zhang, Lingling Tan, Yuecheng Zhan, Wenbin Hu, Qi Xiao, Zhiwei Liu, Guangmei Zhang, Weinan E, Peijie Zhou, Han Wen*, Yi Judy Zhu*, Tiannan Guo*.
bioRxiv preprint. 10 Feb, 2025. doi: https://doi.org/10.1101/2025.02.07.637070.
DDA-BERT: leveraging transformer architecture pre-training for data-dependent acquisition mass spectrometry-based proteomics
A Jun#, Pu Liu#, Yingying Sun#, Jiaying Lin, Xiaofan Zhang, Zongxiang Nie, Yuqi Zhang, Ziyuan Xing, Yi Chen*, Tiannan Guo*.
bioRxiv preprint. 15 Nov, 2024. https://doi.org/10.1101/2024.11.13.623394
DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis
Zhiwei Liu#, Pu Liu#, Yingying Sun#, Zongxiang Nie, Xiaofan Zhang, Yuqi Zhang, Yi Chen*, Tiannan Guo*.
bioRxiv preprint. 12 Nov, 2024. https://doi.org/10.1101/2024.11.11.622930
iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control.
Huanhuan Gao#, Yi Zhu#*, Dongxue Wang#, Zongxiang Nie#, He Wang#, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He#, Tiannan Guo#
Nature Communications 16, 892 (2025). https://doi.org/10.1038/s41467-024-54871-1.
Integral-Omics: Serial Extraction and Profiling of Metabolome, Lipidome, Genome, Transcriptome, Whole Proteome and Phosphoproteome Using Biopsy Tissue
Wei Li, Jing Sun, Rui Sun, Yujuan Wei, Junke Zheng*, Yi Zhu*, Tiannan Guo*.
Analytical Chemistry. 2025 Jan 7. doi: 10.1021/acs.analchem.4c04421. Epub ahead of print. PMID: 39772508.
AI-empowered perturbation proteomics for complex biological systems
Liujia Qian, Rui Sun, Ruedi Aebersold, Peter Bühlmann, Chris Sander*, Tiannan Guo*.
Cell Genomics. 2024, 100691. DOI: https://doi.org/10.1016/j.xgen.2024.100691.
Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics
Zhen Dong#, Wenhao Jiang#, Chunlong Wu, Ting Chen, Jiayi Chen, Xuan Ding, Shu Zheng, Kiryl D Piatkevich*, Yi Zhu*, Tiannan Guo*.
Nature Communications. 2024 Oct 30;15(1):9378. doi: 10.1038/s41467-024-53683-7. PMID: 39477916.
Spatially resolved proteomics via tissue expansion
Lu Li#, Cuiji Sun#, Yaoting Sun#, Zhen Dong#, Runxin Wu, Xiaoting Sun, Hanbin Zhang, Wenhao Jiang, Yan Zhou, Xufeng Cen, Shang Cai, Hongguang Xia, Yi Zhu, Tiannan Guo* & Kiryl D. Piatkevich*
Nature Communications. 2022 Nov 30;13(1):7242. doi: 10.1038/s41467-022-34824-2. PMID: 36450705.
Artificial intelligence defines protein-based classification of thyroid nodules
Yaoting Sun#, Sathiyamoorthy Selvarajan#, Zelin Zang#, Wei Liu#, Yi Zhu#, Hao Zhang#, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy bin Syed Abdillah, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Z. Li*, Oi Lian Kon*, N. Gopalakrishna Iyer*, Tiannan Guo*.
Cell Discovery. 2022 Sep 6;8(1):85. doi: 10.1038/s41421-022-00442-x. Erratum in: Cell Discov. 2022 Sep 30;8(1):100. PMID: 36068205.
High-throughput proteomic sample preparation using pressure cycling technology
Xue Cai#, Zhangzhi Xue, Chunlong Wu, Rui Sun, Liujia Qian, Liang Yue, Weigang Ge, Xiao Yi, Wei Liu, Chen Chen, Huanhuan Gao, Jing Yu, Luang Xu, Yi Zhu*, Tiannan Guo*.
Nature Protocols. 2022 Oct;17(10):2307-2325. doi: 10.1038/s41596-022-00727-1. PMID: 35931778.
High-Throughput Proteomics and AI for Cancer Biomarker Discovery
Qi Xiao#, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu*, Tiannan Guo*.
Advanced Drug Delivery Reviews. 2021 Sep. 176: 113844. doi: 10.1016/j.addr.2021.113844. PMID: 34182017.
Multi-organ Proteomic Landscape of COVID-19 Autopsies
Xiu Nie#, Liujia Qian#, Rui Sun#, Bo Huang#, Xiaochuan Dong#, Qi Xiao#, Qiushi Zhang#, Tian Lu, Liang Yue, Shuo Chen, Xiang Li, Yaoting Sun, Li Lu, Luang Xu, Li Yan, Ming Yang, Zhangzhi Xue, Shuang Liang, Xuan Ding, Chunhui Yuan, Li Peng, Wei Liu, Xiao Yi, Mengge Lyu, Guixiang Xiao, Xia Xu, Weigang Ge, Jiale He, Jun Fan, Junhua Wu, Meng Luo, Xiaona Chang, Huaxiong Pan, Xue Cai, Junjie Zhou, Jing Yu, Huanhuan Gao, Mingxing Xie, Sihua Wang, Guan Ruan, Hao Chen, Hua Su, Heng Mei, Danju Luo, Dashi Zhao, Fei Xu, Yan Li, Yi Zhu*, Jiahong Xia*, Yu Hu*, Tiannan Guo*.
Cell. 2021 Feb.184(3): 775-791.e14. doi: 10.1016/j.cell.2021.01.004. PMID: 33503446.
Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Bo Shen #, Xiao Yi #, Yaoting Sun #, Xiaojie Bi #, Juping Du #, Chao Zhang #, Sheng Quan #, Fangfei Zhang, Rui Sun, Liujia Qian, Weigang Ge, Wei Liu, Shuang Liang, Hao Chen, Ying Zhang, Jun Li, Jiaqin Xu, Zebao He, Baofu Chen, Jing Wang, Haixi Yan, Yufen Zheng, Donglian Wang, Jiansheng Zhu, Ziqing Kong, Zhouyang Kang, Xiao Liang, Xuan Ding, Guan Ruan, Nan Xiang, Xue Cai, Huanhuan Gao, Lu Li, Sainan Li, Qi Xiao, Tian Lu, Yi Zhu*, Huafen Liu*, Haixiao Chen*, Tiannan Guo*.
Cell. 2020 Jul 9;182(1):59-72.e15. doi: 10.1016/j.cell.2020.05.032. PMID: 32492406.
High-throughput Proteomic analysis of FFPE tissue samples facilitates tumor stratification
Yi Zhu#, Tobias Weiss#, Qiushi Zhang, Rui Sun, Bo Wang, Xiao Yi, Zhicheng Wu, Huanhuan Gao, Xue Cai, Guan Ruan, Tiansheng Zhu, Chao Xu, Sai Lou, Xiaoyan Yu, Ludovic Gillet, Peter Blattmann, Karim Saba, Christian D. Fankhauser, Michael B. Schmid, Dorothea Rutishauser, Jelena Ljubicic, Ailsa Christiansen, Christine Fritz, Niels J. Rupp, Cedric Poyet, Elisabeth Rushing, Michael Weller, Patrick Roth, Eugenia Haralambieva, Silvia Hofer, Chen Chen, Wolfram Jochum, Xiaofei Gao, Lirong Chen, Qing Zhong, Peter J. Wild*, Ruedi Aebersold*, Tiannan Guo*.
Molecular Oncology. 2019 Sep;13(11): 2305-2328. doi: 10.1002/1878-0261.12570. PMID: 31495056.
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Tiannan Guo#, Petri Kouvonen, Ching Chiek Koh, Ludovic C Gillet, Witold E Wolski, Hannes L Röst, George Rosenberger, Ben C Collins, Lorenz C Blum, Silke Gillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold*.
Nature Medicine. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. PMID: 25730263.
