精选论文

Note: *, co-corresponding; #, co-first author.

Full list of publications:
29

Large-scale metaproteomics of human gut microbiota reveals microbial functions in metabolic diseases and aging

Shuang Liang#, Yingying Sun#, Zelei Miao#, Bang-yan Li#, Ziyuan Xing, Yuting Xie , Enci Cai, Sainan Li, Pu Liu, Min Yang, Menglei Shuai, Wanglong Gou, Wenhao Jiang, Youming Wang, Huanhuan Gao, Ke Zhang, Jing Yu, Xue Cai, Xingbing Wang, Yi Zhu*, Yu-ming Chen*, Ju-Sheng Zheng*, Tiannan Guo*.

Cell Metabolism. 2026 Mar 13:S1550-4131(26)00055-Cell Metabolism0. doi: 10.1016/j.cmet.2026.02.012. Epub ahead of print. PMID: 41831436.

28

A targeted proteomics assay for the preoperative diagnosis of thyroid nodules

Xue Cai#, Yaoting Sun#, Dingcun Luo#, Hao Zhang#, Wenjun Wei#, Yifeng Zhang#, Weigang Ge#,Jing Liu, Guan Ruan, Lu Li, Lingling Tan, Luang Xu, Dong Xu, Haixia Guan, Jiang Zhu, Wanyuan Chen, Qiushi Zhang, Huijuan Si, Juntao Qiu, Zhangzhi Xue, Zhiqiang Gui, Haitao Zheng, Gaosong Wu, Jianhua Wang, Lei Xie, Guang Chen, Guoyang Wu, Lei Liang, Chuang Chen, Xianghui He, Meiping Shen, Jianbiao Wang, Minghua Ge, Deguang Zhang, Liang Zhou, Yijun Wu, Hui Shi, Fan Wu, Zhihong Wang, Hong Han, Jing Yao, Zhiyan Liu, Mingzhao Xing, Kennichi Kakudo, Yibo Gao, Wen Tian*, Huixiong Xu*, Yi Zhu*, Yu Wang*, Tiannan Guo*, We-TEC Investigators.

Cell Reports Medicine. 2026 Mar 10:102664. doi: 10.1016/j.xcrm.2026.102664. Epub ahead of print. PMID: 41812663.

27

Multimodal AI-enabled mass spectrometry-based expansion proteomics for whole-slide at single-cell resolution

Shuaiyao Wang#, Zhen Dong#*, Chunlong Wu, Jiayi Chen, Changao Li, Jianpeng Sheng, Xiang Li, Yi Chen*, Tiannan Guo*.

LangTaoSha Preprint Server. 2026 Feb. 20. DOI: 10.65215/LTSpreprints.2026.02.20.000134.

26

ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning

Mengge Lyu, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Pu Liu, Sai Zhang, Xiangqing Li, Rui Sun*, Yi Chen*, Tiannan Guo*.

Nature Communications. 2026 Jan 22;17(1):1949. doi: 10.1038/s41467-026-68686-9. PMID: 41571643; PMCID: PMC12929803.

25

Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma

Yan Zhou*, Yingrui Wang*, Xiao Shi*, Jiatong Wang*, Zelin Zang*, Likun Zhang*, Zhiqiang Gu, Xue Cai, Pingping Hu, Jiaxi Wang, Hanqing Liu, Zhihong Wang, Haixia Guan, Xiaohong Wu, Cenkai Shen, Yi He, Mo Li, Hao Zhang, Jianbiao Wang , Yijun Wu, Chuang Chen , Yi Zhu, Yaoting Sun#, Zhiyan Liu#, Yu Wang#, Tiannan Guo#.

Nature Communications. 2026 Jan 14;17(1):432. doi: 10.1038/s41467-025-67533-7. PMID: 41535264; PMCID: PMC12804720.

24

Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Huanhuan Gao#, Yuecheng Zhan#, Yuanqi Liu#, Zhiyi Zhu, Yuxiu Zheng, Liqin Qian, Zhangzhi Xue, Honghan Cheng, Zongxiang Nie, Weigang Ge, Senlin Ruan, Jiaxu Liu, Jikai Zhang, Yingying Sun, Lei Zhou, Dongyue Xun, Yingrui Wang, Heyun Xu*, Huiwen Miao*, Yi Zhu*, Tiannan Guo*.

EMBO Molecular Medicine. 2026 Jan;18(1):275-296. doi: 10.1038/s44321-025-00346-9. Epub 2025 Dec 5. PMID: 41350775; PMCID: PMC12808129.

23

Expansion omics: from expansion microscopy to spatial omics

Zhen Dong#*, Weirong Xiang#, Wenhao Jiang, Tiannan Guo*.

Molecular Systems Biology. 2026 Feb;22(2):165-178. doi: 10.1038/s44320-025-00171-9. Epub 2025 Dec 1. PMID: 41326779; PMCID: PMC12864849.

22

Protein restriction reprograms the multi-organ proteomic landscape of mouse aging

Tian Lu#, Yuting Xie#, Yingrui Wang, Xiling Lin, Xue Cai, Yuqi Zhang, Zongxiang Nie, Chang Su, Wanglong Gou, Hong Zhang, Jing Wang, Yan Zhong, Zeyin Lai, Jingjing Xiang, Peng-Fei Shan, Ju-Sheng Zheng, Huijun Wang, Yi Zhu*, Tiannan Guo*.

Cell. 2025 Dec 11;188(25):7309-7326.e20. doi: 10.1016/j.cell.2025.10.004. Epub 2025 Oct 24. PMID: 41138729.

21

A standardized framework for circulating blood proteomics

Xue Cai, Philipp E. Geyer, Yasset Perez-Riverol, Gilbert S. Omenn, Lianhua Dong, Robert Winkler, Sara Ahadi, Philip Lössl, Xiaobo Yu, Cheng Chang, Markus Ralser, Connie R. Jimenez, Yang Zhao, Yu-Ju Chen, Terence C. W. Poon, Nicolai Bache, Leming Shi, Xinhua Dai, Ziyue Wang, Yi Zhu, Xiang Fang, Jochen M. Schwenk*, Jennifer E. Van Eyk*, Uwe Völker*, Tiannan Guo*.

Nature Genetics. 2025 Oct;57(10):2371-2380. doi: 10.1038/s41588-025-02319-7. Epub 2025 Sep 23. PMID: 40987950.

20

Tissue expansion enables proteomics at improved spatial resolution

Zhen Dong#, Wenhao Jiang#, Tiannan Guo*

Trends in Biochemical Sciences. 2025 Oct;50(10):945-946. doi: 10.1016/j.tibs.2025.06.002. Epub 2025 Jun 21. PMID: 40545409.

19

A protein-based classifier for differentiating follicular thyroid adenoma and carcinoma

Yaoting Sun#, He Wang#, Lu Li#, Jianbiao Wang#, Wanyuan Chen#, Li Peng#, Pingping Hu, Jing Yu, Xue Cai, Nan Yao, Yan Zhou, Jiatong Wang, Yingrui Wang, Liqin Qian, Weigang Ge, Mengni Chen, Feng Yang, Zhiqiang Gui, Wei Sun, Zhihong Wang, Minghua Ge, Yi He, Guangzhi Wang, Yongfu Zhao, Huanjie Chen, Xiaohong Wu, Yuxin Du, Wenjun Wei, Fan Wu, Dingcun Luo, Xiangfeng Lin, Haitao Zheng, Xin Zhu, Bei Wei, Jiafei Shen, Jincao Yao, Zhennan Yuan, Tong Liu, Jun Pan, Yifeng Zhang, Yangfan Lv, Qiaonan Guo, Qijun Wu, Tingting Gong, Ting Chen, Shu Zheng, Jingqiang Zhu, Hanqing Liu, Chuang Chen, Hong Han, Sathiyamoorthy Selvarajan, Michael Mingzhao Xing, Kennichi Kakudo, Erik K Alexander, Yijun Wu, Yu Wang, Dong Xu, Hao Zhang, Xiu Nie, Oi Lian Kon, N Gopalakrishna Iyer, Zhiyan Liu, Yi Zhu*, Haixia Guan*, Tiannan Guo*; We-TEC Investigators.

EMBO Molecular Medicine. 2025. 17(7):1519-1538. doi: 10.1038/s44321-025-00242-2. Epub 2025 May 29. PMID: 40442320; PMCID: PMC12254270.

18

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets

Jaco C. Knol#, Mengge Lyu#, Franziska Böttger#, Madalena Nunes Monteiro#, Thang V. Pham, Frank Rolfs, Andrea Vallés-Martí, Tim Schelfhorst, Richard R. de Goeij-de Haas, Irene V. Bijnsdorp, Shuaiyao Wang, Fangfei Zhang, Jun A, Bart A. Westerman, Barbara Sitek, Janne Lehtiö, Jan Koster, Jan N.M. IJzermans, Hanneke W.M. van Laarhoven, Maarten F. Bijlsma, Jan Paul Medema, Alex A. Henneman, Sander R. Piersma, Ruud H. Brakenhoff, Jacqueline Cloos, Valentina Cordo’, Daphne de Jong, Geert Kazemier, Danijela Koppers-Lalic, Mariette Labots, Tessa Y.S. Le Large, John W.M. Martens, Jules P.P. Meijerink, Madiha Mumtaz, Chantal Scheepbouwer, Robby E. Kibbelaar, David P. Noske, Renske D.M. Steenbergen, Nicole C.T. van Grieken, Winan van Houdt, Elisa Giovannetti, Geert J.L.H. van Leenders, Jos Jonkers, Tong Liu, Meisi Yan, Xiaolu Zhan, Tiannan Guo*, Connie R. Jimenez*.

Cancer Cell. 2025 Jul 14;43(7):1328-1346.e8. doi: 10.1016/j.ccell.2025.05.003. Epub 2025 May 29. PMID: 40446800.

17

Grow AI Virtual Cells: Three Data Pillars and Closed-Loop Learning

Liujia Qian, Zhen Dong & Tiannan Guo*.

Cell Research. 2025 May;35(5):319-321. doi: 10.1038/s41422-025-01101-y. PMID: 40128605; PMCID: PMC12012092.

16

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.

15

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.

14

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*.

Nature Communications. 2025 Apr 14;16(1):3530. doi: 10.1038/s41467-025-58866-4. PMID: 40229248.

13

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 2025 Jan 21;16(1):892. doi: 10.1038/s41467-024-54871-1. PMID: 39837863; PMCID: PMC11751188.

12

Longitudinal serum proteome mapping reveals biomarkers for healthy ageing and related cardiometabolic diseases

Jun Tang#, Liang Yue#, Ying Xu#, Fengzhe Xu#, Xue Cai, Yuanqing Fu, Zelei Miao, Wanglong Gou, Wei Hu, Zhangzhi Xue, Kui Deng, Luqi Shen, Zengliang Jiang, Menglei Shuai, Xinxiu Liang, Congmei Xiao, Yuting Xie, Tiannan Guo*, Yu-ming Chen* & Ju-Sheng Zheng*.

Nature Metabolism 2025 Jan;7(1):166-181. doi: 10.1038/s42255-024-01185-7. Epub 2025 Jan 13. PMID: 39805987; PMCID: PMC11774760.

11

AI-empowered perturbation proteomics for complex biological systems

Liujia Qian, Rui Sun, Ruedi Aebersold, Peter Bühlmann, Chris Sander*, Tiannan Guo*.

Cell Genomics. 2024 Nov 13;4(11):100691. doi: 10.1016/j.xgen.2024.100691. Epub 2024 Nov 1. PMID: 39488205; PMCID: PMC11605689.

10

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.

9

Proteomic landscape of epithelial ovarian cancer

Liujia Qian#, Jianqing Zhu#, Zhangzhi Xue#, Yan Zhou#, Nan Xiang#, Hong Xu#, Rui Sun, Wangang Gong, Xue Cai, Lu Sun, Weigang Ge, Yufeng Liu, Ying Su, Wangmin Lin, Yuecheng Zhan, Junjian Wang, Shuang Song, Xiao Yi, Maowei Ni, Yi Zhu*, Yuejin Hua*, Zhiguo Zheng*, Tiannan Guo*.

Nature Communications. 2024 Jul 31;15(1):6462. doi: 10.1038/s41467-024-50786-z. PMID: 39085232.

8

Population serum proteomics uncovers a prognostic protein classifier for metabolic syndrome

Xue Cai#, Zhangzhi Xue#, Fang-Fang Zeng#, Jun Tang#, Liang Yue#, Bo Wang#, Weigang Ge, Yuting Xie, Zelei Miao, Wanglong Gou, Yuanqing Fu, Sainan Li, Jinlong Gao, Menglei Shuai, Ke Zhang, Fengzhe Xu, Yunyi Tian, Nan Xiang, Yan Zhou, Peng-Fei Shan, Yi Zhu*, Yu-ming Chen*, Ju-Sheng Zheng*, Tiannan Guo*

Cell Reports Medicine. 2023 Sep 19;4(9). doi: https://doi.org/10.1016/j.xcrm.2023.101172. PMID: 37652016.

7

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.

6

Proteomic and metabolomic profiling of urine uncovers immune responses in patients with COVID-19

Xiaojie Bi#, Wei Liu#, Xuan Ding#, Shuang Liang#, Yufen Zheng#, Xiaoli Zhu#, Sheng Quan#, Xiao Yi, Nan Xiang, Juping Du, Haiyan Lyu, Die Yu, Chao Zhang Luang Xu, Weigang Ge, Jiale He, Guangjun Zhu, Donglian Wang, Hongguo Zhu, Shiyong Chen, Jun Li, Haihong Zhao, Yi Zhu*, Huafen Liu*, Jiaqin Xu*, Bo Shen*, Tiannan Guo*.

Cell Reports. 2022 Jan 18;38(3):110271. doi: 10.1016/j.celrep.2021.110271. PMID: 35026155.

5

SnapShot: Clinical proteomics

Yi Zhu, Ruedi Aebersold, Matthias Mann, Tiannan Guo.

Cell. 2021 Sep 2;184(18):4840-4840.e1. doi: 10.1016/j.cell.2021.08.015. PMID: 34478659.

4

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.

3

DPHL: A DIA pan-human protein mass spectrometry library for robust biomarker discovery

Tiansheng Zhu#, Yi Zhu#*, Yue Xuan#, Huanhuan Gao, Xue Cai, Sander R. Piersma, Thang V. Pham, Tim Schelfhorst, Richard R.D.G. Haas, Irene Bijnsdorp, Rui Sun, Liang Yue, Guan Ruan, Qiushi Zhang, Mo Hu, Yue Zhou, Winan J. Van Houdt, T.Y.S Lelarge, J. Cloos, Anna Wojtuszkiewicz, Danijela Koppers-Lalic, F. Böttger, Chantal Scheepbouwer, R.H Brakenhoff, G.J.L.H. van Leenders, Jan N.M. Ijzermans, J.W.M. Martens, R.D.M. Steenbergen, N.C. Grieken, Sathiyamoorthy Selvarajan, Sangeeta Mantoo, Sze Sing Lee, Serene Jie Yi Yeow, Syed Muhammad Fahmy Alkaff, Nan Xiang, Yaoting Sun, Xiao Yi, Shaozheng Dai, Wei Liu, Tian Lu, Zhicheng Wu, Xiao Liang, Man Wang, Yingkuan Shao, Xi Zheng, Kailun Xu, Qin Yang, Yifan Meng, Cong Lu, Jiang Zhu, Jin’e Zheng, Bo Wang, Sai Lou, Yibei Dai, Chao Xu, Chenhuan Yu, Huazhong Ying, Tony Kiat-hon Lim, Jianmin Wu, Xiaofei Gao, Zhongzhi Luan, Xiaodong Teng, Peng Wu, Shi’ang Huang, Zhihua Tao, N. Gopalakrishna Iyer, Shuigeng Zhou, Wenguang Shao, Henry Lam, Ding Ma, Jiafu Ji , Oi Lian Kon, Shu Zheng, Ruedi Aebersold, Connie R. Jimenez, Tiannan Guo*.

Genomics, Proteomics & Bioinformatics. 2020 Apr;18(2):104-119. doi: 10.1016/j.gpb.2019.11.008. PMID: 32795611.

2

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.

1

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.