SELECTED PUBLICATIONS

SELECTED PUBLICATIONS

[Note: *, co-corresponding; #, co-first author.Full list of publications: Google Scholar, All publications]

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. 2025 Dec 5. doi: 10.1038/s44321-025-00346-9. Epub ahead of print. PMID: 41350775.

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 Oct 24:S0092-8674(25)01133-X. doi: 10.1016/j.cell.2025.10.004. Epub ahead of print. PMID: 41138729.

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.

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

Sun Y#, Wang H#, Li L#, Wang J, Chen W, Peng L, Hu P, Yu J, Cai X, Yao N, Zhou Y, Wang J, Wang Y, Qian L, Ge W, Chen M, Yang F, Gui Z, Sun W, Wang Z, Ge M, He Y, Wang G, Zhao Y, Chen H, Wu X, Du Y, Wei W, Wu F, Luo D, Lin X, Zheng H, Zhu X, Wei B, Shen J, Yao J, Yuan Z, Liu T, Pan J, Zhang Y, Lv Y, Guo Q, Wu Q, Gong T, Chen T, Zheng S, Zhu J, Liu H, Chen C, Han H, Selvarajan S, Xing MM, Kakudo K, Alexander EK, Wu Y, Wang Y, Xu D, Zhang H, Nie X, Kon OL, Iyer NG, Liu Z, Zhu Y*, Guan H*, Guo T*; We-TEC Investigators.

EMBO Molecular Medicine. 2025 May 29. doi: 10.1038/s44321-025-00242-2. Epub ahead of print. PMID: 40442320.

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 May 29. Epub ahead of print.

Proteomic analysis reveals modulation of key proteins in follicular thyroid cancer progression

Xue Cai#, Rui Sun#, Liang Yang#, Nan Yao, Yaoting Sun, Guangmei Zhang, Weigang Ge, Yan Zhou, Zhiqiang Gui, Yu Wang, Haitao Zheng, Dong Xu, Yongfu Zhao, Xiu Nie, Zhiyan Liu, Hao Zhang, Pingping Hu, Honghan Cheng, Zhangzhi Xue, Jiatong Wang, Jing Yu, Chuang Chen, Dingcun Luo, Jingqiang Zhu, Tong Liu, Yifeng Zhang, Qijun Wu, Qiaonan Guo, Wanyuan Chen, Jianbiao Wang, Wenjun Wei, Xiangfeng Lin, Jincao Yao, Guangzhi Wang, Li Peng, Shuyi Liu, Zhihong Wang, Hanqing Liu, Jiaxi Wang, Fan Wu, Zhennan Yuan, Tingting Gong, Yangfan Lv, Jingjing Xiang, Yi Zhu, Lei Xie21, Minghua Ge, Haixia Guan, Tiannan Guo*; We-TEC Investigators.

Chinese Medical Journal. 2025 May 21. doi: 10.1097/CM9.0000000000003645. Epub ahead of print. PMID: 40394764.

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.

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). https://doi.org/10.1038/s42255-024-01185-7.

metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis

Yingying Sun#, Ziyuan Xing#, Shuang Liang#, Zelei Miao, Lai-Bao Zhuo, Wenhao Jiang, Hui Zhao, Huanhuan Gao, Yuting Xie, Yan Zhou, Liang Yue, Xue Cai, Yu-Ming Chen*, Ju-Sheng Zheng*, Tiannan Guo*.

Mol Cell Proteomics. 2024 Sep 13:100840. doi: 10.1016/j.mcpro.2024.100840. Epub ahead of print. PMID: 39278598.

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.

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.

Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets

Rui Sun#, Weigang Ge#, Yi Zhu#, Azin Sayad#, Augustin Luna, Mengge Lyu, Shuang Liang, Luis Tobalina, Vinodh N. Rajapakse, Chenhuan Yu, Huanhuan Zhang, Jie Fang, Fang Wu, Hui Xie, Julio Saez-Rodriguez, Huazhong Ying, William C. Reinhold, Chris Sander, Yves Pommier, Benjamin G. Neel*, Ruedi Aebersold*, Tiannan Guo*

Molecular & Cellular Proteomics. 2023 Jun 19:100602. doi.org/10.1016/j.mcpro.2023.100602. PMID: 37343696.

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

Zhangzhi Xue#, Tiansheng Zhu#, Fangfei Zhang, Cheng Zhang, Nan Xiang, Liujia Qian, Xiao Yi, Yaoting Sun, Wei Liu, Xue Cai, Linyan Wang, Xizhe Dai, Liang Yue, Lu Li, Thang V. Pham, Sander R.Piersma, Qi Xiao, Meng Luo, Cong Lu, Jiang Zhu, Yongfu Zhao, Guangzhi Wang, Junhong Xiao, Tong Liu, Zhiyu Liu, Yi He, Qijun Wu,Tingting Gong, Jianqin Zhu, Zhiguo Zheng, Juan Ye, Yan Li , Connie R.Jimenez*, Jun A*, Tiannan Guo*

Patterns. 2023 Jul 5;4(7):100792. doi: 10.1016/j.patter.2023.100792. PMID: 37521047.

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.

Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding

Shaohua Tang# , Rui Sun# , Weigang Ge# , Tingting Mao# , Liujia Qian# , Chongquan Huang# , Zhouyang Kang# , Qi Xiao , Meng Luo , Qiushi Zhang , Sainan Li , Hao Chen , Wei Liu , Bingjie Wang , Shufei Li , Xiaoling Lin , Xueqin Xu , Huanzheng Li , Lianpeng Wu , Jianyi Dai , Huanhuan Gao , Lu Li , Tian Lu , Xiao Liang , Xue Cai , Guan Ruan , Fei Xu , Yan Li , Yi Zhu* , Ziqing Kong*, Jianping Huang *, Tiannan Guo*.

Cell Discovery. 2022 Jul 25;8(1):70. doi: 10.1038/s41421-022-00441-y. PMID: 35879274.

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.

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.

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.

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.