Selected publications

140

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.

120

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.

113

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.

100

Longitudinal proteomic investigation of COVID-19 vaccination

Yingrui Wang#, Qianru Zhu#, Rui Sun#, Xiao Yi#, Lingling Huang, Yifan Hu, Weigang Ge, Huanhuan Gao, Xinfu Ye, Yu Song, Li Shao, Yantao Li, Jie Li*, Tiannan Guo*, Junping Shi*

Protein & Cell. 2023 Sep 14;14(9):668-682. doi: 10.1093/procel/pwad004. PMID: 36930526.

96

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.

89

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.

88

Tissue-characteristic Expression of Mouse Proteome

Tian Lu, Liujia Qian, Yuting Xie, Qiushi Zhang, Wei Liu, Weigang Ge, Yi Zhu *, Lijia Ma *, Cheng Zhang *, Tiannan Guo *.

Molecular & Cellular Proteomics. 2022 Oct;21(10):100408. doi: 10.1016/j.mcpro.2022.100408. PMID: 36058520.

83

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.

62

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.

53

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.

All publications

48

Phenotype Classification using Proteome Data in a Data-Independent Acquisition Tensor Format

Fangfei Zhang#, Shaoyang Yu#, Lirong Wu#, Zelin Zang, Xiao Yi, Jiang Zhu, Cong Lu, Ping Sun, Yaoting Sun, Sathiyamoorthy Selvarajan, Lirong Chen, Xiaodong Teng, Yongfu Zhao, Guangzhi Wang, Junhong Xiao, Shiang Huang, Oi Lian Kon, Gopalakrishna N. Iyer, Stan Z. Li*, Zhongzhi Luan*, Tiannan Guo*.

Journal of American Society of Mass Spectrometry. 2020 Oct.31(11):2296-2304. doi: 10.1021/jasms.0c00254. PMID: 33104352.

45 Elsevier China Top OA Author Award

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.

42

A circulating extracellular vesicles-based novel screening tool for colorectal cancer revealed by shotgun and data-independent acquisition mass spectrometry

Xi Zheng#, Kailun Xu#, Biting Zhou#, Ting Chen, Yanqin Huang, Qilong Li, Fei Wen, Weiting Ge, Jian Wang, Shaojun Yu, Liang Zhu, Liang Yue, Xue Cai, Qiushi Zhang, Guan Ruan, Tiansheng Zhu, Zhicheng Wu, Yi Zhu, Yingkuan Shao*, Tiannan Guo*, Shu Zheng*.

Journal of Extracellular Vesicles. 2020 Apr 14;9(1):1750202. doi: 10.1080/20013078.2020.1750202. PMID: 32363013.

39

Quantitative proteome landscape of the NCI-60 cancer cell lines

Tiannan Guo*#, Augustin Luna#, Vinodh Rajapakse#, Ching Chiek Koh#, Zhicheng Wu, Wei Liu, Yaoting Sun, Huanhuan Gao, Michael Patrick Menden, Chao Xu, Laurence Calzone, Loredana Martignetti, Chiara Auwerx, Marija Buljan, Amir Banaei-Esfahani, Alessandro Ori, Murat Iskar, Ludovic Gillet, Ran Bi, Jiangnan Zhang, Huanhuan Zhang, Chenhuan Yu, Qing Zhong, Sudhir Varma, Uwe Schmitt, Peng Qiu, Qiushi Zhang, Yi Zhu, Peter J. Wild, Mathew J. Garnett, Peer Bork, Martin Beck, Kexin Liu, Julio Saez-Rodriguez, Fathi Elloumi, William C. Reinhold, Chris Sander, Yves Pommier*, Ruedi Aebersold*.

iScience. 2019 Nov 22;21:664-680. doi: 10.1016/j.isci.2019.10.059. PMID: 31733513.

37

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.

35

Comparative analysis of mRNA degradation and protein degradation in 68 pairs of adjacent prostate tissue samples indicates high stability of proteins

Wenguang Shao#, Tiannan Guo#*, Nora C Toussaint, Peng Xue, Ulrich Wagner, Li Li, Konstantina Charmpi, Yi Zhu, Jianmin Wu, Maria Buljan, Rui Sun, Dorothea Rutishauser, Thomas Hermanns, Christian Daniel Fankhauser, Cedric Poyet, Jelena Ljubicic, Niels Rupp, Jan H. Rüschoff, Qing Zhong, Andreas Beyer, Jaifu Ji, Ben C. Collins, Yansheng Liu, Gunnar Rätsch, Peter J. Wild*, Ruedi Aebersold*.

Nature Communications. 2019 Jun 7;10(1):2524. doi: 10.1038/s41467-019-10513-5. PMID: 31175306.

34

In-depth Serum Proteomics Reveals Biomarkers of Psoriasis Severity and Response to Traditional Chinese Medicine

Meng Xu#, Jingwen Deng#, Kaikun Xu#, Tiansheng Zhu#, Ling Han, Yuhong Yan, Danni Yao, Hao Deng, Dan Wang, Yaoting Sun, Cheng Chang, Xiaomei Zhang, Jiayu Dai, Liang Yue, Qiushi Zhang, Xue Cai, Yi Zhu, Hu Duan, Yuan Liu, Dong Li, Yunping Zhu, Timothy R. D. J. Radstake, Deepak M.W. Balak, Danke Xu*, Tiannan Guo*, Chuanjian Lu* and Xiaobo Yu*.

Theranostics. 2019 Apr 13;9(9):2475-2488. doi: 10.7150/thno.31144. PMID: 31131048.

26

TRIM24 is an oncogenic transcriptional activator in prostate cancer

Anna C. Groner, Laura Cato, Jonas de Tribolet-Hardy, Tiziano Bernasocchi, Hana Janouskova , Diana Melchers, René Houtman, Andrew C. B. Cato, Patrick Tschopp, Lei Gu, Andrea Corsinotti, Qing Zhong, Christian Fankhauser, Christine Fritz, Cédric Poyet, Ulrich Wagner, Tiannan Guo, Ruedi Aebersold, Levi A. Garraway, Peter J. Wild, Jean-Philippe Theurillat*, Myles Brown*.

Cancer Cell. 2016 Jun 13;29(6):846-858. doi: 10.1016/j.ccell.2016.04.012. PMID: 27238081.

24

Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity

Qing Zhong#, Jan H Rüschoff#, Tiannan Guo, Maria Gabrani, Peter J Schüffler, Markus Rechsteiner, Yansheng Liu, Thomas J Fuchs, Niels J Rupp, Christian Fankhauser, Joachim M Buhmann, Sven Perner, Cédric Poyet, Miriam Blattner, Davide Soldini, Holger Moch, Mark A Rubin, Aurelia Noske, Josef Rüschoff, Michael C Haffner, Wolfram Jochum, Peter J Wild*.

Scientific Reports. 2016 Apr 7;6:24146. doi: 10.1038/srep24146. PMID: 27052161.

16

A repository of assays to quantify 10,000 human proteins by SWATH-MS

Rosenberger G#, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R*.

Scientific Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. PMID: 25977788.