PUBLICATIONS

PUBLICATIONS

97

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. 2022.13: 7242.

95

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Gilbert S. Omenn*, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch

Journal of Proteome Research. Publication Date:November 1, 2022. doi.org/10.1021/acs.jproteome.2c00498

94

Integrated proteogenomic characterization of medullary thyroid carcinoma

Xiao Shi#, Yaoting Sun#, Cenkai Shen#, Yan Zhang#, Rongliang Shi#, Fan Zhang#, Tian Liao#, Guojun Lv, Zhengcai Zhu, Lianghe Jiao, Peng Li, Tiansheng Xu,  Ning Qu, Naisi Huang, Jiaqian Hu, Tingting Zhang, Yanzi Gu, Guangqi Qin, Haixia Guan, Weilin Pu, Yuan Li, Xiang Geng, Yan Zhang, Tongzhen Chen, Shenglin Huang, Zhikang Zhang, Shuting Ge, Wu Wang, Weibo Xu, Pengcheng Yu, Zhongwu Lu, Yulong Wang, Liang Guo, Yu Wang*, Tiannan Guo*, Qinghai Ji* & Wenjun Wei*

Cell Discovery. 2022.8(1): 120.

89 Representative Publication

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. 2022.8(1): 85.

86

Quantitative proteomic landscapes of primary and recurrent glioblastoma reveal a protumorigeneic role for FBXO2-dependent glioma-microenvironment interactions

Marcel Buehler#, Xiao Yi#, Weigang Ge, Peter Blattmann, Elisabeth Rushing, Guido Reifenberger, Joerg Felsberg, Charles Yeh, Jacob E. Corn, Luca Regli, Junyi Zhang, Ann Cloos,Vidhya Ravi, Benedikt Wiestler, Dieter Henrik Heiland, Ruedi Aebersold, Michael Weller, Tiannan Guo, Tobias Weiss*.

Neuro-Oncology. 2022. Accepted. 2022 Jul 8;noac169. doi: 10.1093/neuonc/noac169.

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. 2022.8(1): 70.

80

Molecular Subgroups of Intrahepatic Cholangiocarcinoma Discovered by Single-Cell RNA Sequencing-Assisted Multi-Omics Analysis

Xuanwen Bao#, Qiong Li#, Jinzhang Chen#, Diyu Chen#, Chanqi Ye#, Xiaomeng Dai, Yanfang Wang, Xin Li, Xiaoxiang Rong, Fei Cheng, Ming Jiang, Zheng Zhu, Yongfeng Ding, Rui Sun, Chuan Liu, Lingling Huang, Yuzhi Jin, Bin Li, Juan Lu, Wei Wu, Yixuan Guo, Wenguang Fu, Sarah Raye Langley, Vincent Tano, Weijia Fang, Tiannan Guo*, Jianpeng Sheng*, Peng Zhao*, and Jian Ruan*.

Cancer Immunology Research. 2022.10(7): 811-828.

73

Circulating proteome and progression of type 2 diabetes

Wanglong Gou#, Liang Yue#, Xinyi Tang#, Yanyan Wu#, Xue Cai#, Menglei Shuai, Zelei Miao, Yuanqing Fu, Hao Chen, Zengliang Jiang, Jiali Wang, Yunyi Tian, Congmei Xiao, Nan Xiang, Zhen Wu, Yuming Chen*, Tiannan Guo*, JuSheng Zheng*.

The Journal of Clinical Endocrinology & Metabolism. 2022.107(6): 1616–1625.

67

Proteomics profiling of colorectal cancer progression identifies PLOD2 as a potential therapeutic target

Yingkuan Shao#, Kailun Xu#, Xi Zheng, Biting Zhou, Xiuli Zhang, Lin Wang, Yaoting Sun, Dan Li, Ting Chen, Jian Wang, Shaojun Yu, Lifeng Sun, Xiaoming Xu, Shaozhi Dai, Huanhuan Gao, Guan Ruan, Wei Liu, Xue Cai, Tiansheng Zhu, Lina Qi, Jiani Chen, Wangxiong Hu, Xingyue Weng, Yi Zhu, Xueping Xiang, Zhiyuan Hu, Jinfan Li, Lirong Chen, Jimin Shao*, Shu Zheng*, Tiannan Guo*.

Cancer Commun. 2022.42(2): 164-169.

63

Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors

Weigang Ge#, Xiao Liang #, Fangfei Zhang#, Yifan Hu#, Luang Xu, Nan Xiang, Rui Sun, Wei Liu, Zhangzhi Xue, Xiao Yi, Yaoting Sun, Bo Wang, Jiang Zhu, Cong Lu, Xiaolu Zhan, Lirong Chen, Yan Wu, Zhiguo Zheng, Wangang Gong, Qijun Wu, Jiekai Yu, Zhaoming Ye, Xiaodong Teng, Shiang Huang, Shu Zheng, Tong Liu*, Chunhui Yuan*, Tiannan Guo*.

Journal of Proteome Research. 2021.20(12): 5392-5401.

61 COVID-19 Research

Gut microbiota may underlie the predisposition of healthy individuals to COVID-19

Wanglong Gou#, Yuanqing Fu#, Liang Yue#, Geng-dong Chen#, Xue Cai#, Menglei Shuai#, Fengzhe Xu#, Xiao Yi, Hao Chen, Yi Zhu, Mian-li Xiao, Zengliang Jiang, Zelei Miao, Congmei Xiao, Bo Shen, Xiaomai Wu, Haihong Zhao, Wenhua Ling, Jun Wang*, Yu-ming Chen*, Tiannan Guo*, Ju-Sheng Zheng*.

Journal of Genetics and Genomics. 2021.48(9): 792-802.

56 COVID-19 Research

Eleven routine clinical features predict COVID-19 severity uncovered by machine learning of longitudinal measurements

Kai Zhou#, Yaoting Sun#, Lu Li#, Zelin Zang#, Jing Wang#, Jun Li#, Junbo Liang#, Fangfei Zhang, Qiushi Zhang, Weigang Ge, Hao Chen, Xindong Sun, Liang Yue, Xiaomai Wu, Bo Shen, Jiaqin Xu, Hongguo Zhu, Shiyong Chen, Hai Yang, Shigao Huang, Minfei Peng, Dongqing Lv, Chao Zhang, Haihong Zhao, Luxiao Hong, Zhehan Zhou, Haixiao Chen, Xuejun Dong, Chunyu Tu, Minghui Li, Yi Zhu*, Baofu Chen*, Stan Z. Li*, Tiannan Guo*.

Computational and Structural Biotechnology Journal. 2021.19: 3640-3649.

53 Representative Publication/COVID-19 Research

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. 2021.184(3): 775-791.e14.

49

Convergent network effects along the axis of gene expression during prostate cancer progression

Konstantina Charmpi#, Tiannan Guo*#, Qing Zhong#, Ulrich Wagner#, Rui Sun, Nora C Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H Ruschoff, Christian Fankhauser, Karim Saba, Cedric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane Leoni Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, View ORCID Profile Yi Judy Zhu, Maria Rodriguez Martinez, Matteo Manica, Michael C Haffner, Ruedi Aebersold*, Peter J Wild*, Andreas Beyer*.

Genome Biology. 2020.21(1): 302.

48 Representative Publication

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. 2020.31(11): 2296-2304.

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. 2020.18(2): 104-119.

44 COVID-19 Research

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. 2020.182(1): 59-72.

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. 2019.21: 664-680.

37 Representative Publication

High-throughput Proteomics 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. 2019.13(11): 2305-2328.

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. 2019.10(1): 2524.

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. 2016.29(6): 846-858.