PUBLICATIONS

PUBLICATIONS

82

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

Xiaohua 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 volume 8, Article number: 70 (2022)

79

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*, Jian Ruan*

Cancer Immunol Res canimm, 20 May 2022, doi.org/10.1158/2326-6066.CIR-21-1101

78

Proteomic characterization of Omicron SARS-CoV-2 host response

Jianfeng Bao#, Rui Sun#, Jingwen Ai#, Liujia Qian#, Fang Liu#, Hongyu Wang#, Lingling Tan, Xue Cai, Yingqiu Shi, Xiao Liang, Weigang Ge, Jing Wu, Chen Chen, Wenhong Zhang*, Jinsong Huang* & Tiannan Guo*

Cell Discovery, 18 May 2022, doi.org/10.1038/s41421-022-00418-x

77

An open invitation to the Understudied Proteins Initiative

Georg Kustatscher*, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser & Juri Rappsilber*

Nature Biotechnology, May 09, 2022, https://doi.org/10.1038/s41587-022-01316-z

73

Stratification of follicular thyroid tumours using data-independent acquisition proteomics and a comprehensive thyroid tissue spectral library

Yaoting Sun*, Lu Li, Yan Zhou, Weigang Ge, He Wang, Runxin Wu, Wei Liu, Hao Chen, Qi Xiao, Xue Cai, Zhen Dong, Fangfei Zhang, Junhong Xiao, Guangzhi Wang, Yi He, Jinlong Gao, Oi Lian Kon, Narayanan Gopalakrishna Iyer, Haixia Guan, Xiaodong Teng, Yi Zhu*, Yongfu Zhao*, Tiannan Guo*

Molecular Oncology, 23 February 2022, doi.org/10.1002/1878-0261.13198

72

Circulating proteome and progression of type 2 diabetes

Wanglong Gou, MSc#, Liang Yue, BSc#, Xin-yi Tang, MPH, Yan-yan Wu, MPH, Xue Cai, MSc, Menglei Shuai, BSc, Zelei Miao, MPH, Yuanqing Fu, PhD, Hao Chen, BSc, Zengliang Jiang, PhD, Jiali Wang, MPH, Yunyi Tian, MPH, Congmei Xiao, MSc, Nan Xiang, BSc, Zhen Wu, PhD, Yu-ming Chen, PhD*, Tiannan Guo, PhD*, Ju-Sheng Zheng, PhD*

The Journal of Clinical Endocrinology & Metabolism, dgac098, https://doi.org/10.1210/clinem/dgac098

67 Representative Publication

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, Xinke Zhan, Jiale He, Zi Xiong, Shun Zhang, Yanchang Li, Ping Xu, Guangjun Zhu, Donglian Wang, Hongguo Zhu, Shiyong Chen, Jun Li, Haihong Zhao, Yi Zhu*, Huafen Liu*, Jiaqin Xu*, Bo Shen*, Tiannan Guo*

Cell Reports. December 27,2021 doi.org/10.1016/j.celrep.2021.110271

66

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 Communications. 04 December 2021 doi.org/10.1002/cac2.12240

64

Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection

Ying Zhang#, Xue Cai#, Weigang Ge#, Donglian Wang#, Guangjun Zhu#, Liujia Qian#, Nan Xiang, Liang Yue, Shuang Liang, Fangfei Zhang, Jing Wang, Kai Zhou, Yufen Zheng, Minjie Lin, Tong Sun, Ruyue Lu, Chao Zhang, Luang Xu, Yaoting Sun, Xiaoxu Zhou, Jing Yu, Mengge Lyu, Bo Shen, Hongguo Zhu*, Jiaqin Xu*, Yi Zhu*, and Tiannan Guo*

J. Proteome Res. November 16, 2021 doi.org/10.1021/acs.jproteome.1c00525

63

Novel deep learning radiomics model for preoperative evaluation of hepatocellular carcinoma differentiation based on computed tomography data

Yong Ding#, Shijian Ruan#, Yubizhuo Wang#, Jiayuan Shao#, Rui Sun, Wuwei Tian, Nan Xiang, Weigang Ge, Xiuming Zhang, Kunkai Su, Jingwen Xia, Qiang Huang, Weihai Liu, Qinxue Sun, Haibo Dong*, Mylène C. Q. Farias, Tiannan Guo*, Andrey S. Krylov, Wenjie Liang*, Wenbo Xiao, Xueli Bai, Tingbo Liang*

Clin. Transl. Med. 2021;11:e570. doi.org/10.1002/ctm2.570

62

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*

J. Proteome Res. 2021, 20, 12, 5392–5401。 doi.org/10.1021/acs.jproteome.1c00640

61 Representative Publication

SnapShot: Clinical proteomics

Yi Zhu, Ruedi Aebersold, Matthias Mann, Tiannan Guo

Cell. 2021. 184(18):4840-4840 el. doi:10.1016/j.cell.2021.08.015

60 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
Volume 48, Issue 9, 20 September 2021, Pages 792-802
https://doi.org/10.1016/j.jgg.2021.04.002

55 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. doi: 10.1016/2021.06.22

52 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. doi: 10.1016/j.cell.2021.01.004

48

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, Yi Judy Zhu, Maria Rodriguez Martinez, Matteo Manica, Michael C Haffner, Ruedi Aebersold*, Peter J Wild*, Andreas Beyer*

Genome Biology. 14 Dec. 2020,21(302) 10.1186/s13059-020-02188-9

47 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) 10.1021/jasms.0c00254

44 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, Irene Bijnsdorp, Rui Sun, Liang Yue, GuanRuan, Qiushi Zhang, Mo Hu, Yue Zhou, Winan J. Van Houdt, T.Y.S Lelarge, J. Cloos, Anna Wojtuszkiewicz, Danijela Koppers-Lalic, F. Baettger, ChantalScheepbouwer, 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, ZhichengWu, 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 and Bioinformatics. online 2020 Aug 12 10.1016/j.gpb.2019.11.008

43 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 Judy Zhu*, Huafen Liu*, Haixiao Chen*, Tiannan Guo*

Cell. 2020. 182(1): 59-72. doi:10.1016/j.cell.2020.05.032

38

Quantitative proteome landscape of the NCI-60 cancer cell lines

Tiannan Guo*#, Augustin Luna#, Ching Chiek Koh#, Vinodh Rajapakse#, Zhicheng Wu, Michael Patrick Menden, Wei Liu, Yaoting Sun, Yongran Cheng, Laurence Calzone, Loredana Martignetti, Alessandro Ori, Murat Iskar, Ludovic Gillet, Qing Zhong, Sudhir Varma, Uwe Schmitt, Peng Qiu, Yi Zhu, Kexin Liu, Peter Wild, Garnett Mathew, Peer Bork, Martin Beck, Julio Saez-Rodriguez, William Reinhold, Chris Sander, Yves Pommier*, Ruedi Aebersold*

iScience. 2019, 21:664-680. 10.1016/j.isci.2019.10.059

36 Representative Publication

High-throughput Proteomics analysis of FFPE tissue samples facilitates tumor stratification

Yi Zhu#, Tobias Weiss#, Qiushi Zhang, Qing Zhong, Zhicheng Wu, Tiansheng Zhu, Chao Xu, Sai Lou, Bo Wang, Xiaoyan Yu, Ludovic Gillet, Peter Blattmann, Rui Sun, Xiao Yi, Ailsa Christiansen, Karim Saba, Dorothea Rutishauser, Jelena Ljubicic, Christian D. Fankhauser, Michael B. Schmid, 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, Peter J. Wild*, Ruedi Aebersold*, Tiannan Guo*

Molecular Oncology. 2019. 13 (11) :2305-2328. 10.1002/1878-0261.12570

34

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, Ulrich Wagner, Li Li, Konstantina Charmpi, Yi Zhu, Rui Sun, Dorothea Rutishauser, Thomas Hermanns, Christian Daniel Fankhauser, Cedric Poyet, Jelena Ljubicic, Niels Rupp, Jan H. Rüschoff, Qing Zhong, Andreas Beyer, Yansheng Liu, Gunnar Rätsch, Peter J. Wild*, Ruedi Aebersold*

Nature Communications 10, Article number: 2524, 2019. 10.1038/s41467-019-10513-5

25

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. Published online 24 May 2016. 10.1016/j.ccell.2016.04.012

23

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. 6, Article number: 24146 (2016). 10.1038/srep24146

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. 10.1038/sdata.2014.31