PUBLICATIONS

PUBLICATIONS

67

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*, and Tiannan Guo*

J. Proteome Res. 2021, XXXX, XXX, XXX https://doi.org/10.1021/acs.jproteome.1c00640
66

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. https://doi.org/10.1002/ctm2.570
54 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
53 COVID-19 Research

Eleven Routine Clinical Features Predict COVID-19 Severity.

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.
50 Representative Publication

Protein Classifier for Thyroid Nodules Learned from Rapidly Acquired Proteotypes.

Yaoting Sun#, Sathiyamoorthy Selvarajan#, Zelin Zang#, Wei Liu#, Yi Zhu#, Hao Zhang#, Hao Chen, Xue Cai, Huanhuan Gao, Zhicheng Wu, Lirong Chen, Xiaodong Teng, Yongfu Zhao, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy Syed Abdillah, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Qi Xiao, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Kexin Liu, Shu Zheng, Ruedi Aebersold, Stan Z. Li*, Oi Lian Kon*, N. Gopalakrishna Iyer*, Tiannan Guo*.

MedRxived: April 14, 2020 10.1101/2020.04.09.20059741
49 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
47

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 ProfileYi 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
46 Representative Publication

Phenotype Prediction using a Tensor Representation and Deep Learning from Data Independent Acquisition Mass Spectrometry.

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
39 Technological Highlight

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
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
22

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