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.
Identifying patients with rapid progression from hormone-sensitive to castration-resistant prostate cancer: a retrospective study
Chenxi Pan#, Yi He#, He Wang#, Yang Yu#, Lu Li, Lingling Huang, Mengge Lyu, Weigang Ge, Bo Yang*, Yaoting Sun*, Tiannan Guo*, Zhiyu Liu*
medRxiv. Posted October 24, 2022 (Preprint). doi.org/10.1101/2022.10.23.22281406
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
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.
Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification
Tianen He#, Youqi Liu#, Yan Zhou, Lu Li, He Wang, Shanjun Chen, Jinlong Gao, Wenhao Jiang, Yi Yu, Weigang Ge, Hui-Yin Chang, Ziquan Fan, Alexey I. Nesvizhskii*, Tiannan Guo*, and Yaoting Sun*
Journal of Proteome Research. 2022.21(12): 3007-3015.
A prediction model for COVID-19 liver dysfunction in patients with normal hepatic biochemical parameters
Jianfeng Bao#, Shourong Liu#, Xiao Liang#, Congcong Wang, Lili Cao, Zhaoyi Li, Furong Wei, Ai Fu, Yingqiu Shi, Bo Shen, Xiaoli Zhu, Yuge Zhao, Hong Liu, Liangbin Miao, Yi Wang, Shuang Liang, Linyan Wu, Jinsong Huang*, Tiannan Guo*, Fang Liu*
Life Science Alliance. 2022.19;6(1): e202201576.
COVIDpro: Database for mining protein dysregulation in patients with COVID-19
Fangfei Zhang#, Augustin Luna, Tingting Tan, Yingdan Chen, Chris Sander, Tiannan Guo*.
bioRxiv, Posted September 28, 2022. doi.org/10.1101/2022.09.27.509819
Targeted protein degradation reveals RNA Pol II heterogeneity and functional diversity
Yuanjun Li#, Jie Huang#, Junyi Zhu, Lijun Bao, Hui Wang, Yongpeng Jiang, Kai Tian, Rui Wang, Haonan Zheng, Wenjia Duan, Weifeng Lai, Xiao Yi, Yi Zhu, Tiannan Guo, Xiong Ji*.
Molecular Cell, 2022.82(20): 3943-3959.e11.
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.
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. 2022.21(10): 100408.
Integration of protein context improves protein-based COVID-19 patient stratification
Jinlong Gao#, Jiale He#, Fangfei Zhang#, Qi Xiao, Xue Cai, Xiao Yi, Siqi Zheng, Ying Zhang, Donglian Wang, Guangjun Zhu, Jing Wang, Bo Shen, Markus Ralser, Tiannan Guo*, Yi Zhu*.
Clinical Proteomics. 2022.19(1): 31.
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.
An in-library ligation strategy and its application in CRISPR/Cas9 screen of high-order gRNA combinations
Zhike Lu#, Ke Ni#, Yingying Wang#, Yangfan Zhou, Yini Li, Jianfeng Yan, Qingkai Song, Min Liu, Yujun Xu, Zhenxing Yu, Tiannan Guo, Lijia Ma*.
Nucleic Acids Research. 2022.50(11): 6575-6586.
High-throughput proteomic sample preparation using pressure cycling technology
Xue Cai#, Zhangzhi Xue, Chunlong Wu, Rui Sun, Liujia Qian, Liang Yue, Weigang Ge, Xiao Yi, Wei Liu, Chen Chen, Huanhuan Gao, Jing Yu, Luang Xu, Yi Zhu*, Tiannan Guo*.
Nature Protocols. 2022.17(10): 2307-2325.
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.
Proteotypic Differences of Follicular-Patterned Thyroid Neoplasms
Dongdong Huang#, Huifang Zhang, Lu Li, Weigang Ge, Wei Liu, Zhen Dong, Jinlong Gao, Nan Yao, Wenxin Fu, Lingling Huang, Tiannan Guo, Yaoting Sun* and Xiaodong Teng*.
Frontiers in Endocrinology. 2022.13: 854611.
Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues
Huanhuan Gao#, Youqi Liu, Vadim Demichev, Stephen Tate, Chen Chen, Jiang Zhu, Cong Lu, Markus Ralser, Tiannan Guo*, and Yi Zhu*.
Journal of Proteome Research. 2022.21(7): 1686-1693.
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.
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. 2022.8(1): 46.
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. 2022.40(6): 815-817.
Understudied proteins: opportunities and challenges for functional proteomics
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 Methods. 2022.19(7): 774-779.
RAB2A promotes cervical cancer progression as revealed by comprehensive analysis of HPV integration and proteome in longitudinal cervical samples
Yifan Meng*#; Shitong Lin#; Yi Zhou#; Xiao Yi#; Ping Wu; Qing Zhang; Weigang Ge; Canhui Cao; Peipei Gao; Wenhua Zhi; Ting Peng; Juncheng Wei; Wencheng Ding; Ding Ma; Guoliang Li; Qin Yang*; Tiannan Guo*; Xi Zeng*; Peng Wu*.
Clinical and Translational Medicine. 2022.12(3): e767.
Multi-omics in COVID-19: Seeing the unseen but overlooked in the clinic
Tian Lu#, Yingrui Wang, Tiannan Guo*.
Cell Reports Medicine. 2022.3(3): 100580.
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. 2022.16(8): 1611-1624.
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.
sRAGE alleviates SARS-CoV-2-induced pneumonia in hamster
Xiuqin Zhang, Dan Li, Rui Sun, Xinli Hu, Zhiqi Song, Xiaotian Ni, Hua Zhu, Tiannan Guo*, Chuan Qin*, Ruiping Xiao*.
Signal Transduction and Targeted Therapy. 2022.7(1): 36.
PROTREC: A probability-based approach for recovering missing proteins based on biological networks
Weijia Kong, Bertrand Jern, Han Wong, Huanhuan Gao, Tiannan Guo, Xianming Liu, Xiaoxian Du, Limsoon Wong*, Wilson Wen Bin Goh*.
Journal of Proteomics. 2022.250: 104392.
DIA-based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia
Wei Liu#, Yaoting Sun, Weigang Ge, Fangfei Zhang, Lin Gan, Yi Zhu, Tiannan Guo*, Kexin Liu*.
Molecular & Cellular Proteomics. 2022.21(2): 100187
Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF
Zelu Huang, Weijia Kong, Bertrand Jernhan Wong, Huanhuan Gao, Tiannan Guo, Xianming Liu, Xiaoxian Du, Limsoon Wong*, Wilson Wen Bin Goh*.
Journal of Proteomics. 2022.41: 107919.
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. 2022.38(3): 110271
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.
A prostate cancer tissue specific spectral library for targeted proteomic analysis
Rui Sun, Mengge Lyu, Shuang Liang, Weigang Ge, Yingrui Wang, Xuan Ding, Cheng Zhang, Yan Zhou, Shanjun Chen, Lirong Chen, Tiannan Guo*.
Proteomics. 2022.22(7): e2100147.
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, Lyv Mengge , Zhu Bo Shen, Xu Hongguo*, Yi Zhu*, Jiaqin Xu*, Tiannan Guo*.
Journal of Proteome Research. 2022.21(1): 90-100.
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*.
Clinical Translation Medicine. 2021.11(11): e570.
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.
SnapShot: Clinical proteomics
Yi Zhu, Ruedi Aebersold, Matthias Mann, Tiannan Guo.
Cell. 2021.184(18): 4840-4840 el.
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.
Phenotypic characterization of two novel cell line models of castration resistant prostate cancer
Michael C. Haffner*, Akshay Bhamidipati, Harrison K. Tsai, David M. Esopi*, Ajay M. Vaghasia, Jin-Yih Low, Radhika A. Patel, Tam Pham, Nicole Castagna, Jessica Hicks, Nicolas Wyhs, Rudolf Aebersold, Angelo M. De Marzo, William G. Nelson, Tiannan Guo and Srinivasan Yegnasubramanian*.
The Prostate. 2021.81(15): 1159-1171.
METTL9 mediated N1-histidine methylation of zinc transporters is required for tumor growth
Mengyue Lv#, Dan Cao#*, Liwen Zhang, Chi Hu, Shukai Li, Panrui Zhang, Lianbang Zhu, Xiao Yi, Chaoliang Li, Alin Yang, Zhentao Yang, Yi Zhu, Kaiguang Zhang & Wen Pan*.
Protein & Cell. 2021.12(12): 965-970.
On the feasibility of deep learning applications using raw mass spectrometry data
Joris Cadow*, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold and María Rodríguez Martínez*.
Bioinformatics. 2021.37(Suppl_1): i245-i253.
High-Throughput Proteomics and AI for Cancer Biomarker Discovery
Qi Xiao#, Fangfei Zhang, Luang Xu, Liang Yue, Oi Lian Kon, Yi Zhu*, Tiannan Guo*.
Advanced Drug Delivery Reviews. 2021.176: 113844.
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.
The Hippo-TAZ axis mediate vascular endothelial growth factor C in glioblastoma-derived exosomes to promote angiogenesis
Zhengmin Wang#, Yifan Yuan#, Xiong Ji#, Xing Xia#, Zhujun Li, Xiao Yi, Yi Zhu, Tiannan Guo, Yin Wang, Liang Chen*, Ying Liu*.
Cancer Letters. 2021.513: 1-13.
Immunometabolism the CyTOF way
Liujia Qian, Tiannan Guo*.
Immunity. 2021.54(4): 610-613.
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.
Proteomic and metabolomic investigation of serum lactate dehydrogenase elevation in COVID-19 patients
Haixi Yan#, Xiao Liang#, Juping Du#, Zebao He#, Yu Wang, Mengge Lyu ,Liang Yue, Fangfei Zhang, Zhangzhi Xue, Luang Xu, Guan Ruan, Jun Li, Hongguo Zhu, Jiaqin Xu, Shiyong Chen, Chao Zhang, Dongqing Lv ,Zongmei Lin, Bo Shen, Yi Zhu*, Biyun Qian*, Haixiao Chen*, Tiannan Guo*.
Proteomics. 2021.21(15): e2100002.
ProteomeExpert: A Docker image based web-server for exploring, modeling, vis-ualizing, and mining quantitative proteomic data sets
Tiansheng Zhu#, Hao Chen, Xishan Yan, Zhicheng Wu, Xiaoxu Zhou, Qi Xiao, Weigang Ge, Qiushi Zhang, Chao Xu, Luang Xu, Guan Ruan, Zhangzhi Xue, Chunhui Yuan*, Guo-Bo Chen* and Tiannan Guo*.
Bioinformatics. 2021.37(2): 273-275.
BatchServer: a web server for batch effect evaluation, visualization and correction
Tiansheng Zhu, Rui Sun, Fangfei Zhang, Guo-Bo Chen, Xiao Yi, Guan Ruan, Chunhui Yuan, Shuigeng Zhou*, Tiannan Guo*.
Journal of Proteome Research. 2021.20(1): 1079-1086.
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.
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.
PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation
Cai, Xue#; Ge, Weigang#; Yi, Xiao; Sun, Rui; Zhu, Jiang; Lu, Cong; Sun, Ping; Zhu, Tiansheng; Ruan, Guan; Yuan, Chunhui; Liang, Shuang; Lyu, Mengge; Huang, Shiang; Zhu, Yi*; Guo, Tiannan*.
Journal of Proteome Research. 2021.20(1): 279-288.
Generating Proteomic Big Data for Precision Medicine
Liang Yue#, Fangfei Zhang#, Rui Sun, Yaoting Sun, Chunhui Yuan, Yi Zhu, Tiannan Guo*.
Proteomics. 2020.20(21-22): e1900358.
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.
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.
Data-Independent Acquisition Mass Spectrometry and Software Tools: a Glimpse in 2020
Fangfei Zhang#, Weigang Ge, Guan Ruan, Xue Cai, Tiannan Guo*.
Proteomics 2020.20(17-18): e1900276.
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. 2020.9(1): 1750202.
Accelerated Lysis and Proteolytic Digestion of Biopsy-level Fresh Frozen and FFPE Tissue Samples Using Pressure Cycling Technology
Gao, Huanhuan#; Zhang, Fangfei; Liang, Shuang; Zhang, Qiushi; Lyu, Mengge; Qian, Liujia; Liu, Wei; Ge, Weigang; Chen, Chen; Yi, Xiao; Zhu, Jiang; Lu, Cong; Sun, Ping; Liu, Kexing; Zhu, Yi *; Guo, Tiannan *.
Journal of Proteome Research. 2020.19 (5): 1982-1990.
Accelerated Protein Biomarker Discovery from FFPE Tissue Samples using Single-shot, Short Gradient Microflow SWATH MS
Rui Sun#, Christie Hunter*#, Chen Chen, Weigang Ge, Nick Morrice, Qiushi Zhang, Xue Cai, Bo Wang, Xiaoyan Yu, Xiaodong Teng, Lirong Chen, Shaozheng Dai, Jian Song, Zhongzhi Luan, Changbin Yu, Ruedi Aebersold, Yi Zhu*, Tiannan Guo*.
Journal of Proteome Research. 2020.19(7): 2732- 2741.
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.
Arabidopsis Proteome and the Mass Spectral Assay Library
Huoming Zhang*#, Pei Liu#, Tiannan Guo#, Huayan Zhao, Dalila Bensaddek, Ruedi Aebersold, Liming Xiong.
Scientific Data. 2019.6(1): 278.
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.
Proteomic investigation of intra-tumor heterogeneity using network-based contextualization — A case study on prostate cancer
Goh, Wilson*#; Zhao, Yaxing#; Sue, Andrew; Guo, Tiannan; Wong, Limsoon*.
Journal of Proteomics. 2019.206: 103446.
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.
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. 2019.9(9): 2475-2488.
Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH
Yi Zhu#, Jiang Zhu#, Cong Lu, Qiushi Zhang, Wei Xie, Ping Sun, Xiaochuan Dong, Liang Yue, Yaoting Sun, Xiao YI, Tiansheng Zhu, Guan Ruan, Ruedi Aebersold*, Shi’ang Huang*, Tiannan Guo*.
Proteomics Clinical Applications. 2019.13(1): e1700179.
Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
Tiannan Guo#, Li Li#, Qing Zhong#, Niels J Rupp, Konstantina Charmpi, Christie E Wong, Ulrich Wagner, Jan H Rueschoff, Wolfram Jochum, Christian Fankhauser, Karim Saba, Cedric Poyet, Peter J Wild*, Ruedi Aebersold*, Andreas Beyer*.
Life Science Alliance. 2018.1(2): e201800042.
High-Throughput Proteomic Analysis of Fresh-Frozen Biopsy Tissue Samples Using Pressure Cycling Technology Coupled with SWATH Mass Spectrometry
Yi Zhu, Tiannan Guo*.
Methods in Molecular Biology. 2018.1788: 279-287.
Towards a one-stop solution for large-scale proteomics data analysis
Yi Zhu, Tiannan Guo*.
Science China Life Sciences. 2018.61(3): 351-354.
Application of Nanosecond Laser Photolysis Protein Footprinting to Study EGFR Activation by EGF in Cells
Yi Zhu, Aida Serra, Tiannan Guo, Jung Eun Park, Qing Zhong, and Siu Kwan Sze*.
Journal of Proteome Research. 2017.16(6): 2282-2293.
A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients
Qing Zhong#, Tiannan Guo#, Markus Rechsteiner, Jan H Rüschoff, Niels Rupp, Christian Fankhauser, Karim Saba, Ashkan Mortezavi, Cédric Poyet, Thomas Hermanns, Yi Zhu, Holger Moch, Ruedi Aebersold, Peter J. Wild*.
Scientific Data. 2017.4: 170014.
Phosphatase POPX2 exhibits dual regulatory functions in cancer metastasis
Songjing Zhang, Ting Weng, Cheruba, Elsie, Tiannan Guo, Hei Chan, Siu Kwan Sze, and Cheng-Gee Koh*.
Journal of Proteome Research. 2017.16(2): 698-711.
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.
Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics Using MicroPestle-Assisted Pressure-Cycling Technology
Shao S, Guo T, Gross V, Lazarev A, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R*.
Journal of Proteome Research. 2016.15(6): 1821-1829.
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. 2016.6: 24146.
Quantitative proteomics signature profiling based on network contextualization
Goh WW*, Guo T, Aebersold R, Wong L.
Biology Direct. 2015.10: 71.
Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry
Shao S, Guo T, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R*.
Proteomics. 2015.15(21): 3711-3721.
Global Metabonomic and Proteomic Analysis of Human Conjunctival Epithelial Cells (IOBA-NHC) in Response to Hyperosmotic Stress
Chen L#, Li J#, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, Chan EC*, Zhou L*.
Journal of Proteome Research. 2015.14(9): 3982-3995.
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Tiannan Guo#, Petri Kouvonen, Ching Chiek Koh, Ludovic C Gillet, Witold E Wolski, Hannes L Röst, George Rosenberger, Ben C Collins, Lorenz C Blum, Silke Gillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold*.
Nature Medicine. 2015.21(4): 407–413.
The methyltransferase Ezh2 controls cell adhesion and migration through direct methylation of the extranuclear regulatory protein talin
Gunawan M#, Venkatesan N#, Loh JT#, Wong JF, Berger H, Neo WH, Li LY, La Win MK, Yau YH, Guo T, See PC, Yamazaki S3, Chin KC4, Gingras AR5, Shochat SG, Ng LG, Sze SK, Ginhoux F, Su IH*.
Nature Immunology. 2015.16(5): 505-516.
Mass spectrometry-based proteomic quest for diabetes biomarkers
Shiying Shao*, Tiannan Guo, Ruedi Aebersold*.
Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics. 2015.1854(6): 519-27.
Quantitative proteomics reveals differential biologicalprocesses in healthy neonatal cord neutrophils and adultneutrophils
Jiang Zhu#, Huoming Zhang*#, Tiannan Guo, Wenying Li, Huiyu Li,YiZhu and Shi’ang Huang*
Proteomics. 2014.14(13-14): 1688-97.
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. 2014.1: 140031.
LEO1 is regulated by PRL-3 and mediates its oncogenic properties in Acute Myeloid Leukemia
Chong PS#, Zhou J#, Cheong LL, Liu SC, Qian J, Guo T, Sze SK, Zeng Q, Chng WJ*.
Cancer Research. 2014.74(11): 3043-3053.
Integrative Transcriptome and Proteome Study to Identify the Signaling Network Regulated by POPX2 Phosphatase
Zhang S, Guo T, Chan H, Sze SK, Koh CG*.
Journal of Proteome Research. 2013.12(6): 2525-2536.
Multidimensional identification of tissue biomarkers of gastric cancer
Tiannan Guo, Lingling Fan, Wai Har Ng, Yi Zhu, Mengfatt Ho, Wei Keat Wan, Kiat Hon Lim, Whee Sze Ong, Sze Sing Lee, Shiang Huang, Oi Lian Kon*, and Siu Kwan Sze*.
Journal of Proteome Research. 2012.11(6): 3405-3413.
Elucidating Structural Dynamics of Integral Membrane Proteins on Native Cell Surface by Hydroxyl Radical Footprinting and Nano LC-MS/MS
Zhu Y, Guo T, Sze SK*.
Methods in Molecular Biology. 2011.790: 287-303.
Investigation of POPX2 Phosphatase Functions by Comparative Phosphoproteomic Analysis
Singh P, Gan CS, Guo T, Phang HQ, Sze SK, Koh CG*.
Proteomics. 2011.11(14): 2891-900.
Simultaneous Analysis of Proteome, Phospho- and Glycoproteome of Rat Kidney Tissue with Electrostatic Repulsion Hydrophilic Interaction Chromatography
Piliang Hao, Tiannan Guo, Siu Kwan Sze*
PloS One. 2011.6(2): e16884.
Global molecular dysfunctions in gastric cancer revealed by an integrated analysis of the phosphoproteome and transcriptome
Tiannan Guo, Sze Sing Lee, Wai Har Ng, Yi Zhu, Chee Sian Gan, Jiang Zhu, Haixia Wang, Shiang Huang, Siu Kwan Sze* and Oi Lian Kon*.
Cellular and Molecular Life Sciences. 2011.68(11): 1983-2002.
Quantitative Proteomics Discloses MET Expression in Mitochondria as a Direct Target of MET Kinase Inhibitor in Cancer Cells
Tiannan Guo, Yi Zhu, Chee Sian Gan, Sze Sing Lee, JiangZhu, Haixia Wang, Xin Li, James Christensen, Shiang Huang, Oi Lian Kon*, Siu Kwan Sze*.
Molecular & Cellular Proteomics. 2010.9(12): 2629-2641.
Novel Application of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) in Shotgun Proteomics: Comprehensive Profiling of Rat Kidney Proteome
Piliang Hao, Tiannan Guo, Xin Li, Sunil S. Adav, Jie Yang, Meng Wei, and Siu Kwan Sze*
Journal of Proteome Research. 2010.9 (7). 3520-3526.
Simultaneous characterization of glyco- and phospho-proteomes of mouse brain membrane proteome with electrostatic repulsion hydrophilic interaction chromatography (ERLIC)
Huoming Zhang, Tiannan Guo, Xin Li, Arnab Datta, Jung Eun Park, Jie Yang, Sai Kiang Lim, James P. Tam, Siu Kwan Sze*.
Molecular & Cellular Proteomics. 2010.9(4):635-647.
Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting
Yi Zhu, Tiannan Guo, Jung Eun Park, Xin Li, Wei Meng, Arnab Datta, Marshall Bern, Sai Kiang Lim*.
Molecular & Cellular Proteomics. 2009.8(8): 1999-2010.
Elucidating the structure of cyclotide by partial acid hydrolysis and LC-MS/MS analysis
Siu Kwan Sze*, Wei Wang, Wei Meng, Randong Yuan, Tiannan Guo, Yi Zhu, James P. Tam*.
Analytical Chemistry. 2009.81(3): 1079-88.
One-step procedure for peptide extraction from in-gel digestion sample for mass spectrometric analysis
Wei Meng, Huoming Zhang, Tiannan Guo, Chhiti Pandey, Yi Zhu, Oi Lian Kon, Siu Kwan Sze*.
Analytical Chemistry. 2008.80(24): 9797-9805.
Hybridization of Pulsed-Q Dissociation and Collision-Activated Dissociation in Linear Ion Trap Mass Spectrometer for iTRAQ Quantitation
Tiannan Guo, Chee Sian Gan, Huoming Zhang, Yi Zhu, Oi Lian Kon, Siu Kwan Sze*.
Journal of Proteome Research. 2008.7(11): 4831-4840.
A Comparative Study of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) versus SCX-IMAC-Based Methods for PhosphopeptideIsolation/Enrichment
Chee Sian Gan, Tiannan Guo, Huoming Zhang, Sai Kiang Lim, Siu Kwan Sze*.
Journal of Proteome Research. 2008.7(11): 4869-4877.
