论文

Note: *, co-corresponding; #, co-first author.

Full list of publications:
192

A targeted proteomics assay for the preoperative diagnosis of thyroid nodules

Xue Cai#, Yaoting Sun#, Dingcun Luo#, Hao Zhang#, Wenjun Wei#, Yifeng Zhang#, Weigang Ge#,Jing Liu, Guan Ruan, Lu Li, Lingling Tan, Luang Xu, Dong Xu, Haixia Guan, Jiang Zhu, Wanyuan Chen, Qiushi Zhang, Huijuan Si, Juntao Qiu, Zhangzhi Xue, Zhiqiang Gui, Haitao Zheng, Gaosong Wu, Jianhua Wang, Lei Xie, Guang Chen, Guoyang Wu, Lei Liang, Chuang Chen, Xianghui He, Meiping Shen, Jianbiao Wang, Minghua Ge, Deguang Zhang, Liang Zhou, Yijun Wu, Hui Shi, Fan Wu, Zhihong Wang, Hong Han, Jing Yao, Zhiyan Liu, Mingzhao Xing, Kennichi Kakudo, Yibo Gao, Wen Tian*, Huixiong Xu*, Yi Zhu*, Yu Wang*, Tiannan Guo*, We-TEC Investigators.

Cell Reports Medicine, 2026 Mar. 10

191

Multimodal AI-enabled mass spectrometry-based expansion proteomics for whole-slide at single-cell resolution

Shuaiyao Wang#, Zhen Dong#*, Chunlong Wu, Jiayi Chen, Changao Li, Jianpeng Sheng, Xiang Li, Yi Chen*, Tiannan Guo*.

LangTaoSha Preprint Server, 2026 Feb. 20. DOI: 10.65215/LTSpreprints.2026.02.20.000134.

190

ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning

Mengge Lyu, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Pu Liu, Sai Zhang, Xiangqing Li, Rui Sun*, Yi Chen*, Tiannan Guo*.

Nature Communications, 2026 Jan 22;17(1):1949. doi: 10.1038/s41467-026-68686-9. PMID: 41571643; PMCID: PMC12929803.

189

Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma

Yan Zhou*, Yingrui Wang*, Xiao Shi*, Jiatong Wang*, Zelin Zang*, Likun Zhang*, Zhiqiang Gu, Xue Cai, Pingping Hu, Jiaxi Wang, Hanqing Liu, Zhihong Wang, Haixia Guan, Xiaohong Wu, Cenkai Shen, Yi He, Mo Li, Hao Zhang, Jianbiao Wang , Yijun Wu, Chuang Chen , Yi Zhu, Yaoting Sun#, Zhiyan Liu#, Yu Wang#, Tiannan Guo#.

Nature Communications. 2026 Jan 14;17(1):432. doi: 10.1038/s41467-025-67533-7. PMID: 41535264; PMCID: PMC12804720.

188

SARS-CoV-2 peptide fragments selectively dysregulate specific immune cell populations via Gaussian curvature targeting

Zhang Y#, Silvestre-Roig C#, Fu H#, Alimohamadi H#, Mandal T, Chen JW, Luo EW, Anda J, Linard Matos AL, Richter M, Mennella A, Lee H, Chan LC, Wang Y, Wang N, Wang H, Wang X, Lee CK, Ghosh S, Matsui T, Weiss TM, Guo T, Zhang M, Li D, Wolfgang MC, Hagan RS, Li MMH, Gunzer M, Sickmann A, Frasca L, Yeaman MR, Lande R, Cui Q, Soehnlein O, Wong GCL*.

Proceedings of the National Academy of Sciences of the United States of America. 2026 Jan 13;123(2):e2521841122. doi: 10.1073/pnas.2521841122. Epub 2026 Jan 8. PMID: 41505524.

187

Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Huanhuan Gao#, Yuecheng Zhan#, Yuanqi Liu#, Zhiyi Zhu, Yuxiu Zheng, Liqin Qian, Zhangzhi Xue, Honghan Cheng, Zongxiang Nie, Weigang Ge, Senlin Ruan, Jiaxu Liu, Jikai Zhang, Yingying Sun, Lei Zhou, Dongyue Xun, Yingrui Wang, Heyun Xu*, Huiwen Miao*, Yi Zhu*, Tiannan Guo*.

EMBO Molecular Medicine. 2025 Dec 5. doi: 10.1038/s44321-025-00346-9. Epub ahead of print. PMID: 41350775.

186

The suprachiasmatic nucleus regulates brown fat thermogenesis in male mice through an adrenergic receptor ADRB3-S100B signaling pathway

Yizhun Zeng, Xiaopeng Song, Qi Chen, Yue Gu, Jie Zhang, Tao Zhou, Zhihao Li, Tao Wang, Le Chang, Hongwei Yao, Yan Wang, Liyan Miao, Liujia Qian, Tiannan Guo, Yong Zhang, Sonia Rodriguez-Fernandez, Antonio Vidal-Puig*, Ying Xu*.

Plos Biology. 2025 Dec 4;23(12):e3003534. doi: 10.1371/journal.pbio.3003534. Epub ahead of print. PMID: 41343575.

185

Expansion omics: from expansion microscopy to spatial omics

Zhen Dong#*, Weirong Xiang#, Wenhao Jiang, Tiannan Guo*.

Molecular Systems Biology. 2025 Dec 1. doi: 10.1038/s44320-025-00171-9. Epub ahead of print. PMID: 41326779.

184

Rational tuning of temperature sensitivity of the TRPM8 channel

Lizhen Xu#, Xiao Liang#, Yunfei Wang#, Han Wen#, Wenxuan Zhen, Zhangzhi Xue, Fangfei Zhang, Xiao Yi, Xiaoying Chen, Lidan Hu, Bei Li, Bing Zhang, Zhenfeng Deng ,Wei Yang, Shilong Yang*, Tiannan Guo*, Yi Zhu* & Fan Yang*.

EMBO reports. 2025 Nov 14. doi: 10.1038/s44319-025-00630-2. Epub ahead of print. PMID: 41238795.

183

Cross-ethnic Molecular Signatures Underpin the Adverse Impact of Statin Use on Type 2 Diabetes

Fengzhe Xu#, Min Yang#, Wei Hu#, Shuai Yuan, Xue Cai, Wanglong Gou, Zelei Miao, Bang-yan Li, Liang Yue, Zhangzhi Xue, Menglei Shuai, Luqi Shen, Yuanqing Fu, Tiannan Guo*, Yu-ming Chen*, Ju-Sheng Zheng*

Genomics, Proteomics & Bioinformatics, 2025;, qzaf101, https://doi.org/10.1093/gpbjnl/qzaf101

182

Protein restriction reprograms the multi-organ proteomic landscape of mouse aging

Tian Lu#, Yuting Xie#, Yingrui Wang, Xiling Lin, Xue Cai, Yuqi Zhang, Zongxiang Nie, Chang Su, Wanglong Gou, Hong Zhang, Jing Wang, Yan Zhong, Zeyin Lai, Jingjing Xiang, Peng-Fei Shan, Ju-Sheng Zheng, Huijun Wang, Yi Zhu*, Tiannan Guo*.

Cell. 2025 Oct 24:S0092-8674(25)01133-X. doi: 10.1016/j.cell.2025.10.004. Epub ahead of print. PMID: 41138729.

181

Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples

Zhen Dong#, Chunlong Wu#, Jiayi Chen, Wenhao Jiang, Kiryl D Piatkevich*, Yi Zhu*, Tiannan Guo*.

Nature Protocols. 2025 Oct 9. doi: 10.1038/s41596-025-01256-3. Epub ahead of print. PMID: 41068477.

180

A standardized framework for circulating blood proteomics

Xue Cai, Philipp E. Geyer, Yasset Perez-Riverol, Gilbert S. Omenn, Lianhua Dong, Robert Winkler, Sara Ahadi, Philip Lössl, Xiaobo Yu, Cheng Chang, Markus Ralser, Connie R. Jimenez, Yang Zhao, Yu-Ju Chen, Terence C. W. Poon, Nicolai Bache, Leming Shi, Xinhua Dai, Ziyue Wang, Yi Zhu, Xiang Fang, Jochen M. Schwenk*, Jennifer E. Van Eyk*, Uwe Völker*, Tiannan Guo*.

Nature Genetics. 2025 Oct;57(10):2371-2380. doi: 10.1038/s41588-025-02319-7. Epub 2025 Sep 23. PMID: 40987950.

179

Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy

Chunfu Xiao#, Xiaoge Liu#, Peiyu Liu#, Xinwei Xu, Chao Yao, Chunqiong Li, Qi Xiao, Tiannan Guo, Li Zhang, Yongjun Qian, Chao Wang, Yiting Dong, Yingxuan Wang, Zhi Peng, Chuanhui Han, Qiang Cheng*, Ni A An*, Chuan-Yun Li*.

Cell Genomics. 2025 Jul 14:100928. doi: 10.1016/j.xgen.2025.100928. Epub ahead of print. PMID: 40680745.

178

Spatially resolved C1QC+ macrophage-CD4+ T cell niche in colorectal cancer microenvironment: implications for immunotherapy response

Zhang, H.#, L. Hong#, Z. Dong#, S. Xin#, B. Lin, J. Cheng, W. Tian, B. Li, J. Wang, X. Liu, C. Liu, Y. Jin, Y. Feng, G. Su, X. Sun, Q. Liu, X. Dai, Y. Gao, Z. Tong, L. Liu, X. Zhu, Y. Zheng, P. Zhao, T. Guo*, W. Fang* and X. Bao* .

Cell Discovery. 11(1): 60. https://doi.org/10.1038/s41421-025-00811-2. PMID: 40593467

177

MassNet: billion-scale AI-friendly mass spectral corpus enables robust de novo peptide sequencing

Jun A#, Xiang Zhang#, Xiaofan Zhang#, Jiaqi Wei#, Te Zhang, Yamin Deng, Pu Liu, Zongxiang Nie, Yi Chen, Nanqin Dong, Zhiqiang Gao*, Siqi Sun*, Tiannan Guo*.

bioRxiv preprint. 26 June, 2025. https://www.biorxiv.org/content/10.1101/2025.06.20.660691v1

176

Tissue expansion enables proteomics at improved spatial resolution

Zhen Dong#, Wenhao Jiang#, Tiannan Guo*

Trends in Biochemical Sciences. 2025 June 21. doi: 10.1016/j.tibs.2025.06.002. PMID: 40545409

175

A protein-based classifier for differentiating follicular thyroid adenoma and carcinoma

Sun Y#, Wang H#, Li L#, Wang J, Chen W, Peng L, Hu P, Yu J, Cai X, Yao N, Zhou Y, Wang J, Wang Y, Qian L, Ge W, Chen M, Yang F, Gui Z, Sun W, Wang Z, Ge M, He Y, Wang G, Zhao Y, Chen H, Wu X, Du Y, Wei W, Wu F, Luo D, Lin X, Zheng H, Zhu X, Wei B, Shen J, Yao J, Yuan Z, Liu T, Pan J, Zhang Y, Lv Y, Guo Q, Wu Q, Gong T, Chen T, Zheng S, Zhu J, Liu H, Chen C, Han H, Selvarajan S, Xing MM, Kakudo K, Alexander EK, Wu Y, Wang Y, Xu D, Zhang H, Nie X, Kon OL, Iyer NG, Liu Z, Zhu Y*, Guan H*, Guo T*; We-TEC Investigators.

EMBO Molecular Medicine. 2025 May 29. doi: 10.1038/s44321-025-00242-2. Epub ahead of print. PMID: 40442320.

174

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets

Jaco C. Knol#, Mengge Lyu#, Franziska Böttger#, Madalena Nunes Monteiro#, Thang V. Pham, Frank Rolfs, Andrea Vallés-Martí, Tim Schelfhorst, Richard R. de Goeij-de Haas, Irene V. Bijnsdorp, Shuaiyao Wang, Fangfei Zhang, Jun A, Bart A. Westerman, Barbara Sitek, Janne Lehtiö, Jan Koster, Jan N.M. IJzermans, Hanneke W.M. van Laarhoven, Maarten F. Bijlsma, Jan Paul Medema, Alex A. Henneman, Sander R. Piersma, Ruud H. Brakenhoff, Jacqueline Cloos, Valentina Cordo’, Daphne de Jong, Geert Kazemier, Danijela Koppers-Lalic, Mariette Labots, Tessa Y.S. Le Large, John W.M. Martens, Jules P.P. Meijerink, Madiha Mumtaz, Chantal Scheepbouwer, Robby E. Kibbelaar, David P. Noske, Renske D.M. Steenbergen, Nicole C.T. van Grieken, Winan van Houdt, Elisa Giovannetti, Geert J.L.H. van Leenders, Jos Jonkers, Tong Liu, Meisi Yan, Xiaolu Zhan, Tiannan Guo*, Connie R. Jimenez*.

Cancer Cell. 2025 May 29. Epub ahead of print.

173

Proteomic analysis reveals modulation of key proteins in follicular thyroid cancer progression

Xue Cai#, Rui Sun#, Liang Yang#, Nan Yao, Yaoting Sun, Guangmei Zhang, Weigang Ge, Yan Zhou, Zhiqiang Gui, Yu Wang, Haitao Zheng, Dong Xu, Yongfu Zhao, Xiu Nie, Zhiyan Liu, Hao Zhang, Pingping Hu, Honghan Cheng, Zhangzhi Xue, Jiatong Wang, Jing Yu, Chuang Chen, Dingcun Luo, Jingqiang Zhu, Tong Liu, Yifeng Zhang, Qijun Wu, Qiaonan Guo, Wanyuan Chen, Jianbiao Wang, Wenjun Wei, Xiangfeng Lin, Jincao Yao, Guangzhi Wang, Li Peng, Shuyi Liu, Zhihong Wang, Hanqing Liu, Jiaxi Wang, Fan Wu, Zhennan Yuan, Tingting Gong, Yangfan Lv, Jingjing Xiang, Yi Zhu, Lei Xie21, Minghua Ge, Haixia Guan, Tiannan Guo*; We-TEC Investigators.

Chinese Medical Journal. 2025 May 21. doi: 10.1097/CM9.0000000000003645. Epub ahead of print. PMID: 40394764.

172

PWWP3A disrupts the assembly of VISA/MAVS signalosome to inhibit innate immune response against RNA viruses

Mengling Shi#, Cong Wang#, Zhen Chen#, Yidan Zhou, Liang Yue, Yu Liu, Tiannan Guo, Jun Shang, Haotian Xu, Yu Zhang, Mengcheng Luo*, Caoqi Lei*.

Nature Communications. 2025 May 1;16(1):4084. doi: 10.1038/s41467-025-59421-x. PMID: 40312484; PMCID: PMC12045991.

171

Proteomic profiling in cerebrospinal fluid reveal biomarkers for shunt outcome in idiopathic normal-pressure hydrocephalus

Yuqi Ying#, Jingquan Lin#, Wei Gao#, Liang Yue#, Qingze Zeng, Katrina Bartas, Dayeon Cheong, Hongjie Jiang, Zhe Zheng, Ligen Shi, An Ping, Yuanjian Fang, Feng Yan, Tiannan Guo, Jianmin Zhang*, Hemmings Wu*, Kevin Beier*, Junming Zhu*, Zhoule Zhu*.

Journal of Advanced Research. 2025 Apr 29:S2090-1232(25)00287-5. doi: 10.1016/j.jare.2025.04.043. Epub ahead of print. PMID: 40311753.

170

Integrative proteogenomic characterization reveals therapeutic targets in poorly differentiated and anaplastic thyroid cancers

Zongfu Pan#, Zhuo Tan#, Ning Xu#, Zhenmei Yao#, Chuanming Zheng, Jinbiao Shang, Lei Xie, Jiajie Xu, Jiafeng Wang, Liehao Jiang, Xuhang Zhu, Dingyi Yu, Ying Li, Yulu Che, Yingying Gong, Zhaoyu Qin, Yiwen Zhang, Xiaozhou Zou, Tong Xu, Zhenying Guo, Tiefeng Jin, Tiannan Guo, Wei Wang, Wanyuan Chen, Yaoting Sun,  Weixin Wang, Xiaojun Peng, Changtian Yin, Chen Ding*, Ping Huang*, Minghua Ge*.

Nature Communications. 2025 Apr 16;16(1):3601. doi: 10.1038/s41467-025-58910-3. PMID: 40234451; PMCID: PMC12000556.

169

The dual-targeted transcription factor BAI1 orchestrates nuclear and plastid gene transcription in land plants

Jing Qin#, Yelin Shan#, Hao Liu, Zhangzhi Xue, Yike Xie, Guoxin Yuan, Yiming Zou, Xiaonuan Hao, Yunpeng Zhu, Xuan Shen, Meng Li, Xu Wang, Puyuan Liu, Jinxiu Xu, Yuhua Wang, Peng Zhao, Yuan Chen, Yi Zhu, Min Xu, Ming Yue, Aigen Fu*, Weiguo Zhang*, Beibei Li*.

Molecular Plant. 2025 Mar 31:S1674-2052(25)00108-X. doi: 10.1016/j.molp.2025.03.018. Epub ahead of print. PMID: 40170352.

168

Grow AI Virtual Cells: Three Data Pillars and Closed-Loop Learning

Liujia Qian, Zhen Dong & Tiannan Guo*.

Cell Research. 2025 March 25. https://doi.org/10.1038/s41422-025-01101-y

167

Spatial single-cell proteomics landscape decodes the tumor microenvironmental ecosystem of intrahepatic cholangiocarcinoma

Libing Hong#, Jie Mei#, Xuqi Sun#, Yifan Wu#, Zhen Dong#, Yuzhi Jin, Liaoliao Gao, Jinlin Cheng, Weihong Tian, Chuan Liu, Bin Li, Pingping Hu, Lulu Liu, Shan Xin, Xiaomeng Dai, Peng Zhao, Rongping Guo, Minshan Chen, Jingping Yun, Bo Lin*, Wei Wei*, Weijia Fang*, Xuanwen Bao*.

Hepatology. 2025 Feb 25. doi: 10.1097/HEP.0000000000001283. Epub ahead of print. PMID: 39999448.

166

Mass-spectrometry-based proteomics: from single cells to clinical applications

Tiannan Guo*, Judith A. Steen*, Matthias Mann*.

Nature. 2025 Feb;638(8052):901-911. doi: 10.1038/s41586-025-08584-0. Epub 2025 Feb 26. PMID: 40011722.

165

ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and a multi-database search strategy

Mengge Lyu, Yi Chen*, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Pu Liu, Sai Zhang, Xiangqing Li, Rui Sun*, Tiannan Guo*.

bioRxiv preprint. 23 Feb, 2025. https://doi.org/10.1101/2025.02.18.638804.

164

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Perez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann*, Bing Zhang*, Tiannan Guo*.

arXiv preprint. 21 Feb 2025. https://doi.org/10.48550/arXiv.2502.15867

163

Spatial distribution of the proteome in human body and cancers

Liang Yue#, Wenhao Jiang#, Sainan Li#, Meng Luo#, Ning Fan, Xiaolu Zhan, Kexin Chen, Tian Lu, Fang Guo, Dongwei Li, Weigang Ge, Zongxiang Nie, Mengge Lyu, Jun A, Yingrui Wang, Yingdan Chen, Zhenhai Fu, Nan Xiang, Lu Li, Fengchao Yu, Guo Ci Teo, Alexy I Nesvizhskii, Meng Wang, Michael P. Snyder, Ben Collins, Ruedi Aebersold, Fei Xu, Yi Zhu*, Tong Liu*, Yan Li*, Tiannan Guo*.

bioRxiv preprint. 18 Feb, 2025. https://doi.org/10.1101/2025.02.14.638212

162

A perturbation proteomics-based foundation model for virtual cell construction

Rui Sun#, Liujia Qian#, Yongge Li#, Honghan Cheng, Zhangzhi Xue, Xuedong Zhang, Lingling Tan, Yuecheng Zhan, Wenbin Hu, Qi Xiao, Zhiwei Liu, Guangmei Zhang, Weinan E, Peijie Zhou, Han Wen*, Yi Judy Zhu*, Tiannan Guo*.

bioRxiv preprint. 10 Feb, 2025. doi: https://doi.org/10.1101/2025.02.07.637070.

161

DDA-BERT: leveraging transformer architecture pre-training for data-dependent acquisition mass spectrometry-based proteomics

A Jun#, Pu Liu#, Yingying Sun#, Jiaying Lin, Xiaofan Zhang, Zongxiang Nie, Yuqi Zhang, Ziyuan Xing, Yi Chen*, Tiannan Guo*.

bioRxiv preprint. 15 Nov, 2024. https://doi.org/10.1101/2024.11.13.623394

160

DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis

Zhiwei Liu#, Pu Liu#, Yingying Sun#, Zongxiang Nie, Xiaofan Zhang, Yuqi Zhang, Yi Chen*, Tiannan Guo*.

Nature Communications. 2025 Apr 14;16(1):3530. doi: 10.1038/s41467-025-58866-4. PMID: 40229248.

159

Hemithyroidectomy Versus Total Thyroidectomy for Sporadic Medullary Thyroid Cancer: A Chinese Nationwide Large-Scale Cohort Study

Xiao Shi#, Cenkai Shen#, Chuqiao Liu#, Likun Zhang#, Yuxin Du#, Hao Zhang, Hongwei Liu, Jianbiao Wang, Chuang Chen, Yijun Wu, Chunyan Zhang, Zimeng Li, Haitao Tang, Min Yin, Xiaoqi Mao, Shuyi Liu, Yaoting Sun, Yan Zhou, Wenjun Wei, Naisi Huang, Zhihong Wang, Zhiqiang Gui, Hanqing Liu, Jiaxi Wang, Jian Li, Cuiwei Li, Shiyu Xiang, Liang Guo, Yan Zhang, Yi He, Tiannan Guo*, Qinghai Ji*, Zhiyan Liu*, Yu Wang*.

Journal of the National Comprehensive Cancer Network. 2025 Feb 6:1-8. doi: 10.6004/jnccn.2024.7088. Epub ahead of print. PMID: 39919373.

158

iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control.

Huanhuan Gao#, Yi Zhu#*, Dongxue Wang#, Zongxiang Nie#, He Wang#, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He#, Tiannan Guo#

Nature Communications 16, 892 (2025). https://doi.org/10.1038/s41467-024-54871-1.

157

Longitudinal serum proteome mapping reveals biomarkers for healthy ageing and related cardiometabolic diseases

Jun Tang#, Liang Yue#, Ying Xu#, Fengzhe Xu#, Xue Cai, Yuanqing Fu, Zelei Miao, Wanglong Gou, Wei Hu, Zhangzhi Xue, Kui Deng, Luqi Shen, Zengliang Jiang, Menglei Shuai, Xinxiu Liang, Congmei Xiao, Yuting Xie, Tiannan Guo*, Yu-ming Chen* & Ju-Sheng Zheng*.

Nature Metabolism (2025). https://doi.org/10.1038/s42255-024-01185-7.

156

Comprehensive Mass Spectral Libraries of Human Thyroid Tissues and Cells

Lu Li#, Wenhao Jiang#, Wenjun Wei, Gnana P Krishnamoorthy, Pingping Hu, Mengni Chen, Vera Tiedje, Adrián Acuña-Ruiz, He Wang, Zhihong Wang, Jianbiao Wang, Hanqing Liu, Wanyuan Chen, Haixia Guan, Chuang Chen, Hao Zhang, Yu Wang, James A Fagin, Tiannan Guo, Yi Zhu, Yingrui Wang*, Jianqing Gao*, Yaoting Sun*.

Scientific Data. 2024 Dec 28;11(1):1448. doi: 10.1038/s41597-024-04322-9. PMID: 39732735; PMCID: PMC11682198.

155

AI-driven eyelid tumor classification in ocular oncology using proteomic data.

Linyan Wang#, Xizhe Dai#, Zicheng Liu#, Yaxing Zhao#, Yaoting Sun, Bangxun Mao, Shuohan Wu, Tiansheng Zhu, Fengbo Huang, Nuliqiman Maimaiti#, Xue Cai, Stan Z Li*, Jianpeng Sheng*, Tiannan Guo*, Juan Ye*.

npj Precision Oncology. 2024 Dec 23;8(1):289. doi: 10.1038/s41698-024-00767-8. PMID: 39715816.

154

π-HuB: the proteomic navigator of the human body.

Fuchu He, Ruedi Aebersold, Mark S Baker, Xiuwu Bian, Xiaochen Bo, Daniel W Chan, Cheng Chang, Luonan Chen, Xiangmei Chen, Yu-Ju Chen, Heping Cheng, Ben C Collins, Fernando Corrales, Jürgen Cox, Weinan E, Jennifer E Van Eyk, Jia Fan, Pouya Faridi, Daniel Figeys, George Fu Gao, Wen Gao, Zu-Hua Gao, Keisuke Goda, Wilson Wen Bin Goh, Dongfeng Gu, Changjiang Guo, Tiannan Guo, Yuezhong He, Albert J R Heck, Henning Hermjakob, Tony Hunter, Narayanan Gopalakrishna Iyer, Ying Jiang, Connie R Jimenez, Lokesh Joshi, Neil L Kelleher, Ming Li, Yang Li, Qingsong Lin, Cui Hua Liu, Fan Liu, Guang-Hui Liu, Yansheng Liu, Zhihua Liu, Teck Yew Low, Ben Lu, Matthias Mann, Anming Meng, Robert L Moritz, Edouard Nice, Guang Ning, Gilbert S Omenn, Christopher M Overall, Giuseppe Palmisano, Yaojin Peng, Charles Pineau, Terence Chuen Wai Poon, Anthony W Purcell, Jie Qiao, Roger R Reddel, Phillip J Robinson, Paola Roncada, Chris Sander, Jiahao Sha, Erwei Song, Sanjeeva Srivastava, Aihua Sun, Siu Kwan Sze, Chao Tang, Liujun Tang, Ruijun Tian, Juan Antonio Vizcaíno, Chanjuan Wang, Chen Wang, Xiaowen Wang, Xinxing Wang, Yan Wang, Tobias Weiss, Mathias Wilhelm, Robert Winkler, Bernd Wollscheid, Limsoon Wong, Linhai Xie, Wei Xie, Tao Xu, Tianhao Xu, Liying Yan, Jing Yang, Xiao Yang, John Yates, Tao Yun, Qiwei Zhai, Bing Zhang, Hui Zhang, Lihua Zhang, Lingqiang Zhang, Pingwen Zhang, Yukui Zhang, Yu Zi Zheng, Qing Zhong, Yunping Zhu & π-HuB Consortium.

Nature. 2024 Dec;636(8042):322-331. doi: 10.1038/s41586-024-08280-5. Epub 2024 Dec 11. Erratum in: Nature. 2024 Dec 23. doi: 10.1038/s41586-024-08555-x. PMID: 39663494.

153

Association of the EAT-Lancet diet, serial measures of serum proteome and gut microbiome, and cardiometabolic health: a prospective study of Chinese middle-aged and elderly adults

Kui Deng#, Luqi Shen#, Zhangzhi Xue#, Bang-yan Li#, Jun Tang, Hui Zhao, Fengzhe Xu, Zelei Miao, Xue Cai, Wei Hu, Yuanqing Fu, Zengliang Jiang, Xinxiu Liang, Congmei Xiao, Menglei Shuai, Wanglong Gou, Liang Yue, Yuting Xie, Ting-yu Sun, Tiannan Guo, Yu-ming Chen*, Ju-Sheng Zheng*.

The American Journal of Clinical Nutrition. In press. https://doi.org/10.1016/j.ajcnut.2024.10.011

152

Integral-Omics: Serial Extraction and Profiling of Metabolome, Lipidome, Genome, Transcriptome, Whole Proteome and Phosphoproteome Using Biopsy Tissue

Wei Li, Jing Sun, Rui Sun, Yujuan Wei, Junke Zheng*, Yi Zhu*, Tiannan Guo*.

Analytical Chemistry. 2025 Jan 7. doi: 10.1021/acs.analchem.4c04421. Epub ahead of print. PMID: 39772508.

151

Mitochondrial Proteome Defined Molecular Pathological Characteristics of Oncocytic Thyroid Tumors

Lu Li, Likun Zhang, Wenhao Jiang, Zhiqiang Gui, Zhihong Wang, Hao Zhang, Yi He, Yi Zhu, Tiannan Guo, Haixia Guan*, Zhiyan Liu*, Yaoting Sun*, Jianqing Gao*.

Endocr Pathol. 2024 Nov 4. doi: 10.1007/s12022-024-09834-z. Epub ahead of print. PMID: 39495444.

150

Proteomic profiling of gliomas unveils immune and metabolism-driven subtypes with implications for anti-nucleotide metabolism therapy

Jinsen Zhang#, Rui Sun#, Yingying Lyu#, Chaxian Liu#, Ying Liu, Yuan Feng, Minjie Fu, Peter Jih Cheng Wong, Zunguo Du, Tianming Qiu, Yi Zhang, Dongxiao Zhuang, Zhiyong Qin, Yu Yao, Wei Zhu, Tiannan Guo, Wei Hua*, Hui Yang*, Ying Mao*.

Nature Communications. 2024 Nov 19;15(1):10005. doi: 10.1038/s41467-024-54352-5. PMID: 39562821.

149

AI-empowered perturbation proteomics for complex biological systems

Liujia Qian, Rui Sun, Ruedi Aebersold, Peter Bühlmann, Chris Sander*, Tiannan Guo*.

Cell Genomics. 2024, 100691. DOI: https://doi.org/10.1016/j.xgen.2024.100691.

148

The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.

Gilbert S. Omenn*, Sandra Orchard, Lydie Lane, Cecilia Lindskog, Charles Pineau, Christopher M. Overall, Bogdan Budnik, Jonathan M. Mudge, Nicolle H. Packer, Susan T. Weintraub, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Uwe Völker, Gong Zhang, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch*.

Journal of Proteome Research. 2024 Dec 6;23(12):5296-5311. doi: 10.1021/acs.jproteome.4c00776. Epub 2024 Nov 8. PMID: 39514846.

147

Spatial proteomics of single cells and organelles on tissue slides using filter-aided expansion proteomics

Zhen Dong#, Wenhao Jiang#, Chunlong Wu, Ting Chen, Jiayi Chen, Xuan Ding, Shu Zheng, Kiryl D Piatkevich*, Yi Zhu*, Tiannan Guo*.

Nature Communications. 2024 Oct 30;15(1):9378. doi: 10.1038/s41467-024-53683-7. PMID: 39477916.

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metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis

Yingying Sun#, Ziyuan Xing#, Shuang Liang#, Zelei Miao, Lai-Bao Zhuo, Wenhao Jiang, Hui Zhao, Huanhuan Gao, Yuting Xie, Yan Zhou, Liang Yue, Xue Cai, Yu-Ming Chen*, Ju-Sheng Zheng*, Tiannan Guo*.

Mol Cell Proteomics. 2024 Sep 13:100840. doi: 10.1016/j.mcpro.2024.100840. Epub ahead of print. PMID: 39278598.

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Individualizing the lifesaving journey for calciphylaxis: addressing rapidly progressive attacks with multidimensional and AI research for regenerative medicine

Ningning Wang*, Andrea Angioi, Nicolas Hanset, Xiaoxue Ye, Shijiu Lu, Yi Zhu.

Ren Fail. 2024 Dec;46(2):2392846. doi: 10.1080/0886022X.2024.2392846. Epub 2024 Sep 5. PMID: 39234636.

144

Proteomic landscape profiling of primary prostate cancer reveals a 16-protein panel for prognosis prediction

Rui Sun#, Jun A#, Haolan Yu#, Yan Wang#, Miaoxia He#, Lingling Tan, Honghan Cheng, Jili Zhang, Yingrui Wang, Xiaochen Sun, Mengge Lyu, Min Qu, Lingling Huang, Zijian Li, Wenhui Zhang, Kunpeng Ma, Zhenyang Dong, Weigang Ge, Yun Zhang, Xuan Ding, Bo Yang, Jianguo Hou, Chuanliang Xu, Linhui Wang, Yi Zhu, Tiannan Guo*, Xu Gao*, Chenghua Yang*.

Cell Reports Medicine. 2024 Aug 20; 5(8):101679. Doi: https://doi.org/10.1016/j.xcrm.2024.101679. PMID: 39168102.

143

Prediction of overall survival in stage II and III colon cancer through machine learning of rapidly-acquired proteomics

Kailun Xu#, Xiaoyang Yin#, Hui Chen#, Yuhui Huang, Xi Zheng, Biting Zhou, Xue Cai, Huanhuan Gao, Miaomiao Tian, Sijun Hu, Shu Zheng, Changzheng Yuan*, Yongzhan Nie*, Tiannan Guo* & Yingkuan Shao*

Cell Discovery. 2024 Aug 13;10(1):85. doi: 10.1038/s41421-024-00707-7. PMID: 39134531.

142

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.