主要论文（*：通讯作者）
- Zhang P, Zhang Q, Li S*. Advancing Cancer Prevention through AI-based Integration of Traditional and Western Medicine. Cancer Discovery 2024
- Zhang Q, Yang M, Zhang P, Wu B, Wei X, Li S*. Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods. Cancer Biology & Medicine 2024;21(4):312-330
- P Zhang, D Zhang, W Zhou, L Wang, B Wang, T Zhang, S Li*. Network pharmacology: towards the artificial intelligence-based precision traditional Chinese medicine. Briefings in Bioinformatics 2023;25(1):bbad518
- Zhang P, Wang B, Li S*. Network-based cancer precision prevention with artificial intelligence and multi-omics. Science Bulletin 2023;68(12):1219-1222
- S Zhang, K Yang, Z Liu, X Lai, Z Yang, J Zeng, S Li*. DrugAI: a multi-view deep learning model for predicting drug–target activating/inhibiting mechanisms. Briefings in Bioinformatics 2023;24(1): bbac526
- P Zhang, S Li*. Human cross-tissue cell atlases: unprecedented resources towards systematic understanding of physiology and diseases. Signal Transduction and Targeted Therapy 2022;7(1):352
- Hou S, Zhang P, Yang K, Wang L, Ma C, Li Y, Li S*. Decoding multilevel relationships with the human tissue-cell-molecule network. Briefings in Bioinformatics 2022; bbac170
- Zhang Y, Chen L, Li S*. CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network with Single-Cell Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022;19(2):819-829.
- Li S*. Network Pharmacology Evaluation Method Guidance - Draft. World Journal of Traditional Chinese Medicine 2021;7(1):146-154.
- Zhou W, Yang K, Zeng J, Lai X, Wang X, Ji C, Li Y, Zhang P, Li S*. FordNet: recommending traditional Chinese medicine formula via deep neural network integrating phenotype and molecule. Pharmacological Research 2021:105752 (Be- Zhou W, Lai X, Wang X, Yao X, Wang W, Li S*. Network pharmacology to explore the anti-inflammatory mechanism of Xuebijing in the treatment of sepsis. Phytomedicine 2021;85:153543
- Sun J, Wang X, Xu R, Mao D, Shen D, Wang X, Qiu Y, Han Y, Lu X, Li Y, Che Q, Zheng L, Peng P, Kang X, Zhu R, Jia Y, Wang Y, Liu L, Chang Z, Ji J, Wang Z, Liu Q, Li S*, Sun F*, Ni J*. HP1c regulates development and gut homeostasis by suppressing Notch signaling through Su(H). EMBO Reports 2021;22(4):e51298
- Yuan Z, Zhou Q, Cai L, Pan L, Sun W, Qumu S, Yu S, Feng J, Zhao H, Zheng Y, Shi M, Li S, Chen Y*, Zhang XR*, Zhang MQ*. SEAM: a Spatial single nuclEar metAboloMics method for dissecting tissue microenvironment. Nature Methods 2021; 18(10):1223-1232
- Guo J*, Zhang P, Zhou L, You L, Liu Q, Zhang Z, Sun B, Liang Z, Lu J, Yuan D, Tan A, Sun J, Liao Q, Dai M, Xiao G, Li S*, Zhang T*. Prognostic and predictive value of a five-molecule panel in resected pancreatic ductal adenocarcinoma: A multicenter study. EBioMedicine 2020; 55: 102767
- Ding Q, Hou S, Zu S, Zhang Y, Li S*. VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models. Bioinformatics 2020;36(11):3610-3612.
- Zhang P, Yang M, Zhang Y, Xiao S, Tai X, Tan A, Du S, Li S*. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Reports 2019; 27,1934-1947（F1000 "Exceptional" paper）
- Guo Y, Bao C, Ma D, Cao Y, Li Y, Xie Z*, Li S*. Network-based combinatorial CRISPR-Cas9 screens identify synergistic modules in human cells. ACS Synthetic Biology 2019;8:482-490 (Cover)
- Cui J, Cui H, Yang M, Du S, Li J, Li Y, Liu L, Zhang X*, Li S*. Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade. Protein & Cell 2019;10: 496-509
- Tan A, Huang H, Zhang P, Li S*. Network-based cancer precision medicine: a new emerging paradigm. Cancer Letters 2019; 458;39-45.
- Liao S, Han L, Zheng X, Wang X, Zhang P, Wu J, Liu R, Fu Y, Sun J, Kang X, Wang S, Liu K, Fan TP*, Li S*, Zheng X*. Tanshinol borneol ester, a novel synthetic small molecule angiogenesis stimulator inspired by botanical formulations for angina pectoris. British Journal of Pharmacology 2019;176:3143–3160.
- Zheng J, Wu M, Wang H, Li SS, Wang X, Li Y, Wang D, Li S*. Network pharmacology to unveil the biological basis of health strengthening herb medicine in cancer treatment. Cancers 2018;10(11):461:1-23
- Guo Y, Nie Q, MacLean A, Li Y, Lei J*, Li S*. Multiscale modeling of inflammation-induced tumorigenesis reveals competing oncogenic and onco-protective roles for inflammation. Cancer Research 2017;77(22):6429-6441
- Qi Q, Li R, Li H, Cao Y, Bai M, Fan X, Wang S, Zhang B*, Li S*. Identification of the anti-tumor activity and mechanisms of nuciferine through a network pharmacology approach. Acta Pharmacologica Sinica 2016;37:963-972
- Li S*. Mapping ancient remedies: applying a network approach to traditional Chinese medicine. Science 2015;350(6262 Supplement):S72-S74 (传统医学增刊)
- Zu S, Chen T, Li S*. Global optimization-based inference of chemogenomic features from drug-target interactions. Bioinformatics 2015;31(15):2523-2529
- Liang X, Li H, Li S*. A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-wei-di-huang Pill as a case study. Molecular BioSystems 2014,10(5):1014-1022 (Cover)
- Li S*, Zhang B. Traditional Chinese medicine network pharmacology: theory, methodology and application. Chinese Journal of Natural Medicines 2013;11(2):110-120
- Zhao S, Li S*. A co-module approach for elucidating drug-disease associations and revealing their molecular basis. Bioinformatics 2012;28(7):955-961
- Chen Y, Gu J, Li D, Li S*. Time-course network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in vascular endothelial cells. Bioinformatics 2012;28(1):1-4
- Li S*, Zhang B, Zhang NB. Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Systems Biology 2011;5(S1):S10 (Faculty of 1000 "Must Read" paper)
- 李梢. 网络靶标：中药方剂网络药理学研究的一个切入点.中国中药杂志 2011;36:2017-2020（领跑者5000论文）
- Li S*, Zhang B, Jiang D, Wei YY, Zhang NB. Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. BMC Bioinformatics 2010;11(S11):S6
- Zhao S, Li S*. Network-based relating pharmacological and genomic spaces for drug target identification. PLoS ONE 2010;5(7):e11764 （Highlighted by Nature China）
- Ma T, Tan C, Zhang H, Wang M, Ding W, Li S*. Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network. Molecular BioSystems 2010;6:613-619
- Wu X, Jiang R, Zhang MQ, Li S*. Network-based global inference of human disease genes. Molecular Systems Biology 2008;4:189, pages:1-11 （Highlighted by 2009 American Medical Informatics Association Summit on Translational Bioinformatics, and Highlight Track in ISMB 2009）
- Zhang J, Ma T, Li YD, Li S*. dbNEI2.0: building multilayer network for drug-NEI-disease. Bioinformatics 2008;24:2409-2411
- Li S*, Zhang Z, Wu L, Zhang X, Li Y, Wang Y. Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Systems Biology 2007;1(1):51-60
- 李梢. 基于生物网络调控的方剂研究模式与实践. 中西医结合学报 2007;5(5):1-5
- Li S*, Wu LJ, Zhang ZQ. Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 2006;22:2143-2150
- Li S*, Lu A, Li B, Wang Y. Circadian rhythms on hypothalamic-pituitary-adrenal axis hormones and cytokines of collagen induced arthritis in rats. Journal of Autoimmunity 2004;22(4):277-285
- 李梢,王永炎,季梁,李衍达. 复杂系统意义下的中医药学及其案例研究. 系统仿真学报 2002;14(11):1429-1432
学术专著：
- 李梢（主编）.网络药理学.清华大学出版社 2022
Li S (editor). Network Pharmacology. Springer Press, Tsinghua University Press 2021
