· Network Pharmacology and Bioinformatics, with applications in inflammation, cancer, and traditional Chinese medicine

· Sep. 1998 ~ Jul. 2001 Beijing University of Traditional Chinese Medicine, M.D.

· Sep. 1995 ~ Jul. 1998 Wannan College of Medicine, M.S.

· Sep. 1990 ~ Jul. 1995 Beijing University of Traditional Chinese Medicine, B.S.

· Dec. 2020 ~ Director, Institute for TCM-X, Beijing, Tsinghua University

· 2013 ~ Adjunct professor, Department of Pharmacology & Pharmaceutical Sciences, School of Medicine, Tsinghua University

· 2011 ~ Adjunct professor, School of Life Sciences, Tsinghua University

· Dec. 2009 ~ Professor, Tsinghua University

· Oct. 2008 ~ PhD Candidate Supervisor, Tsinghua University

· Sep. 2017 ~ Director, TCM-X Center, TNList (Tsinghua National Lab for Information Science & Technology)

· Feb. 2006 ~ Deputy Director, Bioinformatics Division, TNList (Tsinghua National Lab for Information Science & Technology)

· Dec. 2004 ~ Nov. 2009: Associate Professor, MOE Key Lab of Bioinformatics, Department of Automation, Tsinghua University

· Sep. 2003 ~ Nov. 2004: Assistant Professor, MOE Key Lab of Bioinformatics, Department of Automation, Tsinghua University

· Sep. 2001 ~ Jul. 2003: Postdoctoral Research Fellow, MOE Key Lab of Bioinformatics, Department of Automation, Tsinghua University

· 2024 ~ Member of European Academy of Sciences and Arts

· 2023 ~ Leading Expert in High-Level Key Disciplines of the National Administration of Traditional Chinese Medicine

· 2022 ~ Fellow of the Royal Society of Chemistry

· 2022 ~ Fellow of the Royal Society of Biology

· 2022 ~ Chairman, Specialty Committee of Biomedical Big Data, Chinese Society of Bioengineering

· 2015 ~ Chairman, Specialty Committee of Network Pharmacology, World Federation of Chinese Medicine Societies

· 2014 ~ Vice chairman, Specialty Committee of Network Pharmacology, Chinese Pharmacological Society

· 2018 ~ Vice chairman, Specialty Committee of Biomarkers, Chinese Research Hospital Association

· 2014 ~ Vice chairman, Specialty Committee of Dose-response Relationship Study of Chinese Prescription, 

World Federation of Chinese Medicine Societies

· 2023 ~ Editorial Board Member, Pharmacological Research

· 2017 ~ Member of the standing committee, Specialty Committee of Integrative Oncology, Chinese Anti-cancer Association

· 2017 ~ Editorial Board Member, Chinese Medicine

· 2014 ~ Editorial Board Member, Chinese Journal of Integrative Medicine

· 2013 ~ Editorial Board Member, Scientific Reports

· 2012 ~ Editorial Board Member, Evidence-Based Complementary and Alternative Medicine

· 2012 ~ Editorial Board Member, Journal of Traditional Chinese Medicine

· 2012 ~ Editorial Board Member, Chinese Journal of Natural Medicines

· 2014 ~ Editorial Board Member, Journal of Chinese Pharmaceutical Sciences

· 2014 ~ Editorial Board Member, Chinese Herbal Medicines

· 2011 ~ Editorial Board Member, China Journal of Chinese Materia Medica

· 2018-2019: Lead guest editor: Research Topic on “Network Pharmacology and Traditional Medicine”, Frontiers in Pharmacology

· 2012-2013: Lead guest editor: Special Issue on "Network Pharmacology in Traditional Chinese Medicine", 

Evidence-Based Complementary and Alternative Medicine

· 2012, 2014: Guest editor: Special Issue on "Evidence-Based ZHENG, a Traditional Chinese Medicine Syndrome", 

Evidence-Based Complementary and Alternative Medicine

· Jun. 2017 Chair: The 2nd International Forum on TCM Network Pharmacology, Specialty Committee of Network Pharmacology, 

World Federation of Chinese Medicine Societies

· Nov. 2015 Chair: The 1st International Forum on TCM Network Pharmacology, Specialty Committee of Network Pharmacology, 

World Federation of Chinese Medicine Societies

· Oct. 2013 Lead Scientist and Chair: The 86th Academic salon on Network Pharmacology, China Association for Science and Technology

· Dec. 2010 Co-Chair, The 228th Youth Scientist Forum ofChinaAssociation for Science and Technology

· Dec. 2009 Co-Chair, The 209th Youth Scientist Forum ofChinaAssociation for Science and Technology

· Nov. 2004 Co-Chair, The 1st International Symposium on Bioinformatics and Traditional Chinese Medicine

· Outstanding Award, China Pharmaceutical Development Award (2023)

· China Excellence Patent Award (2023)

· International Award for Contribution to Chinese Medicine (the 1st Prize, 2020)

· World's Top 2% Scientists (2019/2020/2021/2022, Stanford University)

· Highly Cited Chinese Researchers (2020/2021/2022, Elsevier)

· Li Shizhen Pharmaceutical Innovation Award. China Association of Chinese Medicine (2019)

· Leading talents in science and technological innovation, National "Ten-Thousand talents" Program (2019)

· Young and middle-aged leading talents in science and technology innovation, Ministry of Science and Technology (2018)

· National Science Fund for Distinguished Young Scholars, National Natural Science Foundation of China (2012)

· National Education Award, Ministry of Education (the 2nd Class) (2009)

· National Science & Technology Award,China(the 2nd Class) (2004)

· National Excellent Doctoral Dissertation, China (2003)

· Grand Challenges 2015—Young Scientists (Ministry of Science & Technology, Bill & Melinda Gates Foundation, 2015)

· Top 1% highly cited Chinese authors in Royal Society of Chemistry journals in 2015 (2016)

· Mao Yi-Sheng Science and Technology Award for Beijing Youth (2009)

· Beijing Teaching Achievement Award (the 1st Class) (2008)

· New Century Excellent Talents in University, MOE (2007)

· Excellent Postdoc Fellow of Tsinghua University (2004)

· Beijing Science & Technology Award (2002)

· Anhui Province Science & Technology Award (2000)

Traditional Chinese Medicine (TCM) is characterized by its holistic thinking in treating a patient as an imbalanced system, and the use of various herbal formulae in restoring the balance of human body. The holistic philosophy and patient-tailored treatment of TCM shares a lot with the key idea of current systems biology and precision medicine. However, it is very challenging to unveil the biological basis of TCM by current reductionist "one target, one drug" approach due to the complexity of both the chemical compositions of herb formula and the biological systems of patients. In the big data era, we devoted to create a novel “network target” approach to offer bright prospects in understanding TCM from a systems perspective, narrow the gap between Eastern and Western medical practices, and help achieve the TCM-based precision medicine. The following is the Conception, methods and application of our approach.

Conception. In 2007, Jan., we for the first time constructed the bio-molecular network for Cold/Hot Syndromes, a pair of thousand-year-old concepts in TCM, and revealed the network regulation mechanism of corresponding Hot/Cold herb formulae ^{[Li et al. IET Systems Biology 2007.1]}. We also proposed a biological network-based TCM research paradigm in 2007, Sep. ^{[Li. J Chin Integr Med 2007.9]}. (Afterwards, Hopkins introduced the term “network pharmacology” in 2007, Oct. ^{[Hopkins. Nature Biotechnology 2007.10]} and considered it as the next paradigm in drug discovery ^{[Hopkins. Nature chemical biology 2008]}). We further proposed a new concept of “network target” and established a new approach based on network target analysis, which emphasizes that treating the biological networks underlying complex diseases or TCM Syndrome as a therapeutic target to understand drug (herb) actions.

Methods. With over a decade efforts, we created a set of computational models and algorithms to determine the network target underlying disease and herbal formula. These algorithms as able to predict the network interaction among herbs, compounds, biomolecules, phenotypes, and diseases and/or TCM syndromes, and to screen synergistic multi-compounds from herbal formulae in a high-throughput way.

Application. The effectiveness of the network target approach has been demonstrated by the follow-up clinical and experimental investigations. For examples, we revealed and validated the metabolism-immune imbalanced molecular network and identified network biomarkers for Cold / Hot syndrome during the occurrence and development of cancer, especially in patients with gastritis and precancerous lesions. Furthermore, with the Cold / Hot network as “network target”, we discovered the active compounds, network regulation mechanism, and modern indications from some classic herbal formulae in regulating related complex diseases. Some of the results made the headline in The Wall Street Journal ^[link] and selected as one of "The world top 10 news of TCM, 2014" ^[link]. Recently, we also validated the effectiveness of our methods in decipher the networks underlying different diseases, e.g. CIPHER in predicting high risk genes or modules for hepatocellular carcinoma in collaboration with Prof. Wang HY’s lab ^{[Su et al. Hepatology 2015; Lin et al. Gastroenterology 2017]}.

Google Scholar Citations

2023

- Peng Zhang, Boyang Wang, Shao Li*. Network-based cancer precision prevention with artificial intelligence and multi-omics. Science bulletin 2023 Jun 30;68(12):1219-1222

- Boyang Wang, Wuai Zhou, Huan Zhang, Weihua Wang, Bo Zhang*, Shao Li*. Exploring the effect of Weifuchun capsule on the Toll-like receptor pathway mediated HES6 and immune regulation against chronic atrophic gastritis. Journal of Ethnopharmacology 2023; 303:115930

- Shao Li, Jianxin Chen, Yuanjia Hu, Min Ye. Editorial: Network pharmacology and AI. Journal of Ethnopharmacology. 2023 May;307:116260.

- Changzheng Ma, Peng Zhang, Shiyu Du, Yan Li, Shao Li*. "Construction of Tongue Image-Based Machine Learning Model for Screening Patients with Gastric Precancerous Lesions" Journal of Personalized Medicine 2023; 13, no. 2: 271.

- Siqin Zhang, Kuo Yang, Zhenhong Liu, Xinxing Lai, Zhen Yang, Jianyang Zeng, Shao Li*. DrugAI: a multi-view deep learning model for predicting drug–target activating/inhibiting mechanisms, Briefings in Bioinformatics, Volume 24, Issue 1, January 2023, bbac526

2022

· Peng Zhang, Shao Li*. Human cross-tissue cell atlases: unprecedented resources towards systematic understanding of physiology and diseases. Signal Transduction and Targeted Therapy 2022; 7: 352

· S Hou, P Zhang, K Yang, L Wang, C Ma, Y Li, S Li*. Decoding multilevel relationships with the human tissue-cell-molecule network. Briefings in Bioinformatics 2022;23(5):bbac170.

· Siqin Zhang, Kuo Yang, Zhenhong Liu, Xinxing Lai, Zhen Yang, Shao Li*. DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms. Briefings in Bioinformatics 2022; bbac526

· 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.

· W Zhou, H Zhang, X Wang, J Kang, W Guo, L Zhou, H Liu, M Wang, R Jia, X Du, W Wang, B Zhang*, S Li*. Network pharmacology to unveil the mechanism of Moluodan in the treatment of chronic atrophic gastritis. Phytomedicine. 2022;95:153837.

· J Cui, S Hou, B Liu, M Yang, L Wei, S Du, S Li*. Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients. BMC Medical Genomics 2022;15(1):60

2021

· Shao Li* et al. Network Pharmacology Evaluation Method Guidance-Draft. World Journal of Traditional Chinese Medicine 2021;7(1):146-154 [pdf]

· 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 (Best Research Articles Published in the Journal in 2020/2021)

· Jin Sun, Xia Wang, Rong-Gang Xu, Decai Mao, Da Shen, Xin Wang, Yuhao Qiu, Yuting Han, Xinyi Lu, Yutong Li, Qinyun Che, Li Zheng, Ping Peng, Xuan Kang, Ruibao Zhu, Yu Jia, Yinyin Wang, Lu-Ping Liu, Zhijie Chang, Jun-Yuan Ji, Zhao Wang, Qingfei Liu, Shao Li*, Fang-Lin Sun*, Jian-Quan Ni*. 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

· Wuai Zhou, Xinxing Lai, Xin Wang, Xiaoqing Yao, Weihua Wang, Shao Li*. Network pharmacology to explore the anti-inflammatory mechanism of Xuebijing in the treatment of sepsis. Phytomedicine 2021;85:153543

· Siqin Zhang, Xinxing Lai, Xin Wang, Zhenzhong Wang, Liang Cao, Xinzhuang Zhang, Wei Xiao*, Shao Li*. Deciphering the pharmacological mechanisms of Guizhi-Fuling capsule on primary dysmenorrhea through network pharmacology. Frontiers in Pharmacology 2021: 613104 [pdf]

· Pang H, Jiang Y, Li J, Wang Y, Nie M, Xiao N, Wang S, Song Z, Ji F, Chang Y, Zheng Y, Yao K, Yao L, Li S, Li P, Song L*, Lan X*, Xu Z*, Hu Z*. Aberrant NAD + metabolism underlies Zika virus-induced microcephaly. Nature Metabolism 2021;3(8):1109-1124

· Xin Wang, Ziyi Wang, Jiahui Zheng, Shao Li*. TCM network pharmacology: A new trend towards combining computational, experimental and clinical approaches. Chinese Journal of Natural Medicines 2021;19:1-11 [pdf]

· Nan Xiao, Meng Nie, Huanhuan Pang, Bohong Wang, Jieli Hu, Xiangjun Meng, Ke Li, Xiaorong Ran, Quanxin Long, Haijun Deng, Na Chen, Shao Li, Ni Tang*, Ailong Huang*, Zeping Hu*. Host metabolite-cytokine correlation landscape in SARS-CoV-2 infection. Nature Communications 2021;12: 1618 [pdf]

2020

· Guo J#*, Zhang P#, Zhou Li#, 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 (cover) [link]

· 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;36:3610-3612 [link]

· 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 (Regular Paper) (Accepted) [link]

· Wang X, Wu M, Lai X, Zheng J, Hu M, Li Y, Li S*. Network Pharmacology to Uncover the Biological Basis of Spleen-Qi-Deficiency Syndrome and Herbal Treatment. Oxidative Medicine and Cellular Longevity 2020:2974268 [link]

· Lai X, Wang X, Hu Y, Su S, Li W, Li S*. Network Pharmacology and Traditional Medicine (Editorial). Frontiers in Pharmacology [link]

2019

· Zhang P, Yang M, Zhang Y, Xiao S, Lai 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 [link] (F1000 Recommendation: "Exceptional"；Reported by GenomeWeb)

· 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 [link]

· 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) [link]

· Tan A, Huang H, Zhang P, Li S*. Network-based cancer precision medicine: a new emerging paradigm. Cancer Letters 2019;458;39-45 [link]

· 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 (DBZ), a novel synthetic small molecule angiogenesis stimulator inspired by botanical formulations for angina pectoris. British Journal of Pharmacology 2019;176:3143–3160 [link]

2018

· 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 [pdf]

· Ting-Ting Zhang, Rui Xue, Xin Wang, Shi-Wen Zhao, Lei An, Yun-Feng Li, You-Zhi Zhang*, Shao Li*. Network-Based Drug Repositioning: a Novel Strategy for Discovering Potential Antidepressants and Their Mode of Action. European Neuropsychopharmacology 2018;28:1137-1150 [link]

· Zuo J, Wang X, Liu Y, Ye J, Liu Q, Li Y*, Li S*. Integrating network pharmacology and metabolomics study on anti-rheumatic mechanisms and antagonistic effects against methotrexate-induced toxicity of Qing-Luo-Yin. Frontiers in Pharmacology 2018; 9:1472; 17pages [link]

· Zhang B, Wang X, Li Y, Wu M, Wang S, Li S*. Matrine is identified as a novel macropinocytosis inducer by a network target approach. Frontiers in Pharmacology 2018; 9;10:1-11 [link]

· Qiao H, Wang F, Xu R, Sun J, Zhu R, Mao D, Ren X, Wang X, Jia Y, Peng P, Shen D, Liu L, Chang Z, Wang G, Li S, Ji J, Liu Q, Ni J*. An efficient and multiple target transgenic RNAi technique with low toxicity in Drosophila. Nature Communications 2018; 9(1):4160 [link]

2017

· Guo Y, Nie Q, MacLean AL, Li Y, Lei J*, Li S*. Multiscale modeling of inflammation-induced tumorigenesis reveals competing oncogenic and oncoprotective roles for inflammation. Cancer Research 2017;77(22):6429–6441 [link] (Report)

· D Xi*, T Bao, Qi Chen, S Chen, Y Cheng, J Cullen, D Frank, J Friedberg, I Kronish, J Lee, M Levine, P Li, S Li, W Lu, J Mao, S Keefe, L Rubinstein, M Shah, L Standish, C Paller, E Chu. State of the Science: Cancer Complementary and Alternative Medicine Therapeutics Research—NCI Strategic Workshop Highlights of Discussion Report. JNCI Monographs 2017;52:lgx003 [link]

· Lin X, Hu L, Gu J, Wang R, Li L, Tang J, Zhang B, Yan X, Zhu Y, Hu C, Zhou W, Li S, Liu J, Gonzalez F, Wu M, Wang H*, Chen L*. Choline Kinase Alpha mediates interactions between the Epidermal Growth Factor Receptor and mTORC2 in hepatocellular carcinoma cells to promote drug resistance and xenograft tumor progression. Gastroenterology 2017;152:1187–1202 [link]

2016

· 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 [pdf]

· Shao Li*. Exploring traditional Chinese medicine by a novel therapeutic concept of network target. Chinese Journal of Integrative Medicine 2016;22(9):647-652 (Feature Article) [pdf]

2015

· Shao Li*. Mapping ancient remedies: applying a network approach to traditional Chinese medicine. Science 2015;350(6262 Suppl):S72-S74 [pdf] [link] (Report)

· Songpeng Zu, Ting Chen, Shao Li*. Global optimization-based inference of chemogenomic features from drug-target interactions. Bioinformatics 2015;31(15):2523-9 [pdf]

· Wu M, Lu P, Shi L*, Li S*. Traditional Chinese patent medicines for cancer treatment in China: a nationwide medical insurance data analysis. Oncotarget 2015;6(35):38283-38295 [pdf]

· Zhang B, Lu C, Bai M, He X, Tan Y, Bian Y, Xiao C, Zhang G, Lu A*, Li S*. Tetramethylpyrazine identified by a network pharmacology approach ameliorates methotrexate-induced oxidative organ injury. Journal of Ethnopharmacology 2015;175:638-647 [pdf]

· Su B, Luo T, Zhu J, Fu J, Zhao X, Chen L, Zhang H, Ren Y, Yu L, Yang X, Wu M, Feng G, Li S, Chen Y*, Wang H*. Interleukin-1β/IRAK-1 inflammatory signaling contributes to persistent Gankyrin activation during hepatocarcinogenesis. Hepatology 2015;61(2):585–597 [Abstract]

· Li Y, Li R, Ouyang Z, Li S*. Herb network analysis for a famous TCM doctor’s prescriptions on treatment of rheumatoid arthritis. Evidence-Based Complementary and Alternative Medicine 2015: 451319 [pdf]

2014

· Xujun Liang, Huiying Li, Shao Li*. A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-wei-di-huang Pill as a case study. Molecular BioSystems 2014,10:1014-1022 [pdf] (Cover article) (Selected as “HOT article”)

· Li H, Zhao L, Zhang B, Jiang Y, Wang X, Guo Y, Liu H, Li S*, Tong X*. A network pharmacology approach to determine active compounds and action mechanisms of Ge-Gen-Qin-Lian decoction for treatment of Type 2 diabetes. Evidence-based Complementary and Alternative Medicine 2014: 495840 [pdf]

· Wang L, Wang Y, Hu Q, Li S*. Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks. CPT: Pharmacometrics and Systems Pharmacology 2014;3:e146 [pdf]

· Liang X, Li H, Tian G, Li S*. Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer. Scientific Reports 2014;4,4985 [pdf]

· Shao Li*, Taiping Fan, Wei Jia, Aiping Lu, Weidong Zhang. Network pharmacology in traditional Chinese medicine. Evidence-based Complementary and Alternative Medicine 2014: 138460 (Editorial) [pdf]

2013

· Li S*, Zhang B (2013) Traditional Chinese medicine network pharmacology: theory, methodology and application. Chinese Journal of Natural Medicines 11(2):110-120 [pdf] (Most Cited Chinese Journal of Natural Medicines Article)

· Li R, Ma T, Gu J, Liang X, Li S* (2013) Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients. Scientific Reports 3:1543 [pdf] (Highlight Research in The 3rd Annual Translational Bioinformatics Conference)

· Bo Zhang, Xu Wang, Shao Li* (2013) An integrative platform of TCM network pharmacology and its application on an herbal formula, Qing-Luo-Yin. Evidence-based Complementary and Alternative Medicine 456747 [pdf]

· Zhang B, Liu L, Zhao S, Wang X, Liu L, Li S* (2013) Vitexicarpin acts as a novel angiogenesis inhibitor and its target network. Evidence-based Complementary and Alternative Medicine 278405 [pdf]

· Wang T, Gu J, Yuan J, Tao R, Li Y, Li S* (2013) Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 9(7):1822-1828 [Link]

2012

· Jiang B, Liang X, Chen Y, Ma T, Liu L, Li J, Jiang R, Chen T, Zhang X*, Li S* (2012) Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Scientific Reports 2:936 [pdf]

· Shiwen Zhao, Shao Li* (2012) A co-module approach for elucidating drug-disease associations and revealing their molecular basis. Bioinformatics 28(7):955-961 [Full text]

· Yang Chen, Jin Gu, Dan Li, Shao Li* (2012) Time-course network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in vascular endothelial cells. Bioinformatics 28(1):1-4 [Full text]

· Jin Gu*, Shao Li*. (2012) Towards integrative annotation of the cell-type specific gene functional and signaling map in vascular endothelial cells. Molecular BioSystems 8:2041-2049 [Link]

· Kanawong R, Ajayi T, Ma T, Xu D, Li S*, Duan Y*. (2012) Automated tongue feature extraction for ZHENG classification in traditional Chinese medicine. Evidence-based Complementary and Alternative Medicine 912852:1-14 [pdf] (Reported by ScienceDaily)

2011

· Shao Li*, Bo Zhang, Ningbo Zhang (2011) Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Systems Biology 5(S1):S10 [pdf] (Recommended by Faculty of 1000)

· Shao Li* (2011) Network target: a starting point for traditional Chinese medicine network pharmacology. China Journal of Chinese Materia Medica 36:2017-2020 (In Chinese) [pdf]

· Xin Yao, Han Hao, Yanda Li, Shao Li* (2011) Modularity-based credible prediction of disease genes and detection of disease subtypes on the phenotype-gene heterogeneous network. BMC Systems Biology 5:79 [pdf]

· Le Lu, Yanda Li, Shao Li* (2011) Computational identification of potential microRNA network biomarkers for the progression stages of gastric cancer. International Journal of Data Mining and Bioinformatics 5:519-531 [pdf]

2010

· Shiwen Zhao, Shao Li* (2010) Network-based relating pharmacological and genomic spaces for drug target identification. PLoS ONE 5(7): e11764 [pdf] (Highlighted by Nature China)

· Shao Li*, Bo Zhang, Duo Jiang, Yingying Wei, Ningbo Zhang (2010) Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. BMC Bioinformatics 11(S11):S6 [pdf]

· Tao Ma, Conge Tan, Hui Zhang, Miqu Wang, Weijun Ding, Shao Li* (2010) Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network. Molecular BioSystems 6:613-619 [Link]

· Jin Gu, Yang Chen, Shao Li*, Yanda Li* (2010) Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Systems Biology 4:47 [pdf]

· Han Yan, Bo Zhang, Shao Li*, Qianchuan Zhao* (2010) A formal model for analyzing drug combination effects and its application in TNF-alpha-induced NFkappaB pathway. BMC Systems Biology 4:50 [pdf]

· Yezhou Huang, Shao Li* (2010) Detection of characteristic sub-pathway network for angiogenesis based on the comprehensive pathway network. BMC Bioinformatics 11(S1):S32 [pdf]

· Lisha Li, Ningbo Zhang, Shao Li* (2010) Ranking effects of candidate drugs on biological process by integrating network analysis and Gene Ontology. Chinese Science Bulletin 55:2974-2980 [Link]

· BangpengYao, Shao Li* (2010) ANMM4CBR: a case-based reasoning method for gene expression data classification. Algorithms for Molecular Biology 5:14 [pdf]

· Shao Li, Aiping Lu*, Yongyan Wang (2010) Symptomatic comparison in efficacy on patients with benign prostatic hyperplasia treated with two therapeutic approaches. Complementary Therapies in Medicine 18(1):21-27 [Link]

2009

· Shao Li* (2009) Network systems underlying traditional Chinese medicine syndrome and herb formula (Invited review). Current Bioinformatics 4(3):188-196 [pdf] (Invited Review)

· Shao Li* (2009) Conception and research on the network biomarker of TCM Syndrome. Journal of Traditional Chinese Medicine 50(9):773-776 [pdf]

· Shao Li, Ningbo Zhang, Zhihong Li, Hao Ding, Yongan Ye (2009) Decision tree diagnostic model of Gan-dan damp-heat syndrome and Gan-stangnancy pi-deficiency syndrome in patients with chronic hepatitis B. Chinese Journal of Integrative Medicine 29(11): 993-996 (In Chinese)

2008

· Xuebing Wu, Rui Jiang, Michael Zhang, Shao Li* (2008) Network-based global inference of human disease genes. Molecular Systems Biology 4:189 [pdf] (Highlighted by Nature China; Nature Publishing Group “Featured Article” in FOUR areas: Systems Biology, Pathology & Pathobiology, Genetics, and Biotechnology; Highlighted by 2009 American Medical Informatics Association Summit on Translational Bioinformatics, and Highlight Track in ISMB 2009)

· Jing Zhang, Tao Ma, Yanda Li, Shao Li* (2008) dbNEI2.0: building multilayer network for drug-NEI-disease. Bioinformatics 24:2409-2411 [pdf]

· Guolian Kang, Shao Li*, Jifeng Zhang (2008) Entropy-based models for interpreting life systems in traditional Chinese medicine. Evidence-based Complementary and Alternative Medicine 5:273-279 [pdf]

· Min Wu, Changhua Ma, Ying Wu, Shao Li* (2008) Simultaneous LC analysis of five bioactive alkaloids in an anti-angiogenesis herbal formula, Qing-Luo-Yin. Chromatographia 68:579-585 [Link]

2007

· Shao Li*, Zhongqi Zhang, Lijiang Wu, Xuegong Zhang, Yanda Li, Yongyan Wang (2007) Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Systems Biology 1:51-60 [pdf] (Most-Cited Article in IET Systems Biology)

· Shao Li* (2007) Framework and practice of network-based studies for Chinese herbal formula. Journal of Chinese Integrative Medicine 5(5):489-493 (In Chinese) [pdf]

· Shao Li*, Youhan Fang (2007) Modelling circadian rhythms of protein KaiA, KaiB and KaiC interactions in cyanobacteria. Biological Rhythm Research 38:43-53 [Link]

2006

· Shao Li*, Lijiang Wu, Zhongqi Zhang (2006) Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 22:2143-2150 [pdf]

· Yonglong Zhuang, Shao Li*, Yanda Li (2006) dbNEI: a specific database for neuro-endocrine-immune interactions. Neuroendocrinology Letters 27: 53-59 [pdf]

· Shao Li*, Ruiqin Wang, Yulong Zhang, Xuegong Zhang, A. Joseph Layon, Yanda Li, Mingzhe Chen (2006) Symptom combinations associated with outcome and therapeutic effects in a cohort of cases with SARS. American Journal of Chinese Medicine 34:937-947 [Link]

Before 2005

· Shao Li*, Aiping Lu, Biao Li, Yongyan Wang (2004) Circadian rhythms on hypothalamic-pituitary-adrenal axis hormones and cytokines of collagen induced arthritis in rats. Journal of Autoimmunity 22:277-285 [Link]

· Shao Li, Aiping Lu*, Lian Zhang, Yanda Li (2003) Anti-Helicobacter pylori immunoglobulin G (IgG) and IgA antibody responses and the value of clinical presentations in diagnosis of H. pylori infection in patients with precancerous lesions. World Journal of Gastroenterology 9:755-758

· Shao Li*, Aiping Lu, Yongyan Wang, Yanda Li (2003) Suppressive effects of a Chinese herbal medicine Qing-Luo-Yin extract on the angiogenesis of collagen induced arthritis in rats. American Journal of Chinese Medicine 31:713-720 [Link]

· Shao Li*, Yongyan Wang, Liang Ji, Yanda Li (2002) A discussion and case study of complexities in traditional Chinese medicine. Acta Simulata Systematica Sinica 14(11):1429-1432 (In Chinese)

1. Li S*, Zhang NB, Zhang B. A network target-based approach for evaluating multicomponent synergy. Proceedings of the 4th International Conference on Computational Systems Biology (ISB 2010), 2010:51-58

2. Li YJ, Ma T, Lu L, Li S*. Networking drugs and diseases in the context of neuro-endocrine-immune system. Proceedings of the 3rd International Conference on BioMedical Engineering and Informatics (BMEI 2010), 2010:1-5

3. Zhang B, Xu ZY, A LY, Li S*. AngioIQ: a novel automated localization approach for angiogenesis image quantification. Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics, 2009:1-5

4. Gu J, Li S, Chen Y, Li YD. Integrative computational identifications of the signaling pathway network related to TNF-alpha stimulus in vascular endothelial cells. Proceedings of the International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS 2009), 2009:422-427

5. Li LS, Zhang NB, Li S*. Network approach for prioritizing drug candidate on gliomas. Proceedings of the 7th Asia Pacific Bioinformatics Conference, Poster No. PE2-19, Tsinghua University Press. 2009

6. Bao Y, Liu Y, Ma T, Lin Y, Li S*. Identifying phenotype-dependent modules in signaling pathway. The 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008), Poster No. 08, Stanford, California,USA, Aug. 26-29, 2008

7. Yan H, Li S, Zhao QC*. A formal model for analyzing and predicting combination effects for biosystems based on Bliss independence method. The 4th Annual RECOMB Satellite on Systems Biology, Poster No. 248, MIT / Broad Institute,USA, Oct. 29-Nov. 2, 2008

8. Yan B, Xu X, Wu X, Li S, van Waes C, Chen Z*. Integrative analysis of biomarkers that contribute to the metastatic process of head and neck cancer. NIH Research Festival 2008. Poster No. Bioinfo-18, Bethesda,USA. Oct. 14-17, 2008

9. Wu X, Zhang MQ, Li S*. Global inference of human phenotype-genotype associations by integrating interactome, phenome and diseasome (Extended Abstract). Proceedings of the 8th International Conference on Systems Biology (ICSB 2007), CaliforniaUSA. Oct. 2007. Poster No. I25 [pdf]

10. Zhou T*, Li S. Multi-target identification in intracellular regulation networks. Proceedings of the 26th Chinese Control Conference 2007:112-116

11. Lu X, Huang Y, Zhang B, Li S. Application of mixture designs for detection and characterization of multi-drug synergism. Proceedings of the 1st International Conference on Bioinformatics and Biomedical Engineering, 2007: 409-413

12. Zhang C, Li S*. Modeling of neuro-endocrine-immune network via subject oriented literature mining. Proceedings of the 4th International Conference on Bioinformatics of Genome Regulation and Structure, 2004,2:167-170

13. Li S, Hu Y, Wang Y, Lu A. The effects of Cold and Heat property herbal formula on collagen induced arthritis in rats (Poster). Proceedings of the 2nd International Scientific Conference on Complementary, Alternative & Integrative Medical Research, Sponsored by NIH and Harvard Medical School, Abstracts printed by Elsevier Science Press, 2002

1. Shao Li, Chunfu Wu, Zunjian Zhang, Weidong Zhang (editor). Network Pharmacology: A New Way to the Modernization of Traditional Chinese Medicine. Beijing, China: China Science and Technology Press, 2014

2. Shao Li, Le Lu. Computational Systems Biology Approaches for Deciphering Traditional Chinese Medicine. Basics of Bioinformatics. Springer Berlin Heidelberg. 2013:337-368

3. Xuebing Wu, Shao Li. Cancer Gene Prediction Using a Network Approach. Chapter 11. Cancer Systems Biology (Ed. Edwin Wang). Series: Chapman & Hall/CRC Mathematical & Computational Biology,USA: CRC Press, 2010: 191-212 [Link]

4. Shao Li. A network biology approach for understanding traditional Chinese medicine. Advances in Pharmacology and Clinics of Chinese Material Medica - Book seven. People's Medical Publishing House 2010: 265-290 (In Chinese)

5. Shao Li. Chief Editor. 100 TCM Practitioners in Latest 100 Years: Li Ji-ren & Zhang Shun-hua. Beijing: China Press of Traditional Chinese Medicine, 2004

6. Shao Li. Deputy Chief Editor. Essential of Traditional Chinese Medicine: Researches on Xin An’s Medicine. Beijing: Hua Xia Publishing House, 1999

7. Shao Li. Deputy Chief Editor. A General Survey on Atrophy Disease. Beijing: People’s Health Press, 1996

8. Shao Li. General Theory of Seal Cutting. Beijing: Academy Press, 1993

1. Network-based cancer precision integrative medicine. The 2nd international Forum on Chinese and Western Medicine of the National Cancer Center. 2019.10.26 Beijing

2. Network-based precision Chinese medicine on cancer. 2019 NSFC-NCI Integrative Oncology Workshop. 2019.4.24 Beijing

3. Network pharmacology to unveil the biological basis of traditional Chinese medicine. The 66th Annual Meeting of the Society for Medicinal Plant and Natural Product Research. 2018.8.27, Shanghai

4. Unveiling the biological basis of traditional Chinese medicine by network pharmacology. The 4th International Summit on Innovative Drug Discovery in Chinese Medicine: Network Pharmacology and Big Data Analysis. 25-26 Aug. 2018, Hongkong

5. Network-based integrative studies on inflammation-induced tumorigenesis. ICSB 2018 (The 8th International Workshop on Cancer Systems Biology) 2018.6.30, Changchun

6. Traditional Chinese Medicine network pharmacology. Systems Biology for Efficacy/Toxicological Risk Assessment Workshop. Unilever (China) Investing Company 2017.4.27, Shanghai (Keynote Speech)

7. Modern biological interpretation for TCM practice: Cold / Hot Syndrome as a case study. The 4th International Workshop of Basic and Translational Cancer Research. 2017.4.21-23, Guiyang

8. Network-based TCM precision medicine. The 7th International Conference on Computational Systems-Biology and Bioinformatics (CSBio2016), 19-22nd, Dec. 2016, Macau (Keynote Speech)

9. From prediction to discovery: TCM network pharmacology in the big data era. Bio-med and Innovative Medical Devices 2016. 2016.11.29

10. Network target: a new approach towards TCM precision medicine. World Life Science Conference (WLSC2016). Organized by China Association of Science and Technology and the China Union of Life Science Societies. 2016,11,1-3 Beijing

11. Development of TCM network pharmacology in the big data era. International Symposium on Clinical and Translational Medicine 2016 (ISCTM 2016), Organized by Chinese Academy of Engineering, Chinese Academy of Sciences, and US NIH Clinical Center. 2016.9.24-26. Shanghai

12. Network Pharmacology and Computational Modeling to Traditional Chinese Medicine Research. The State of Science Cancer Complementary and Alternative Medicine Therapeutic Research. NIH/NCI. 2016. 5.24-26, Maryland, USA (photo)

13. Network pharmacology: a new mode for traditional medicine research. The 16th International Congress on Ethnopharmacology, International Society for Ethnopharmacology, 2016.5.16-18, Guangxi

14. Network target: a breakthrough point of TCM Network Pharmacology. The Founding Conference of Specialized Committee of TCM Network Pharmacology, World Federation of Chinese Medicine Societies, & the First Academic Conference of TCM Network Pharmacology. 2015, Nov. 20-22, Beijing (Keynote Speech)

15. Methodology and application of network pharmacology in Traditional Chinese Medicine. 2015 Grand Challenges Annual Meeting (Gates Foundation, MOST), Beijing, China 2015, Oct. 20

16. Network target: a novel approach to decipher traditional Chinese medicine. Symposium of "Exploring Traditional Medicine", IAMP (The interacademy medical panel), 23-24 Sep. 2015, Beijing

17. Network-based analysis of traditional Chinese medicine on cancer. The Fifth International Workshop on Cancer Systems Biology (ICSB 2015). July 11-12, 2015, Changchun

18. Network pharmacology: accelerates biomarker and drug discovery from traditional Chinese medicine. The Third International Workshop of Basic and Translational Cancer Research. Hefei, 2015,4,10-12

19. TCM network pharmacology: towards the modernization of Chinese medicine. The 13th Meeting of Consortium for Globalization of Chinese Medicine (CGCM), Bioinformatics Pre-meeting Workshop. 2014,8,26 (Special talk)

20. Understanding traditional Chinese medicine by a network pharmacology approach. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013) 2013, Dec. 18-20 (Keynote Speech)

21. Network pharmacology and the interdisciplinary study of TCM. International Conference on Interdisciplinary Study on Traditional Chinese Medicine. 2013,10,11-14, Hangzhou

22. Network pharmacology: a new approach to explore traditional Chinese medicine. The 4th International Conference on the Modernization of Traditional Chinese Medicine. 2013, 9,26-27 Chengdu

23. Network analysis: towards evidence-based traditional Chinese medicine. 2013 International Conference on Intelligence Science and Big Data Engineering (IScIDE2013). 2013, July 31-Aug. 2. Beijing

24. Network pharmacology for discovering traditional Chinese medicine. The 2nd International Workshop of Basic and Translational Cancer Research. Hefei, 2013,1,27-29

25. Network approaches to Translational Chinese medicine. The International Conference on Translational Biomedical Informatics. Taicang, Dec. 8-10, 2012

26. Network Biology and Network Pharmacology in Traditional Chinese Medicine: theory, methodology and application. International Conference on System and Network Biology and Traditional Chinese Medicine. Adelaide, Australia, Nov,10-15, 2012 (Keynote Speech)

27. Methodology & application of network pharmacology in traditional Chinese medicine. Shanghai International Conference on Traditional Chinese Medicine and Natural Medicine 2012,10,20-21

28. A network pharmacology methodology and its applications in traditional Chinese medicine. 2011 International Conference of Genomics. Oct. 24, 2011 (Invited talk)

29. A Network Pharmacology Approach to Explore the Action Mechanism of Herbal Formulae. 13th Annual Meeting of China Association for Science and Technology. International Forum on the Development of Traditional Chinese Medicine. Sep. 21-23, 2011 Tianjin

30. Network-based Studies of Cancer Genes, Drugs and Traditional Chinese Medicine. International Workshop on Cancer Systems Biology (ICSB) Changchun, 2-6 July, 2011

31. Understanding the biological basis of traditional Chinese medicine and acupuncture from a network perspective. International Symposium on Acupuncture Research – Past, Present and Future. Oct. 16-18, 2010, Hefei (Keynote Speech)

32. Recent Progress in Systems Bioinformatics-based TCM Research. The 4th International Symposium on Bioinformatics, Systems Biology and Traditional Chinese Medicine. Chengdu, Apr. 29, 2010

33. Biological network systems underlying traditional Chinese medicine. 2009 International Workshop on Bioinformatics and Systems Biology in Traditional Chinese Medicine Research, the International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. Shanghai, Aug. 2009

34. Bioinformatics and the modernization of traditional Chinese medicine. The 9th International Conference on Signal Processing. Beijing, Oct. 2008 (Keynote Speech)

35. TCM bioinformatics and the analysis of Cold/Hot ZHENG-related network. The 2nd International Symposium on Bioinformatics, Systems Biology and Traditional Chinese Medicine. Shanghai, May 2007 (Keynote Speech)

36. Systems bioinformatics studies for TCM ZHENG and Fu-Fang. Nanjing International Forum of Traditional Chinese Medicine. Nanjing, Oct. 2008 (Invited talk)

37. A network approach for studying TCM ZHENG and Fu Fang. The International Symposium on From Structure to Systems based Drug Discovery. Beijing, Aug. 2007

38. Information and system: A new approach to the modernization of traditional Chinese medicine. The 1st International Symposium on Bioinformatics and Traditional Chinese Medicine. Chengdu, Nov. 2004 (Keynote Speech)