Shao Li (李梢)

Professor

Deputy Director, Bioinformatics Division, TNList

Tsinghua University, Beijing 100084, China

Tel: +86 10 62797035

E-mail: shaoli “at” mail.tsinghua.edu.cn

中文版http://bioinfo.au.tsinghua.edu.cn/member/lishao/

 

 

Main research interests

 

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

 

Education background

 

·   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.

 

Academic experiences

 

·   Dec. 2009 ~ Present: Full Professor, Tsinghua University

·   Oct. 2008 ~ Present: PhD Candidate Supervisor, Tsinghua University

·   Feb. 2006 ~ Present: 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

 

Academic activities and membership

 

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

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

·   2012 ~  Guest Professor, China Academy of Chinese Medical Sciences

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

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

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

·   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

·   Lead guest editor: Special Issue on “Network Pharmacology in Traditional Chinese Medicine”, Evidence-Based Complementary and Alternative Medicine

·   Guest editor: Special Issue on “Evidence-Based ZHENG, a Traditional Chinese Medicine Syndrome”, Evidence-Based Complementary and Alternative Medicine

·   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 of China Association for Science and Technology

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

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

 

Awards

 

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

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

·   National Outstanding Young Scientist Award, China (2012)

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

·   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, China (2007)

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

·   Excellent Postdoc Fellow of Tsinghua University (2004)

·   National Excellent Doctoral Dissertation, China (2003)

·   Beijing Science & Technology Award (2002)

·   Anhui Province Science & Technology Award (2000)

 

Research overview

  

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 (Table 1), 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 (Table 2) 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 (Table 3). 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].

 

Table 1. Conception development in Li Lab

Conception

Reference

Constructed biological network for Cold / Hot syndromes, and revealed the network regulation mechanism of Hot / Cold herb formulae

IET Systems Biology 2007

Proposed the network-based TCM research framework

J Chin Integr Med 2007

Proposed the “Phenotype network-Biological network-Herb network”

Current Bioinformatics 2009

Proposed the concept of “Network biomarker” for TCM syndrome

JTCM 2009

Proposed the concept of “Network target

BMC Systems Biology 2011; CJCMM 2011

Proposed the TCM network pharmacology

CJCMM 2011; CJNM 2013

Proposed the network target-based effect on/off model

Science 2015(Suppl)

 

Table 2. Algorithm development for the network target analysis in Li Lab

Category

Name

Description

Reference

Network for disease / TCM syndrome

LMMA

Disease-specific biological network construction

Bioinformatics 2006

CIPHER

Network-based prediction for disease genes

Molecular Systems Biology 2008

CSPN

Disease-specific pathway network construction

BMC Bioinformatics 2010a

ClustEx

Disease-specific responsive gene module identification

BMC Systems Biology 2010a

 

CIPHER-HIT

Modularity-based disease gene prediction

BMC Systems Biology 2011a

 

sGSCA

Pathway crosstalk network analysis

Molecular BioSystems 2013

Network as a target for drug / herbs

drugCIPHER

Network-based prediction for drug (herbal ingredient) targets

PLoS ONE 2010

GIFT

Chemogenomic features of drug-target interaction inference

Bioinformatics 2015

DMIM

Herb network construction and co-module analysis

BMC Bioinformatics 2010b

NADA

Network-based assessment for drug (herbal ingredient) action

Chinese Science Bulletin 2010

NIMS

Network-based identification of synergistic drug combinations

BMC Systems Biology 2011b

 

SAF

Synergism assessment factor for drug combination

BMC Systems Biology 2010b

 

SidePro

Network-based inferring proteins related to drug side effects

Quantitative Biology 2015

Drug-gene-disease co-module

comCIPHER

Drug-gene-disease co-module analysis

Bioinformatics 2012a

DGPsubNet

Drug-gene-disease coherent subnetwork analysis

CPT: PSP 2014

dbNEI

Multilayer network for drug-NEI-disease

Bioinformatics 2008

 

Table 3. Applications of the network target approach in TCM

 

Subjects

Discovery from the network target analysis

Reference

TCM Syndrome & related diseases

Cold syndrome / Hot syndrome

Network construction, topological temperature measure

IET Syst Biol 2007

Cold syndrome patients

Validated the network by microarray

Mol BioSyst 2010

Different stage of gastritis patients with Cold / Hot syndrome

Imbalance of metabolism-immune, network biomarker

Sci Rep 2013

Tongue coating of atrophic gastritis patients

Cold / Hot microbe network

Sci Rep 2012

Cold / Hot network related biological processes or diseases

Angiogenesis network

Bioinformatics 2006 Bioinformatics 2012b

Cold / Hot network related biological processes or diseases

Inflammation, angiogenesis, and cancer related pathway networks

BMC Bioinfo 2010

Mol BioSyst 2012

Mol BioSyst 2013

A mouse model of colitis-associated colorectal cancer

Microbe and molecule networks including Hot hub nodes

Sci Rep 2014

Herb medicine

Qing-Luo-Yin (QLY, a Hot-Cooling formula)

Wen-Luo-Yin (WLY, a Cold-Warming formula)

Network regulation for Cold / Hot Syndrome

IET Syst Biol 2007

61 herbs or compounds including QLY ingredients

Anti-angiogenesis synergistic combination screening

BMC Syst Biol 2011

Qing-Luo-Yin

Jun-Chen-Zuo-Shi network regulation

ECAM 2013a

Mining Qing-Luo-Yin from 871 clinical prescriptions

Network effects on rheumatoid arthritis

ECAM 2015

Man-Jing-Zi (Vitex rotundifolia), a cool herb

New activity of anti-tumor angiogenesis

ECAM 2013b

Wu-Tou decoction, a formula similar to WLY

Network effects on rheumatoid arthritis

Sci Rep 2015

Wu-Tou decoction, a formula similar to WLY

Cold-Warming (thermogenesis)-associated pathway target

Oncotarget 2016

Tetramethylpyrazine from Chuan-Xiong (Ligusticum wallichii Franchat), a warm herb

Ameliorating methotrexate-induced oxidative organ injury

J Ethnopharmacol 2015

3865 herbal formulae including Liu-Wei-Di-Huang

Herb network and co-module for treating different diseases

BMC Bioinfo 2010

Liu-Wei-Di-Huang formula, a Yin-nourishing formula

Network regulation mechanism, potential new activity of anti-tumorigenesis and active compounds

Mol BioSyst 2014

Ge-Gen-Qin-Lian decoction, a Hot-Cooling formula

Network effects on type 2 diabetes

ECAM 2014

Nuciferine extracted from lotus leaves, a Hot-Cooling herb

Anti-tumor activity and mechanisms

APS 2016

Chinese patent medicines for cancer treatment

A nationwide 51,382 cancer patients data analysis

Oncotarget 2015

 

 

Selected Publications (*: Corresponding author)

Google Scholar Citations

2017

·   Xi D*, Bao T, Chen Q, Chen S, Cheng Y, Cullen J, Frank D, Friedberg J, Kronish I, Lee J, Levine M, Li S, Lu W, Mao J, Keefe S, Rubinstein L, Standish L, Studzinski G, Wan Y, Wang G, Yan J, Yang C, Yang P, Yeung S, Zhou G, Paller C, Chu E. State of the Science: Cancer Complementary and Alternative Medicine Therapeutics Research - NCI Strategic Workshop Highlights of Discussion Report. JNCI: Journal of the National Cancer Institute (Accepted)

·   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]

·   Huang Q, Xu L, Qu W, Ye Z, Huang W, Lin J, Li S*, Ma H*. TLC Bioautography-guided Isolation of Antioxidant Activity Components of Extracts from Sophora flavescens Ait. European Food Research and Technology 2017 [link]

 

2016

·   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]

·   Zhang Y, Mao X, Guo Q, Bai M, Zhang B, Liu C, Sun Y, Li S*, Lin N*. Pathway of PPAR-gamma coactivators in thermogenesis: a pivotal traditional Chinese medicine-associated target for individualized treatment of rheumatoid arthritis. Oncotarget 2016;7(13):15885-15900 [pdf]

·   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]

·   Wang T, Xie Y, Tan A, Li S, Xie Z*. Construction and characterization of synthetic microRNA cluster for multiplex RNA interference in mammalian cells. ACS Synthetic Biology 2016;5(11):1193-1200 [link]

·   Ding F, Tan A, Ju W, Li X, Li S*, Ding J*. The prediction of key cytoskeleton components involved in glomerular diseases based on a protein-protein interaction network. PLoS ONE 2016;11(5):e0156024 [pdf]

·   Zhang Y, Mao X, Guo Q, Lin N, Li S*. Network pharmacology-based approaches capture the essence of Chinese herbal medicines. Chinese Herbal Medicines 2016;8:107-116 [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]

·   Zhang Y, Bai M, Zhang B, Liu C, Guo Q, Sun Y, Wang D, Wang C, Jiang Y, Lin N*, Li S*. Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation. Scientific Reports 2015; 5: 9463 [pdf]

·   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]

·   Rui Li, Ting Chen*, Shao Li*. Network-based method to infer the contributions of proteins to the etiology of drug side effects. Quantitative Biology 2015;3(3):124-134 [pdf]

·   Shi Y, Chen G, Xiao C, Wang H, Li Y, Zhang J, Li S, Xia Y, Ren J, Guleng B*. Dragon (repulsive guidance molecule b, RGMb) is a novel gene that promotes colorectal cancer growth. Oncotarget 2015;6(24):20540-20554

·   Tang J, Li L, Huang W, Sui C, Yang Y, Lin X, Hou G, Chen X, Fu J, Yuan S, Li S, Wen W, Tang S, Cao D, Wu M, Chen L*, Wang H*. MiR-429 increases the metastatic capability of HCC via regulating classic Wnt pathway rather than epithelial-mesenchymal transition. Cancer Letters 2015;364(1):33-43

·   Zhao X, Fu J, Xu A, Yu L, Zhu J, Dai R, Su B, Luo T, Li N, Qin W, Wang B, Li S, Chen Y*, Wang H*. Gankyrin drives malignant transformation of chronic liver damage-mediated fibrosis via Rac1/JNK pathway. Cell Death & Disease 2015;6:e1751

·   C Xiao, M Xiao, H Xu, H Wang, X Chen, Y Liu, P Li, Y Shi, Y Nie, S Li, K Wu, Z Liu, J Ren*, B Guleng*. Exome sequencing identifies novel compound heterozygous IFNA4 and IFNA10 mutations as a cause of impaired function in Crohn's disease patients. Scientific Reports 2015;5:10514.

·   Y Kumar, J Yang, T Hu, L Chen, Z Xu, L Xu, X Hu, G Tang, J Wang, Y Li, W Poon, W Wan, L Zhang, W Mat, F Pun, P Lee, T Cheong, X Ding, S Ng, S Tsang, J Chen, P Zhang, S Li, H Wang*, H Xue*. Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response. BMC Medical Genomics 2015;8:42

 

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*, Xuegong Zhang. Tongue-Coating Microbiome Characterized by the Next-Generation Sequencing and Traditional Tongue Diagnosis. Encyclopedia of Metagenomics 2014 Springer [link]

·   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 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)

·   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)

·   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]

·   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]

·   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]

·   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]

·   Yan Li, Shao Li*, Aiping Lu (2006) Comparative analysis via data mining on the clinical features of western medicine and Chinese medicine in diagnosing rheumatoid arthritis. Chinese Journal of Integrative Medicine 26:988-989 (In Chinese)

 

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)

 

Selected Conference Papers or Posters

 

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), California USA. 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

 

Books & Book Chapters

 

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

 

Keynote Speech / Invited Talk at International Conferences

 

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

2.      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

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

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

5.      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

6.      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

7.      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)

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

9.      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)

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

11.   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

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

13.   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

14.   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)

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

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

17.   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

18.   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

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

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

21.   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)

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

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

24.   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

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

26.   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)

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

28.   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

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

30.   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)

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

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

33.   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)

 

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