M.D. Ph.D., Professor
Deputy Director, Bioinformatics
Division, TNList
Tel: +86 10 62797035
E-mail: 
中文版：http://bioinfo.au.tsinghua.edu.cn/member/lishao/
Main
research interests
·
Drug-Gene-Disease Networks: Interaction between Diseases,
Drugs and Molecular Networks, with application to Cancer and
neuro-endocrine-immune disorders
·
TCM Network Pharmacology: Network-based drug discovery
and development from traditional Chinese medicine (TCM)
Education
background
·
Sep. 1998 ~ Jul. 2001
·
Sep. 1995 ~ Jul. 1998
·
Sep. 1990 ~ Jul. 1995
Academic
experiences
·
Dec. 2009 ~ Present: Full
Professor,
·
Oct. 2008 ~ Present: PhD
Candidate Supervisor,
·
Feb. 2006 ~ Present: Deputy
Director, Bioinformatics Division, TNList
(Tsinghua National Lab for Informatics Science & Technology)
·
Dec. 2004 ~ Nov. 2009: Associate Professor, MOE Key Laboratory of
Bioinformatics, Department of Automation,
·
Sep. 2003 ~ Nov. 2004: Assistant
Professor, MOE Key Laboratory of Bioinformatics, Department of Automation,
Tsinghua University
·
Sep. 2001 ~ Jul. 2003: Postdoctoral
Research Fellow, MOE Key Laboratory of Bioinformatics, Department of
Automation, Tsinghua University
Academic
activities and membership
· 2012 ~ Guest Professor, China Academy of Chinese
Medical Sciences
· 2011 ~ Adjunct
professor, School of Life Sciences, Tsinghua University
· 2011 Guest editor, Evidence-Based Complementary and Alternative Medicine
· 2011 ~ Editorial
Board Member, China Journal of Chinese Materia Medica
·
2010
~ Editorial Board Member, International Journal of Functional
Informatics and Personalized Medicine
·
2010
~ Editorial Board Member, Chinese Journal of Electronics
·
2010
~ Editorial Board Member, World Science and Technology-Modernization
of Traditional Chinese Medicine
· 2009 ~ Editorial
Board Member, World Journal of Gastrointestinal Oncology
· 2008 ~ Editorial Advisory Board Member, The Open Systems Biology Journal (Bentham)
· Reviewer: Trends in Molecular Medicine, American Journal of Gastroenterology, PLoS ONE, Bioinformatics, BMC Systems Biology, Rheumatology, Evidence-Based Complementary and Alternative Medicine, Complementary
Therapies in Medicine, BMC Complementary and Alternative Medicine, Artificial
Intelligence in Medicine …
· Referee:
The Royal Society of New Zealand “Marsden Fund”, National Nature Science
Foundation of China (NSFC)…
· Dec.
2010 Co-Chair, The 228th Youth Scientist Forum of
· Dec.
2009 Co-Chair, The 209th Youth Scientist Forum of
· Jan.
2009 Poster Co-Chair, APBC2009
· Nov.
2004 Co-Chair, The 1st International Symposium on Bioinformatics and Traditional Chinese
Medicine
Awards
·
National Education
·
Mao Yi-Sheng Science and
Technology Award for
·
·
New Century Excellent Talents in
·
National Science & Technology
·
Excellent Postdoc Fellow of
·
National Excellent Doctoral Dissertation, China (2003)
·
·
Grants
1. NSFC Key Project (2010~2013): System modeling and regulatory mechanism of disease-oriented biomolecular networks (PI: Shao Li)
2. NSFC Project (2009~2011): Angiogenesis network-based study for the multi-target synergistic effect of herbal formula (PI: Shao Li)
3. NSFC Project (2007~2009): Multilayer network analysis and clinical investigation for Cold/Hot ZHENG (TCM Syndrome) (PI: Shao Li)
4. National Key Technology Support Program, China (2006~2009): Computational systems biology approaches for studying ZHENG (TCM Syndrome) (PI: Shao Li)
5.
National 863 Hi-tech
research and development program of
6.
Key Project of Ministry of
Education,
7.
Foundation for the Author of
National Excellent Doctoral Dissertation of
8. NSFC Key Project (2003~2006): Genome informatics for the Cold/Hot ZHENG (TCM Syndrome) in patients with rheumatoid arthritis (PI: Aiping Lu & Shao Li)
9. NSFC Project (2003~2005): Understanding biological mechanisms of the Cold/Hot ZHENG (TCM Syndrome) in the context of the neuro-endocrine-immune network (PI: Shao Li)
Invited
Talks
1.
A
network pharmacology methodology and its applications in traditional Chinese
medicine. 2011 International Conference
of Genomics. Oct. 24, 2011 (Invited
talk)
2.
Network approaches to bridge the gap between traditional
Chinese medicine and systems biology. TCM-driven
systems biology, personalised medicine and healthcare IT. Sep 27, 2011,
Tsinghua U (Keynote Speech)
3.
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 (Invited talk)
4.
Network-based
Studies of Cancer Genes, Drugs and Traditional Chinese Medicine. International
Workshop on Cancer Systems Biology (ICSB)
5.
The potential advantages of the network target approaches
in creating new Chinese medicine. Capital summit for the scientific and technological
innovation on the prevention and control of major diseases. Dec. 5, 2010,
6.
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 (Plenary
Presentation)
7.
Network
target-based researches on traditional Chinese herbal formula. Xiangshan Meeting.
8.
Systems Bioinformatics and the modernization of TCM. Xiangshan Meeting.
9.
Multilayer networks underlying disease and
drug. Invited
talk at National Laboratory of Pattern Recognition,
10.
Recent Progress in Systems Bioinformatics-based TCM
Research. The 4th International Symposium on Bioinformatics, Systems Biology
and Traditional Chinese Medicine.
11.
Network-based Studies on Complex Diseases and Traditional Chinese
Medicine. Invited talk at GlaxoSmithKline R&D China, Apr., 2010
12.
Understanding
traditional Chinese medicine by systems biology approaches. Tsinghua-PICB
workshop, Feb., 2010 (Invited talk)
13.
How to design the research framework for ZHENG (TCM
Syndrome)? Xiangshan Meeting.
14. Network biomarker identification
for ZHENG (TCM Syndrome)
in traditional Chinese medicine. Tsinghua-CKI Workshop, Nov. 2009 (Invited talk)
15. 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 (Invited talk)
16.
Bioinformatics and the modernization of traditional
Chinese medicine. The 9th International Conference on Signal Processing.
17.
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)
18.
Systems bioinformatics studies for TCM ZHENG and Fu-Fang.
19.
TCM Systems biology: A framework of phenotype network -
biological network - herbal network. The Seminar on Computational Systems
Biology. Shanghai, Aug. 2008 (Invited talk)
20.
A network approach for studying TCM ZHENG and Fu Fang.
The International Symposium on From Structure to Systems based Drug
Discovery.
21.
Progress of computational systems biology-based
studies for TCM. Xiangshan Meeting.
22.
Information and system: A new approach to the
modernization of traditional Chinese medicine. The 1st International
Symposium on Bioinformatics and Traditional Chinese Medicine.
Selected
Journal Publications
(Selected from >80
Journal Papers. *: Corresponding author)
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 annotating the
cell-type specific gene functional and signaling map in vascular endothelial
cells.
Molecular
BioSystems (Accepted)
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 (Accepted)
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] (Faculty of 1000 Medicine,
F1000 Factor = 8)
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]
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]
Shiwen Zhao, Shao Li*
(2010) Network-based relating pharmacological and genomic spaces for drug target
identification.
PLoS ONE 5(7): e11764 [pdf] (Research
highlights in Nature China)
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] (Selected for the Virtual Journal
of Biological Physics Research 7(19), April 1, 2010, issued by American Institute of Physics and the American Physical
Society)
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 2010;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]
Shao Li* (2009) Network systems underlying traditional Chinese medicine syndrome and herb
formula.
Current Bioinformatics 4(3):188-196 [pdf] (Invited Review)
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 2009; 29(11): 993-996.(In Chinese)
Xuebing Wu, Rui Jiang, Michael Zhang, Shao
Li* (2008) Network-based global inference of human disease
genes.
Molecular Systems Biology 4:189 [pdf] (Nature Publishing Group “Featured Article” in FOUR areas:
Systems Biology, Pathology & Pathobiology, Genetics, and Biotechnology; Research
highlights in Nature China;
Highlighted by 2009 American Medical Informatics Association
Jing
Zhang, Tao Ma, Yanda Li, Shao Li*
(2008) dbNEI2.0:
building multilayer network for drug-NEI-disease.
Bioinformatics 24:2409-2411 [pdf] (Highlighted by “Computational Molecular Biology at NIH”)
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]
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] (“Top 4 Accessed Article” among all the papers published in IET Systems Biology, during Jan 2009)
Shao Li*,
Youhan Fang (2007) Modelling
circadian rhythms of protein KaiA, KaiB and KaiC
interactions in cyanobacteria.
Biological Rhythm Research 38:43-53 [Link]
Shao Li*
(2007) Framework
and practice of network-based studies for Chinese herbal formula.
Journal of Chinese Integrative Medicine 2007,5(5):489-493 (In Chinese) [pdf]
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 2006;26:988-989 (In Chinese)
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 2002;14(11):1429-1432 (In Chinese)
Selected
Conference Papers or Posters
1.
Li S*,
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
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,
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,
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,
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)
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
Books
& Book Chapters
1. 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]
2. 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)
3. Shao Li. Chief Editor. 100
TCM Practitioners in Latest 100 Years: Li Ji-ren & Zhang Shun-hua.
4. Shao Li. Deputy Chief Editor.
Essential of Traditional Chinese Medicine: Researches on Xin An’s Medicine.
5. Shao Li. Deputy Chief Editor.
A General Survey on Atrophy Disease.
6. Shao Li. General Theory of Seal
Cutting.
Invention
Patents
· Shao Li, Ningbo Zhang, Bo Zhang. Method of Network-Based Identification of Multicomponent Synergy and Compositions for Use as Effective Component of Anti-Angiogenesis Medicines. US Patent: 12/436,844
·
Shao
Li, Ningbo Zhang, Bo Zhang. Network-based methods for identification of drug synergy.
China Invention Patent: ZL200810239284.4
·
Shao Li, Min Wu. Composition
and its use as effective constituent of a medicine having anti-angiogenesis
synergy effect.
· Shao Li, Shiwen Zhao. A method of network-based identification for drug targets and drug actions. Applying for Invention Patents, 201010218468.X
Software
& Database
1.
CIPHER (References: Wu et al., Molecular Systems Biology 2008; Wu et
al., ICSB 2007; Wu & Li, Cancer Systems Biology 2010)
2.
dbNEI (References: Zhang et al., Bioinformatics 2008; Zhuang et al., Neuroendocrinology
Letters 2006)