LEMING SHI, Ph.D.
(Data Mining, Bioinformatics, Chemoinformatics, Biochips, and Drug Discovery)
Center for Toxicoinformatics
To meet the challenges of information explosion in genomics, proteomics, metabonomics, combinatorial chemistry, high-throughput screening, and biochips by using my extensive expertise in data mining, chemoinformatics, bioinformatics, computational chemistry, and chemometrics for the discovery, development, and regulation of better medicine and healthcare for human beings.
Ph.D. in Computational Chemistry 9/1988-7/1991
of Computational Chemistry,
M.Sc. in Computational Chemistry and Chemometrics 9/1985-7/1988
of Modern Chemistry,
B.Sc. in Analytical Chemistry 9/1981-7/1985
of Chemistry and Chemical Engineering,
EMPLOYMENT AND MAIN RESPONSIBILITIES
Computational Chemist (Principal Investigator in Biochemoinformatics) 4/2003-Present
Co-founder, Director of Informatics 5/2001-4/2003
Chipscreen Biosciences, Ltd.,
Senior Scientist 7/2000-5/2001
Senior Research Chemist 8/1999-6/2000
Cyanamid Company (a subsidiary of American Home Products Corp., now Wyeth),
Senior Computational Chemist 12/1997-8/1999
R.O.W. Sciences, Inc. (now
Northrop Grumman Information Technology),
Visiting Fellow 9/1995-12/1997
of Molecular Pharmacology, National Cancer Institute, NIH,
Research Associate 9/1994-9/1995
Assistant and Associate Research Professor 7/1991-8/1994
of Computational Chemistry,
Assistant and Vice President 7/1992-8/1994
1. Systems biology and toxicology
2. Data mining for DNA microarray gene expression profiling, SELDI-TOF protein profiling, and NMR metabolic profiling
3. Knowledge discovery, data mining, and visualization in chemistry and biology
4. Bioinformatics, chemoinformatics, toxicoinformatics, and chemometrics
5. Identification of disease-related genes
6. Computer-aided drug design and toxicity prediction
7. Structure-based drug design
8. Molecular diversity analysis and combinatorial library design
9. Pharmacophore identification and 3D database searching
10. Databases, expert systems, machine learning, and artificial intelligence
11. Chemical and biological information exchange on the WWW
1. Extensive (18 years) experience in programming, algorithm development, and application of state-of-the-art technologies of statistics, expert systems, machine learning, and artificial intelligence in solving challenging problems in chemistry and biology
2. Formal training and extensive programming experience in Statistics, Data Structures, Software Engineering, Databases, Artificial Intelligence, Expert Systems, Pattern Recognition, Fuzzy Set Theory, Neural Networks, Genetic Algorithms, Chemical Structure Processing, Molecular Diversity Analysis, etc.
3. Broad knowledge on chemistry, biology, pharmacology, and toxicology
4. Understanding of human diseases, such as cancer, endocrine disruption, and diabetes
5. Familiarity with the drug development process and FDA drug reviewing procedures
6. Extensive laboratory experience in UV/Vis, FTIR, FTNIR, GC, HPLC, AAS, etc.
7. Strong publication records (80+ papers and book chapters)
8. Creative, self-motivated, diligent, team-worker, and a quick learner
1. Platforms: PC, Macintosh, DEC Vax, DEC Alpha, IBM and SGI workstations
2. Operating Systems: DOS, Windows/NT, VMS, and Unix/Linux
3. Languages: Basic, Fortran, Pascal, LISP, Prolog, C, C++, SAS/JMP, S-Plus, Matlab, HTML, Visual Basic, Tcl/Tk, Perl, and CGI
4. Molecular Modeling and bioinformatics: Sybyl, Cerius2, InsightII, CODESSA/AMPAC, APEX-3D, MOE, MOPAC, Gaussian, Quanta/CHARMm; Protein and DNA sequence analysis packages (e.g. GCG)
5. Databases and Diversity Analysis: Oracle, Access, ISIS/Base/Host/Chemscape, Unity, Catalyst, Chem-X, Concord, Corina, NCI drug information system, Cambridge structural database, Brookhaven protein data bank, Protein and nucleic acid sequence databases, DiverseSolutions, Legion/Selector
6. Genetic Linkage Analysis: SOLAR, SLINK, LINKAGE and FASTLINK.
Chemistry and Biology: Partners in
Decoding the Genome,
The Second Committee Meeting of IUPAC
Task Force on Biochips and Nanotechnology,
International Forum on
First Committee Meeting of IUPAC Task Force on Biochips and Nanotechnology,
Expression and Proteomics in Environmental Health Research, National Institutes of
American Chemical Society National Meeting,
International Forum on Biochip
Innovative Computational Applications:
The Interface of Library Design, Bioinformatics, Structure Based Drug Design
and Virtual Screening,
1999 Keystone Symposia on Endocrine
Drug Discovery Technology'98: Breaking
the Bottleneck: Innovation and Speed in Drug Discovery,
DNA Microarray: Current Technology and
Future Applications Workshop,
Short course on clustering during the
Joint Annual Meeting of the Classification Society of North America and the
215th American Chemical Society National
17. American Chemical Society Short Course on Molecular Biology and Recombinant DNA Technology, Dallas, Texas, March 27-28, 1998.
18. Principles of Toxicology (3 credit hours course), NIH, 1997.
19. From Molecules to the Market: FDA Drug Reviewing Procedures (3 credit hours course), FDA/NIH, 1997.
EDITORIAL ADVISORY BOARD
and Applied Chemistry (
Review of Molecular Diagnostics (
1. Journal of Chemical Information and Computer Science
2. Journal of Medicinal Chemistry
3. Molecular Pharmacology
5. Briefings in Bioinformatics
6. Trends in Biotechnology
8. Computers and Applied Chemistry
9. Expert Review of Molecular Diagnostics
10. Journal of VLSI Signal Processing
11. Pattern Analysis & Applications
12. Journal of Biopharmaceutical Statistics
13. Journal of Biomedical Nanotechnology
14. Frontiers in Bioscience
15. Journal of Computational Chemistry
16. Machine Learning
17. Biotechnology and Bioengineering
1. The Department of
2. The Department of
3. The National Institutes of Health (NIH),
4. The Food and Drug Administration (FDA),
5. The Environmental Protection Agency (EPA),
6. American Society for
HONORS AND OTHER SPECIAL SCIENTIFIC RECOGNITION
of the USEPA Review Panel on Computational Toxicology & Endocrine Disruptors:
Use of Systems Biology in Hazard Identification & Risk Assessment,
2. Member of the USEPA Review Panel on the Development of High-Throughput Screening Approaches for the Endocrine Disruptor Program, Washington, DC, May, 2003. Invited.
3. Interviewed and reported by Science magazine several times for work on microarrays, bioinformatics, and chemoinformatics, see e.g. http://www.sciencemag.org/content/vol285/issue5429/netwatch.shtml; http://www.sciencemag.org/feature/e-market/benchtop/dnamicro.shl; http://www.sciencemag.org/feature/e-market/benchtop/dnachips.shl
and reported by BioInform magazine on
5. Member of the IUPAC (International
6. First Place Award Winner from Shenzhen Municipal Government for Honoring Oversea Chinese Returnees with Extraordinary Contribution to Shenzhen’s High-Tech Industry, 2002. (Cash award of 120,000 RMB, approx. 15,000 USD)
7. Principal Investigator of three bioinformatics
grants awarded by
of the Scientific Committee of the First Critical Assessment of Microarray Data
Analysis (CAMDA’00), Duke University,
9. Marquis Who's Who in Science and Engineering, Millennium Edition (5th), 2000
11. NIH Forgarty Research Fellowship Award, NIH, Bethesda, Maryland, 1995-1997
Education Committee of China Award for the Advancement of Science and
Technology, for a project on Chemometrics and Chemical Derivation Enhanced Fluorimetry,
13. Education Committee of Hunan Province Award for the Advancement of Science and Technology, for a project on the Research and Application of Chemical Derivation Enhanced Fluorimetry, Changsha, China, 1996
14. Ministry of Mechanical Engineering of China Award for the Advancement of Science and Technology, for a project on the Application of Chemometrics for Data Resolution in Chemistry, Beijing, China, 1995
Invited Speaker of the Japanese Chemical Society at its Third
Graduate Student Award,
Graduate Student Award, Univ. Sci. & Tech. of
1. American Association for the Advancement of Science (AAAS), since 1995
2. American Chemical Society (ACS), since 1994
3. International Chemometrics Society (ICS), since 1994
Classification Society of
5. Society for Biomolecular Screening (SBS), since 2001
for Laboratory Automation (
7. QSAR and Modelling Society, since 1995
8. Chinese Chemical Society (CCS), since 1986
Gerald W. Stockton, Ph.D.
Former Senior Group Leader
Roger G. Perkins, M.Sc.
Director, Scientific Computation
Northrop Grumman Information Technology
(870) 543-7049, 543-7382
John N. Weinstein, M.D., Ph.D.
Laboratory of Molecular Pharmacology
National Cancer Institute
National Institutes of Health
(301) 496-9571, 402-0752(Fax)
Gilles Klopman, Ph.D.
Charles F. Mabery Professor of Research
Department of Chemistry
(216) 368-3618, 368-5921(Fax)
LIST OF PUBLICATIONS (100+ manuscripts and book chapters)
1. Shi L, Tong W, Fang H, Goodsaid F, Frueh FW, Han T, Fuscoe JC, and Casciano DA. QA/QC: Challenges and pitfalls facing the microarray community and regulatory agencies. Expert Review of Molecular Diagnostics, 4(6), 761-777 (2004).
2. Tan Y, Shi L, Tong W, Wang C. Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data. Nucleic Acids Research, 33(1), 56-65 (2004).
3. Shi L, Tong W, Fang H, Fuscoe JC, and Casciano DA. The reality of cross-platform comparability of microarray technology. Science, submitted as Letter, Dec 6, (2004).
4. Shi L, Tong W, Fang H, Scherf U, Han J, Puri RK, Frueh FW, Goodsaid FM, Su Z, Chen JJ, Han T, Fuscoe JC, Xu ZA, Hong H, Xie Q, Perkins RG, and Casciano DA. Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential. Nucleic Acids Research, in preparation (2005).
5. Shi L, Tong W, SU Z, Han T, Han J, Puri RK, Frueh FW, Goodsaid FM, Fang H, Branham WS, Chen JJ, Xu ZA, Harris SC, Hong H, Xie Q, Perkins RG, Fuscoe JC. Characteristics and implications of microarray scanner calibration curves. BMC Bioinformatics, submitted (2005).
6. Fuscoe JC, Branham WS, Melvin CD, Desai VG, Moland CL, Han T, Shi L, Scully A, Delongchamp RR. Technical issues involved in obtaining reliable data from microarray experiments. Regulatory Research Perspectives, 4(2), 2004.
7. Fang H, Tong W, Perkins R, Shi L, Hong H, Cao X, Xie Q, Yim SH, Ward JM, and Dragan YP. Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. BMC Bioinformatics, submitted (2005).
8. Hong H, Dragan YP, Epstein J, Tong W, Teitel C, Chen B, Xie Q, Fang H, Shi L, and Perkins R. Quality control and quality assessment in data analysis for identification of biomarker proteins using surface-enhanced laser description/ionization (SELDI) time-of flight (TOF) mass spectrometry. BMC Bioinformatics, submitted (2005).
9. Liao C, Liu B, Shi L, Zhou J, Lu XP. Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators. European Journal of Medicinal Chemistry, in press (2004)
10. Li Z, Liao C, Ko BC, Shan S, Tong EH, Yin Z, Pan D, Wong VK, Shi L, Ning ZQ, Hu W, Zhou J, Chung SS, Lu XP. Design, synthesis, and evaluation of a new class of noncyclic 1,3-dicarbonyl compounds as PPARalpha selective activators. Bioorganic and Medicinal Chemistry Letter, 14(13), 3507-3511 (2004).
11. Tan Y, Shi L, Wang C, Hwang GTG, Tong W. Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Computational Biology and Chemistry, 28(3), 235-243 (2004).
12. Tong W, Xie Q, Hong H, Shi L, Fang H, Perkins R, Petricoin EF. Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity. Environmental Health Perspectives, 112, 1249-1254 (2004).
13. Tong W, Xie Q, Hong H, Fang H, Shi L, Perkins R, Petricoin EF. Using decision forest to classify prostate cancer samples based on SELDI-TOF MS data – assessing chance correlation and prediction confidence. Environmental Health Perspectives, 112(16), 1622-1627 (2004).
14. Su ZQ, Pan DS, Shan S, Hu WM, Ning ZQ, Li ZB, Shi LM, Liao CZ, Zhang DJ, Qiao W, Lu XP. The Important role of biochemoinformatics in drug discovery and development. Chinese Journal of New Drug. In press (2004).
15. Fang H, Tong W, Shi L, Jakab RL, Bowyer JF. cDNA arrays are sensitive tools for detecting significant differences in gene expression patterns within brain regions. DNA and Cell Biology, 23(10), 661-674 (2004).
16. Hong H, Tong W, Perkins R, Fang H, Xie Q, Shi L. Multi-class decision forest - a novel pattern recognition method for multi-class classification in microarray data analysis. DNA and Cell Biology, 23(10), 685-694 (2004).
17. Tong W, Harris S, Cao X, Fang H, Shi L, Sun H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Casciano D. Development of public toxicogenomics software for microarray data management and analysis. Mutation Research, 549(1-2), 241-253 (2004).
18. Su ZQ, Lu XP, Shi LM. The application of
multithreading parallel and distributed computing in construction of Oracle
database for storage and retrieval of chemical structure data. Computers and Applied Chemistry (
19. Shi LM. Advances in the mining of DNA microarray data. Manuscript in preparation (2003). [This manuscript is based on information I provided on www.gene-chips.com under "Data Mining" section. This site was reviewed favorably by Science magazine, 1999 August 6; 285(5429):799, and many other sites/journals]
20. Liao C, Xie A, Shi L, Zhou J, Lu X. Eigen value analysis of peroxisome proliferator-activated receptor γ agonists. Journal of Chemical Information and Computer Sciences, 44(1), 230-238 (2004).
21. Liao C, Xie A, Zhou J, Shi L, Li Z, Lu X. 3D QSAR studies on peroxisome proliferator-activated receptor γ agonists using CoMFA and CoMSIA. Journal of Molecular Modeling, 10(3), 165-177 (2004).
22. Xie A, Liao C, Li Z, Ning Z, Hu W, Lu X, Shi L, Zhou J. Quantitative structure-activity relationship study of histone deacetylase inhibitors. Current Medicinal Chemistry – Anti-cancer Agents, 4(3), 273-299 (2004).
23. Xie A, Liao C, Li Z, Ning Z, Hu W, Lu X, Shi L, Zhou J. Quantitative structure-activity relationship study of bisphosphonates. Internet Electronic Journal of Molecular Design, 3, 622-650 (2004).
24. Xie AH, Liao CZ, Li ZB, Ning ZQ, Hu WM, Lu XP, Zhou JJ, Shi LM. Design, synthesis, and biological activities of novel histone deacetylase inhibitors. manuscript in preparation (2004).
25. Xie AH, Li BY, Shan S, Deng T, Li ZB, Ning ZQ, Hu WM, Shi LM, Zhou JJ, Lu XP. New development of histone deacetylase inhibitors as anticancer agents. Chinese Journal of New Drugs, In press (2004).
27. Liao CZ, Xie AH, Li ZB, Lu XP, Zhou JJ, Shi LM. Construction of a virtual combinatorial chemical library by using SMILES strings for the discovery of anti type 2 diabetic drugs. manuscript in preparation (2004).
28. Shi L, Tong W, LU XP. Biochemoinformatics: integrating bioinformatics and chemoinformatics for drug discovery and development, European Biopharmaceutical Review, 59-62, Autumn (2003). Invited review
W, Cao X, Harris S, Sun H, Fang H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins
R, Shi L, Casciano D. ArrayTrack - supporting
toxicogenomic research at the U.S. Food and
30. Shi L, Hu W, Su Z, Lu X, Tong W. Chapter 13: Microarrays: technologies and applications. in Fungal Genomics, Volume 3 of Applied Mycology and Biotechnology, D. K. Arora and G. G. Khachatourians (Editors), Elsevier Science, pp.271-293 (2003). ISBN: 0-444-51442-2. Invited book chapter
31. Su ZQ, Liao CZ, Xie AH,
Lu XP, Shi LM. An Oracle database for efficient storage
and retrieval of chemical structure data. Computers and Applied
32. Shi LM, Su ZQ, Xie AH, Liao CZ, Qiao W, Zhang DJ, Shan S, Pan DS, Li ZB, Ning ZQ, Hu WM, Lu XP. An integrated biochemoinformatics system for drug discovery: managing and mining chemical structure information, biological activity fingerprints, and gene expression profiling patterns. in The Frontiers of Biochip Technologies, W.L. Xing and J. Cheng (Editors), Kluwer Academic Press, in press (2004). Invited book chapter
L. DNA chip technology: more interesting applications to open up in Life
Sciences, in “50 Years of DNA”,
pp.57-59, April 2003. ISBN 0-9545135-0-9. (A Business Weekly publication in association with The Wellcome Trust,
34. Tong W, Welsh WJ, Shi L, Fang H, Perkins R. Structure-activity relationship approaches and applications. Environmental Toxicology and Chemistry, 22(8), 1680-95 (2003).
LM, Tong WD. Data mining: an integrated approach
for drug discovery. in Biochips: Technology and Applications, W.L Xing and J. Cheng
36. Liao CZ, Deng T, Shan S, Pan DS, Li ZB, Ning ZQ, Hu WM, Shi LM, Zhou JJ, Lu XP. Current strategies of developing novel anti type 2 diabetic drugs via PPAR. Chinese Journal of New Drugs, 13(1), (2004).
37. Shi LM. An integrated biochemoinformatics system and its applications to drug discovery. in Facing the Frontiers of the World’s Life Sciences – Recent Innovative Progresses in Functional Genomics and Biochips Made by Some Chinese Universities, Department of Education of China, (2002).
38. Shi L, Tong W, Fang H, Xie Q, Hong H, Perkins R, Wu J, Tu M, Blair RM, Branham WS, Waller C, Walker J, Sheehan DM. An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity. SAR QSAR Environ Res 13(1):69-88 (2002).
39. Hong H, Tong W, Fang H, Shi L, Qian X, Wu J, Perkins R, Walker JD, Braham W, Sheehan D. Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts. Environ Health Perspectives 110(1), 29-36 (2002).
40. Branham WS, Dial SL, Moland CL, Hass B, Blair R, Fang H, Shi L, Tong W, Perkins R, Sheehan DM. Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor. Journal of Nutrition, 132, 658-664 (2002).
41. Shi L, Arrays, molecular diagnostics, personalized therapy, and informatics (invited editorial). Expert Review of Molecular Diagnostics, 1(4), 363-365 (2001).
W, Perkins R, Wu J, Shi L, Tu M, Fang H, Blair R, Branham W, Sheehan DM.
An integrated computational approach for prioritizing potential estrogens. Proceeding
of the International Symposium on Environmental Endocrine Disruptors, Dec,
43. Fan Y, Shi LM, Kurt KW, Pommier Y, Weinstein JN. Quantitative structure-antitumor activity relationships of camptothecin analogues: cluster analysis and genetic algorithm-based studies. Journal of Medicinal Chemistry, 44(20), 3254-3263 (2001).
44. Fang H, Tong W, Shi LM, Blair R, Perkins R, Branham W, Hass BS, Xie Q, Dial SL, Moland CL, Sheehan DM. Structure-activity relationships of estrogens for a large diverse set of natural, synthetic and environmental chemicals. Chem. Res. Toxicol., 14(3), 280-294 (2001).
45. Shi L M, Fang H, Tong W, Wu J, Perkins R, Blair R, Branham WS, Sheehan DM. QSAR models using a large diverse set of estrogens. Journal of Chemical Information and Computer Sciences, 41(1), 186-195 (2001).
LM, Fan Y, Lee JK,
47. Blair RM, Fang H, Branham WS, Hass B, Dial SL, Moland CL, Tong W, Shi L, R. Perkins, and D. M. Sheehan. The estrogen receptor relative binding affinities of 188 natural and xenochemicals: structural diversity of ligands. Toxicological Sciences, 54(1):138-153 (2000).
48. Perkins R, Anson J, Blair R, Branham W, Chen Y, Dial S, Fang H, Hass B, Jackson M, Lu M, Meehan J, Moland C, Nossaman R, Shi LM, Tong W, Welsh W, Sheehan D. The estrogen knowledge base: prototype toxicological knowledge base and predictive models for endocrine disrupting compounds. Society of Environmental Toxicology and Chemistry, Book chapter (2000).
49. Shi LM, Fan Y, Myers TG, Paull KD, Weinstein JN. Mining the anticancer activity database generated by the NCI anticancer drug discovery program using statistical and artificial intelligence techniques. Mathematical Modelling and Scientific Computing, Vol. 9, 1998.
50. Fan Y, Pommier Y, Kohn KW, Shi LM, Weinstein JN. Molecular modeling studies of the DNA - topoisomerase I ternary cleavable complex with camptothecin. Journal of Medicinal Chemistry, 41(13):2216-2226 (1998).
51. Shi LM, Fan Y, Myers TG, Paull KD, Friend SH, Weinstein JN. Mining the NCI anticancer drug discovery database: genetic function approximation for the QSAR study of anticancer ellipticine analogs. Journal of Chemical Information and Computer Sciences, 38(2):189-199 (1998).
52. Shi LM, Myers TG, Fan Y, O'Conner PM, Paull KD, Friend SH, Weinstein JN. Mining the NCI anticancer drug discovery database: cluster analysis of ellipticine analogs with p53-inverse and CNS-selective patterns of activity. Molecular Pharmacology, 52(2):241-251 (1998).
53. Shi LM,
Fan Y, Myers TG, Weinstein JN. Genetic function approximation in the
molecular pharmacology of cancer. Proceedings
of the 1997 International Conference on Neural Networks (ICNN'97), Vol. 4,
54. Klopman G, Shi LM, Ramu A. Quantitative structure-activity relationships study of multidrug resistance reversal agents. Molecular Pharmacology, 52(2):323-334 (1997).
Z, Hu F, Liang B, She H, Li M, Shi L. Neural network in QSAR studies:
estimation and prediction of biological activity for N,N-dimethyl-2-bromo
(substituted phenyl) ethylamine derivatives. J. Med. Chem. of
56. Li Z, Hu F, Liang B, Yu B, Shi LM, Li M, Sakai M. Neural networks in QSAR studies: estimation and prediction of biological activity for N-(substituted phenoxyethyl)cyclopropylamines. Acta Pharm. Sinica (Yaoxue Xuebao) 31(1):38-42 (1996).
57. Li Z, Liu S, Shi L, Pan Z, Lou M, Li M, Yu B. Artificial neural networks (ANN) as applied to quantitative spectroscopic analysis. J. Appl. Sci. (Yingyong Kexue Xuebao) 13(2):179-183 (1995).
58. Fei W, Liang B, Shi L,
An D, Li Z. Effective processing of structural information for organic
compounds using computer - expression and recognition of molecular skeletons. J.
59. Xia SQ, Xu PL, Sun JH, Pan ZX, Zhang MS, Shi LM. Determination of six aromatic compounds by using target factor analysis-UV spectrometry. Fresenius' J. Anal. Chem. 351(2-3):325-327 (1995).
LM. Chapter XVI: Knowledge-based systems in
chemical engineering, in Chinese translation of T.E. Quantrille
& Y.A. Liu's book: Artificial
Intelligence in Chemical Engineering (Academic Press, USA, 1991) (J. Zha, ed.).
LM. Chapter XVII: Artificial neural networks in
chemical engineering, in Chinese translation of T.E. Quantrille
& Y.A. Liu's book: Artificial Intelligence
in Chemical Engineering (Academic Press, USA, 1991) (J. Zha,
62. Li Z, Yu B, Qian F, Shi L, Pan Z, Nie S. Fading recursive filtering aided spectroscopy. An optimal adaptive algorithm, J. Appl. Sci. (Yingyong Kexue Xuebao) 12(1):150-158 (1994).
63. Li ZL., Yaegashi O, Liang BX, Shi LM. Neural networks used in chromatography. (I). Prediction of GC retention parameters. Chem J. Chinese Univ. (Gaodeng Xuexiao Huaxue Xuebao) 15(12):1775-1777 (1994).
64. Yu B, Li M, Liu A, Li Z, Shi L, Pan Z. Some novel methods based on recursive optimal estimation. Applications to analytical chemistry. Analytica Chimica Acta 277(2):199-204 (1993).
65. Zhou J, Xu Z, Shi L, Zhang Y, Cai S. Application of artificial neural networks in prediction of material properties and problem diagnosis of chemical process. Engineering Chemistry and Metallurgy (Huagong Yejin) 14(1):57-62 (1993).
66. Zhong L, Shi L Quantitative analysis of complex spectra using artificial neural networks - analysis of protein in grain by near infrared spectroscopy. Chinese Science Bulletin (Kexue Tongbao) 38(1):68-71 (1993).
X, Shi L. Fuzzy pattern recognition of the mode of fluidization. in Selected Papers of
Engineering Chemistry and Metallurgy (
ZL, Shi LM. Chapter V: Chemometrics: its methodology and application. in Frontiers of Modern
Chemistry (Huaxue Qianyan Luntan) (J. Chen, ed.).
LM Chapter XI: Applications of neural networks in
chemistry. in Frontiers
of Modern Chemistry (Huaxue Qianyan
Luntan) (J. Chen, ed.).
70. Shi L, Lou M, Li M, Li Z. Resolution of overlapped chromatograms by using the Kalman filter. Chinese Science Bulletin (Kexue Tongbao) 37(9):804-806 (1992).
71. Shi L, Liu X, Lin A, Zhuo Z. Kalman filtering spectrophotometric analysis of mixed synthetic colorants. Anal. Chem. (Fenxi Huaxue) 20(12):1365-1368 (1992).
72. Shi L, Zhou J, Liu X, Sun D, Xu Z. Structure-activity relation of chemical hybridizing agent using artificial neural networks. Chemistry (Huaxue Tongbao) (6):46-48, 37 (1992).
73. Shi L, Tang H, Zhou J. Applications of neural networks in chemistry. Chemistry (Huaxue Tongbao) (11):46-49 (1992).
74. Zhong L,Shi L. Quantitative analysis on uv spectra of six amino acids by artificial neural network. Acta Biophysica Sinica (Shengwu Wuli Xuebao) 8(4):706-710 (1992).
75. Shi L, Li Z, Xu Z, Pan Z. Simultaneous analysis of cobalt(II), nickel(II), copper(II), zinc(II), and cadmium(II) by spectrophotometry and the Kalman filter. Journal of Chemometrics 5(3):193-199 (1991).
L, Xu Z, Pan Z, Liu X, Gao Y, Qian
F, Nie S, Li Z. Application of the Kalman filter algorithm to the simultaneous determination
of four amino acids by direct UV spectrophotometry. Journal of Micronutrient Analysis (
77. Li Z, Lin H, Li M, Shi L, Yu R. Fluorimetric study on the inclusion complex reaction of cyclodextrin with phenols. Chem. J. Chinese Univ. (Gaodeng Xuexiao Huaxue Xuebao) 12(1):30-32 (1991).
78. Li Z, Yu R, Shi L, Xu J, Zhang M, Wang Q. Valence-state speciation of sulfur by x-ray fluorescence spectrometry and Kalman filtering. Ana. Chim. Acta 248(1):257-261 (1991).
79. Liu X, Shi L, Xu Z, Pan Z, Li Z, Gao Y. Partial Least-Squares (PLS) regression and spectrophotometry as applied to the analysis of multicomponent mixtures. Chin. Chem. Lett. 2(3):233-236 (1991).
L, Pan Z, Wang Q. Resolution of overlapped x-ray fluorescence
spectra using the Kalman filter. Microcomputer Applications (
81. Shi L, Xu Z, Yan Y, Jin M, Pan Z, Li Z. Rapid determination of protein in millet by Fourier transform near-infrared (FTNIR) diffuse reflectance spectroscopy. Chin. Chem. Lett. 1(3):247-250 (1990).
82. Shi L, Xu Z, Liu X. Fuzzy set theory and its applications in chemistry. Chemistry (Huaxue Tongbao) (7):20-25 (1990).
83. Li ZL, Li ML, Qian F, Shi LM, Yu RQ. Kalman filtering-titrimetry: potentiometric titration of benzalkonium bromide. Acta Pharm. Sinica (Yaoxue Xuebao) 25(1):35-43 (1990).
84. Xu J, Zhang M, Shi L. Representation and recognition of chemical structures. Chemistry (Huaxue Tongbao) (11):58-64, inside back cover (1990).
85. Pan Z, Xia S, Si S, Zhang M, Shi L, Liu X. Target factor analysis: UV spectrophotometry for the simultaneous determination of six amino acids. Journal of Chemometrics 4(4):323-330 (1990).
86. Li Z, Li M, Shi L, Yu R. Study on Kalman filtering titrimetric method. II. Model of thermodynamically non-equilibrium titration. Anal. Chem. (Fenxi Huaxue) 18(11):1044-1047 (1990).
87. Li M, Shi L, Li Z, Yu R. Partial least squares spectrophotometry for simultaneous microdetermination of manganese, copper, zinc and cadmium. Anal. Lab. (Fenxi Shiyanshi) 9(6):12-15 (1990).
88. Li Z, Shi L, Li M, Lin H, Yu R. A highly sensitive and selective method for trace multicomponent analysis - Kalman filtering spectrophotometry. Acta Chim. Sinica (Huaxue Xuebao) 48(11):1101-1107 (1990).
89. Li Z, Li M, Shi L, Yu R. Study of chemical equilibrium by Kalman filtering spectrometry. Chem. J. Chinese Univ. (Gaodeng Xuexiao Huaxue Xuebao) 11(8):825-827 (1990).
90. Xia S, Pan Z, Zhang M,
Liu X, Shi L, Li Z. Determination of aromatic compounds by factor
analysis- spectrophotometry. J. Univ. Sci. & Tech.
91. Shi L, Xu J, Cai W, Zhang M. Expert systems for design of organic synthetic pathways. Chemical World (Huaxue Shijie) 31(4):151-156 (1990).
92. Li Z, Shi L, Li M, Yu R. Kalman filter fluorometry and its application to simultaneous determination of mixture of fluorescent dye. Chem. J. Chinese Univ. (Gaodeng Xuexiao Huaxue Xuebao) 11(3):245-249 (1990).
Z, Qiu X, Shi L, Qian F, Lin H. Inclusion
chromatography and its application in pharmaceutical analysis. J. Pharmaceutical Sci.
94. Li Z, Li M, Lin H, Shi L, Yu R. Study on the linear combination of multiwavelength data - improvement of selectivity for spectrophotometry. Anal. Chem. (Fenxi Huaxue) 18(3):201-205 (1990).
95. Li Z, Shi L, Li M, Yu R. Application and development of organic and azo reagents for inorganic fluorometry analysis. Anal. Chem. (Fenxi Huaxue) 18(8):780-790 (1990).
96. Li Z, Shi L, Li M, Yu R. Chemometrics and its development in spectrophotometric analysis in China. Anal. Chem. (Fenxi Huaxue) 18(6):588-595 (1990).
97. Li M, Shi L, Liu S, Li Z, Yu R. Linear combination of spectrophotometry of multi-wavelength data and its applications. Chem. J. Chinese Univ. (Gaodeng Xuexiao Huaxue Xuebao) 11(7):693-697 (1990).
98. Qian F, Shi L, Li Z. Simultaneous determination of gas mixtures containing propane and n-hexane by IR spectrometry - application of the Kalman filter and multi-wavelength regression method. Physical and Chemical Testing (Lihua Jianyan, Huaxue Fence) 25(3):138-139, 141 (1989).
99. Shi L, Zhang M, Li Z. Expert systems and modern analytical chemistry. Anal. Chem. (Fenxi Huaxue) 17(10):949-956 (1989).
100. Liu X, Lin A, Shi L. Microdetermination of multicomponents with Kalman filtering on the DMS/VIS spectrophotometer-IBM PC/AT on-line system. Anal. Chem. (Fenxi Huaxue) 17(12):1125-1127, 1146 (1989).
Shi L, Zhang M, Liu
X, Lin A, Jia Z. On-line simultaneous determination
of multicomponent mixtures by using UV spectrophotometry and Kalman
filter. Chem. J. of
102. Shi L, Zhang M, Li Z. Expert system and its applications to chemistry. Nature J. (Ziran Zazhi) 11(6):412-416 (1988).
Liu X, Lin A, Shi L, Zhang M. Simultaneous
determination of seven organic compounds by Kalman
filter-spectrophotometry. J. Univ. Sci. & Tech.
104. Li Z, Zhang M, Shi L. Chemometrics: An Outline and Its Progress. Nature J. (Ziran Zazhi) 11(9):675-677 (1988).
105. Yang G, Yu Y, Shi L. On the chromogenic reaction of 6-Br-BTAQS with zinc(II). Anal. Lab. (Fenxi Shiyanshi) 5(6):4-6 (1986).
Yang G, Yu Y, Shi L. Study on the
Synthesis of the New Chromogenic Reagent 6-Br-BTAQS
and Its Application to the Determination of Nickel(II).
107. Li Z, Chen J, Shi L. 5-Br-PADAP as a spectrophotometric reagent for zirconium (IV) in the presence of Tween-80. Chemical Reagents (Huaxue Shiji) 7(6):330-332 (1985).
108. Li Z, Lin H, Shi L, Chen J. Colorimetric reaction of zirconium (IV) with Eriochrome Cyanine R in the presence of surfactants. Anal. Chem. (Fenxi Huaxue) 13(12):920-923 (1985).
Shi L. QC metrics and thresholds for assessing the overall
quality of a microarray study, The 44th Annual Meeting of the Society of
Shi L. Pitfalls and challenges of microarray-based pharmacogenomic
and toxicogenomic studies, International Forum on Biochip Technology 2004 (www.capitalbiochip.com/IFBT2004/),
Shi L. Toxicoinformatics: integrating bioinformatics, chemoinformatics,
and chemometrics for omics-based toxicological
studies, International Conference on Chemometrics and Bioinformatics in
Chemistry and Medicine (cheminfo.tongji.edu.cn/ccba2004/),
Shi L. Quality control (QC) metrics and thresholds for assessing
the overall quality of a microarray study, The 2nd
annual conference of the MidSouth Computational
biology and BIOinformatics Society
(MCBIOS 2004, www.mcbios.org), Peabody
L. ArrayTrack: Managing, analyzing, and interpreting
microarray data in toxicogenomic research at the NCTR/FDA, AMET/Toxicology
special interest group meeting at the 9th Annual Meeting of the
Society for Biomolecular Screening (SBS),
Shi L. Data mining in drug discovery, Symposium at
Shi L, ArrayTrack – Supporting toxicogenomic research at the
XP, Li ZB, Ning ZQ, Shi LM, and Hu WM, Application of chemical genomics
approach in identifying novel PPAR agonists with in vivo anti-diabetic and lipid-modulating activities. Invited
lecture at The 3rd Annual Knowledge Foundation's International Conference on
BIOCHIPS 2003: Technology Development and Application,
9. Shi LM, Su ZQ, Xie AH, Liao CZ,
Qiao W, Zhang DJ, Li ZB,
Ning ZQ, Hu WM, Lu XP, Integrating chemical structures, biological
activity fingerprints, and gene expression profiling for drug discovery. Presentation on “Informatics challenges in
pharmacogenomics” at the 225th
ACS National Meeting,
10. Xie AH, Liao CZ, Li BY, Li ZB, Ning ZQ, Hu WM, Lu XP, Zhou JJ, Shi LM, Quantitative structure-activity relationship study of histone deacetylase inhibitors. Presentation at the 225th ACS National Meeting,
LM. An integrated biochemoinformatics system for
drug discovery. Invited lecture at the International Forum on Biochip
LM. DNA microarray and data mining: from spots to results.
Invited lecture at the XXI WAASPaLM (World Association of Societies of Pathology and
Laboratory Medicine) Congress, Symposium I: Microchips, Microarrays
and Micronisation in Laboratory Diagnostic
LM. DNA microarray and data mining. Invited lecture at the
Chinese Biopharmaceutical Association (CBA) annual meeting,
LM. Data mining: an integrated approach for drug
discovery. Invited lecture at the International Forum on Biochip Technologies,
15. Perkins R, Anson J, Tong W, Branham W, Blair R, Hass B, Fang H, Shi L, Chen Y, Meehan J, Nossaman R, Welsh W, Sheehan D. A knowledge base for mining of endocrine disruptor data, Book of Abstracts, 217th ACS National Meeting, Anaheim, Calif., March 21-25 (1999), CINF-005 Publisher: American Chemical Society, Washington, D. C.
16. Shi LM, Tong W, Perkins R, Chen Y, Tu M, Meehan J, Nossaman R, Welsh WJ, Fang H, Branham W, Blair B, Hass B, Sheehan D. QSAR models for multiple estrogenic endpoints, 1999 Keystone Symposia on Endocrine Disruptors (B5), Granlibakken Resort, Tahoe City, California, January 31 - February 5, 1999.
17. Shi LM, Tong W, Perkins R, Chen Y, Fang H, Poirier L, Sheehan D. Classification methods for toxicity prediction and anticancer drug discovery, Joint Annual Meeting of the Classification Society of North America and the Psychometric Society, Urbana, Illinois, June 17-21, 1998, p98.
18. Shi LM, Fan Y, Myers TG, Weinstein JN. Genetic function approximation in the molecular pharmacology of cancer, Proceedings of the 1997 International Conference on Neural Networks (ICNN'97), Vol. 4, 2490-2493, IEEE, Houston, Texas, 1997. ISBN: 0-7803-4122-8
19. Shi LM, Fan Y, Myers TG, Weinstein JN. Application of cluster analysis and genetic function approximation to the discovery of anticancer drugs, Classification Society of North America 1997 Conference, Washington, DC, June 12-15, 1997. pp32-33.
20. Fan Y, Shi LM, Myers TG, Weinstein JN. Quantitative
structure-activity relationships of camptothecin
analogs, 213th Annual Meeting of the American Chemical Society,
LM, Fan Y, Myers TG, Paull
KD, Weinstein JN. Mining the NCI anticancer drug screen database using genetic
function approximation (GFA) and cluster analysis, 213th Annual Meeting of the
American Chemical Society,
LM, Myers TG, Fan Y, O'Conner PM, Paull KD, Friend SH, Weinstein JN. Mining the NCI
anticancer drug screen database: clustering and QSAR studies on candidate
p53-inverse agents, Proceedings of the American Association for Cancer
Research, vol. 38, p232 (Paper #1563). 88th AACR
1. Lu XP, Li ZB, Ning ZQ, Shi LM, Wu ZW, Deng T. Preparation and pharmaceutical use of novel retinoic acid analogs. Filed with USPTO in 2002. US60/393456.
2. Lu XP, Li ZB, Liao CZ, Shi
LM, Liu ZD, Ning ZQ, Shan S, Deng T, Mao BS. Noncyclic
1,3-dicarbonyl compounds as dual PPAR agonists with
potent antihyperglycemic and antihyperlipidemic
activity. Filed with USPTO on
3. Li ZB, Lu XP, Liao CZ, Shi
LM, Liu ZD, Mao BS, Ning ZQ, Shan S, Deng T. Substituted arylalcanoic acid derivatives as PAPR agonists with potent antihyperglycemic and antihyperlipidemic
activity. Filed with USPTO on
Novermber 26, 2002. US60/429221. WO04048333A1
4. Lu XP, Li ZB, Ning ZQ, Shi LM, Wu ZW, Xie
AH, Shan S. Novel bisphosphonate complexes for the
prevention and treatment of osteoporosis and other bone diseases. Filed with
Chinese patent office in 2002.
5. Lu XP, Li ZB, Xie AH, Shi LM, Li BY, Ning ZQ, Shan S, Deng T. Novel histone deacetylase inhibitors and their pharmaceutical uses. Filed with USPTO in 2003.