LEMING SHI, Ph.D.

(Data Mining, Bioinformatics, Chemoinformatics, Biochips, and Drug Discovery)

 

Home:                    

Office:

14825 Chambery Drive

Center for Toxicoinformatics

Little Rock, AR 72211

National Center for Toxicological Research, US FDA

U.S.A.

3900 NCTR Rd., HFT-020

+1-501-227-8590(H)

Jefferson, AR 72079, USA

+1-501-227-8590(Fax)

+1-870-543-7387(O)

lmshi@helix.nih.gov

+1-870-543-7662(Fax)

lemingshi@yahoo.com

Leming.Shi@fda.hhs.gov

www.gene-chips.com

www.fda.gov/nctr/

 

 

OBJECTIVES

 

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.

 

EDUCATION

 

Ph.D. in Computational Chemistry                                                            9/1988-7/1991

Laboratory of Computational Chemistry, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China. Thesis: Chemometrics-assisted resolution of analytical spectra and studies of structure-activity relationships of pesticides and pharmaceuticals. Supervisor: Prof. Zhihong Xu

 

M.Sc. in Computational Chemistry and Chemometrics                             9/1985-7/1988

Department of Modern Chemistry, University of Science and Technology of China, Hefei, China. Thesis: The design of an expert system for planning organic synthetic pathways and applications of chemometrics in chemistry. Supervisor: Prof. Maosen Zhang

 

B.Sc. in Analytical Chemistry                                                                    9/1981-7/1985

Department of Chemistry and Chemical Engineering, Hunan University, Changsha, China. Thesis: Synthesis of a novel chromogenic reagent, 6-Br-BTAQS, and its applications in analytical chemistry. Supervisor: Prof. Guifa Yang

 

EMPLOYMENT AND MAIN RESPONSIBILITIES

 

Computational Chemist (Principal Investigator in Biochemoinformatics) 4/2003-Present

National Center for Toxicological Research, FDA, Jefferson, Arkansas.  Projects: Quality control and quality assurance of microarrays; Data mining in the areas of genomics, proteomics, and metabonomics as applied to toxicology and drug discovery/development; Systems toxicology.

 

Co-founder, Director of Informatics                                                          5/2001-4/2003

Chipscreen Biosciences, Ltd., Shenzhen, China.  Leading the informatics department to apply state-of-the-art methodologies of computer-aided drug design (CADD) to rationally design novel small molecule drug candidates for treating type 2 diabetes, cancer, osteoporosis, and menopause syndrome; Leading the efforts in designing and implementing an integrated biochemoinformatics software system (TASS) for the efficient storage, management, integration, mining, visualization, and interpretation of various kinds of data (genomics, combinatorial chemistry, HTS, and gene expression profiling) being generated in the Company’s innovative, chemogenomics-based drug discovery programs; Responsible for and successful in grant applications to various funding agencies to support on-going R&D projects in the areas of bioinformatics and chemoinformatics; Responsible for directing several Ph.D. candidates from the Chinese Academy of Sciences.

 

Senior Scientist                                                                                          7/2000-5/2001

BASF Corp., Princeton, New Jersey.  Projects: Data mining for massive gene expression data from DNA microarrays; Design of combinatorial libraries; Data mining for high-throughput screening; Molecular modeling, quantitative structure-activity relationships, pharmacophore identification and 3D database searching, and molecular diversity analysis; Computer-aided molecular design; Supervising and training of organic and computational chemists within the Company to apply cutting-edge methodologies for molecular design and data mining.

 

Senior Research Chemist                                                                           8/1999-6/2000

American Cyanamid Company (a subsidiary of American Home Products Corp., now Wyeth), Princeton, New Jersey.  Projects: Data mining for massive gene expression data from DNA microarrays; Design of combinatorial libraries; Data mining for high-throughput screening; Molecular modeling, quantitative structure-activity relationships, pharmacophore identification and 3D database searching, and molecular diversity analysis; Computer-aided molecular design.  Supervising and training of organic and computational chemists within the Company to apply cutting-edge methodologies for molecular design and data mining.

 

Senior Computational Chemist                                                                  12/1997-8/1999

R.O.W. Sciences, Inc. (now Northrop Grumman Information Technology), National Center for Toxicological Research, FDA, Jefferson, Arkansas.  Projects: Data mining, classification and clustering, QSAR, pharmacophore identification, and molecular diversity analysis for priority setting of tens of thousands of compounds that may bind to the estrogen receptor (ER); Proposed and developed an integrated, "4-Phases" computational approach to priority setting in screening large libraries of compounds; Structure-carcinogenicity/mutagenicity relationships of NTP-tested compounds; Development of a highly rated Web site on gene-chips and DNA microarrays (http://www.gene-chips.com), which was reviewed favorably and recommended several times by Science magazine (1999 August 6; 285(5429): 799, etc.) and cited by journals like Nature.  The high-profile projects at the FDA helped to attract attention from management teams of both FDA and EPA, and resulted in a substantial grant for supporting the research group.

 

Visiting Fellow                                                                                           9/1995-12/1997

Laboratory of Molecular Pharmacology, National Cancer Institute, NIH, Bethesda, Maryland, with Dr. John N. Weinstein.  Projects: Data mining and visualization of large databases (structures, biological activities, and targets or modulators) generated by the NCI anticancer drug discovery program; Identification of CNS- and p53-mutation selective anticancer agents; Pharmacophore identification and 3D database searching; Molecular modeling of DNA-topoisomerase I ternary cleavable complexes with camptothecins.

 

Research Associate                                                                        9/1994-9/1995

Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, with Prof. Gilles Klopman.  Projects: 2D substructural QSAR studies of multidrug resistance reversal agents in cancer; Prediction of carcinogenicity, mutagenicity, and acute toxicity of several sets of diverse compounds; Metabolism study using the META program.

 

Assistant and Associate Research Professor                                               7/1991-8/1994

Laboratory of Computational Chemistry, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China.  Projects: Several award-winning projects on the application of chemometrics and artificial neural networks in molecular design and data mining in analytical chemistry; Developed (in C) a comprehensive chemometrics software package.

 

Assistant and Vice President                                                                      7/1992-8/1994

Beijing BioMat Biotechnology and Material Sciences Engineering Research & Development Center, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China.  Responsible for the overall business development of the Center and negotiations with industrial partners on cooperative projects and technology transfer deals.

 

RESEARCH INTERESTS

 

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

 

PROFESSIONAL EXPERTISE

 

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

 

COMPUTER SKILLS

 

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.

 

RECENT TRAINING/CONFERENCES/SEMINARS

 

1.      Chemistry and Biology: Partners in Decoding the Genome, Bethesda, Maryland, March 15-16, 2004.

2.      The Second Committee Meeting of IUPAC Task Force on Biochips and Nanotechnology, London, U.K., December 2-4, 2002. Invited and funded by the IUPAC.

3.      International Forum on Biochip Technologies, Beijing, China, November 9-13, 2002. Invited and funded by the organizing committee.

4.    The First Committee Meeting of IUPAC Task Force on Biochips and Nanotechnology, Palm Springs, California, January 28, 2002. Invited and funded by the IUPAC.

5.      LabAutomation2002, Palm Springs, California, January 28-30, 2002.

6.      Gene Expression and Proteomics in Environmental Health Research, National Institutes of Health, Bethesda, Maryland, December 3-4, 2001.

7.    221st American Chemical Society National Meeting, San Diego, CA, April 1- 5, 2001.

8.      HTS Technologies, Stuttgart, Germany, December 4-6, 2000. (IBC)

9.      International Forum on Biochip Technologies, Beijing, China, October 11-14, 2000. Invited and funded by the organizing committee.

10.   Bioinformatics Symposium, Princeton University, January 19, 2000.

11.   Innovative Computational Applications: The Interface of Library Design, Bioinformatics, Structure Based Drug Design and Virtual Screening, San Francisco, California, October 25-27, 1999. (IIR)

12.   1999 Keystone Symposia on Endocrine Disruptors (B5), Tahoe City, California, January 31 - February 5, 1999.

13.   Drug Discovery Technology'98: Breaking the Bottleneck: Innovation and Speed in Drug Discovery, Boston, Massachusetts, August 10-13, 1998. (IBC)

14.   DNA Microarray: Current Technology and Future Applications Workshop, Bethesda, Maryland, July 14-15, 1998. (FDA)

15.   Short course on clustering during the Joint Annual Meeting of the Classification Society of North America and the Psychometric Society, Urbana, Illinois, June 17-21, 1998.

16.   215th American Chemical Society National Meeting, Dallas, Texas, March 29 - April 2, 1998.

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

 

1.      Computers and Applied Chemistry (China), since 2000

2.      Expert Review of Molecular Diagnostics (UK), since 2001

 

JOURNAL REFEREE

 

1.      Journal of Chemical Information and Computer Science

2.      Journal of Medicinal Chemistry

3.      Molecular Pharmacology

4.      Bioinformatics

5.      Briefings in Bioinformatics

6.      Trends in Biotechnology

7.      BioTechniques

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

 

GRANT REVIEWER

 

1.       The Department of Energy, USA

2.       The Department of Agriculture, USA

3.       The National Institutes of Health (NIH), USA

4.       The Food and Drug Administration (FDA), USA

5.       The Environmental Protection Agency (EPA), USA

6.       American Society for Microbiology, USA

 

HONORS AND OTHER SPECIAL SCIENTIFIC RECOGNITION

 

1.       Member of the USEPA Review Panel on Computational Toxicology & Endocrine Disruptors: Use of Systems Biology in Hazard Identification & Risk Assessment, Washington, DC, May 11, 2004.

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

4.       Interviewed and reported by BioInform magazine on “Solutions: China’s Chipscreen builds an integrated bio-chemoinformatics system” (http://www.bioinform.com/), BioInform, 7(12), p.3, March 24, 2003

5.       Member of the IUPAC (International Union of Pure and Applied Chemistry) Task Force on Biochips and Microtechnology, since 2001

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 China’s Department of Science and Technology, 2002: a) Informatics system for microarray gene expression; b) Prediction of structure and function of proteins; and c) Grid computing for drug discovery and development

8.       Member of the Scientific Committee of the First Critical Assessment of Microarray Data Analysis (CAMDA’00), Duke University, Durham, N.C., USA

9.       Marquis Who's Who in Science and Engineering, Millennium Edition (5th), 2000

10.    Certified by the U.S. Immigration and Naturalization Service (INS) as a "Person with Extraordinary Ability" in Science, 1997

11.    NIH Forgarty Research Fellowship Award, NIH, Bethesda, Maryland, 1995-1997

12.    State Education Committee of China Award for the Advancement of Science and Technology, for a project on Chemometrics and Chemical Derivation Enhanced Fluorimetry, Beijing, China, 1996

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

15.    Special Invited Speaker of the Japanese Chemical Society at its Third Japan Chemometrics Workshop (Osaka), and Second Japan Computational Chemistry Seminar (Tsukuba), 1992

16.    Outstanding Graduate Student Award, Institute of Process Engineering, Chinese Academy of Sciences, 1990

17.    Outstanding Graduate Student Award, Univ. Sci. & Tech. of China, Hefei, China, 1988

18.    Outstanding Student Award, Hunan University, Changsha, China, 1985

 

PROFESSIONAL SOCIETIES

 

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

4.      Classification Society of North America (CSNA), since 1997

5.      Society for Biomolecular Screening (SBS), since 2001

6.      Association for Laboratory Automation (ALA), since 2001

7.      QSAR and Modelling Society, since 1995

8.      Chinese Chemical Society (CCS), since 1986

 

REFERENCES

 

Gerald W. Stockton, Ph.D.

Former Senior Group Leader

BASF Corp.

391 S. Milton Drive

Yardley, PA 19067

(215) 295-8822

gstockton@comcast.net

 

Roger G. Perkins, M.Sc.

Director, Scientific Computation

Northrop Grumman Information Technology

National Center for Toxicological Research, FDA

Jefferson, AR 72079

(870) 543-7049, 543-7382

rperkins@nctr.fda.gov

 

John N. Weinstein, M.D., Ph.D.

Senior Investigator

Laboratory of Molecular Pharmacology

National Cancer Institute

National Institutes of Health

Bethesda, MD 20892-4225

(301) 496-9571, 402-0752(Fax)

weinstein@dtpax2.ncifcrf.gov

Gilles Klopman, Ph.D.

Charles F. Mabery Professor of Research

Department of Chemistry

Case Western Reserve University

Cleveland, OH 44106

(216) 368-3618, 368-5921(Fax)

gxk6@po.cwru.edu

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 (China), In press (2004).

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).

26.   Xie AH, Li BY, Liao CZ, Li ZB, Lu XP, Shi LM, Zhou JJ. Docking study of HDAC: Implication for the binding mode of benzamide inhibitors. Acta Phys. Chim. Sin. (Wuli Huaxue Xuebao). 20(6), 569-572 (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

29.   Tong 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 Drug Administration National Center for Toxicological Research. Environmental Health Perspectives, 111(15), 1819-1826 (2003).

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 Chemistry (China), 20(5), 556-562 (2003).

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

33.   Shi 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, Cambridge, U.K.; Foreword by U.K. Prime Minister Tony Blair). Invited review

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).

35.   Shi LM, Tong WD. Data mining: an integrated approach for drug discovery. in Biochips: Technology and Applications, W.L Xing and J. Cheng (Editors), Berlin, Springer, pp.71-89, July 2003. ISBN 3-540-00423-8. Invited book chapter

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).

42.   Tong 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, Kobe, Japan, 1999.

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).

46.   Shi LM, Fan Y, Lee JK, Waltham M, Andrews DT, Scherf U, Paull KD, Weinstein JN. Mining and visualizing large anticancer drug discovery databases. Journal of Chemical Information and Computer Sciences, 40(2), 367-379 (2000).

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, 2490-2493, IEEE, Houston, Texas, 1997. ISBN: 0-7803-4122-8

54.   Klopman G, Shi LM, Ramu A. Quantitative structure-activity relationships study of multidrug resistance reversal agents. Molecular Pharmacology, 52(2):323-334 (1997).

55.   Li 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 China (Zhongguo Yaowu Huaxue Zazhi) 6(1):38-42 (1996).

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. Hunan Univ. (Hunan Daxue Xuebao) 22(6):46-52 (1995).

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).

60.   Shi 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.). China Petrochemical Industry Press, Beijing, 394-444 (1994).

61.   Shi 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, ed.). China Petrochemical Industry Press, Beijing, 445-499 (1994).

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).

67.   Liu X, Shi L. Fuzzy pattern recognition of the mode of fluidization. in Selected Papers of Engineering Chemistry and Metallurgy (China) - 1992 (M. Mao, ed.). Science Press, Beijing, 182-189 (1993).

68.   Li ZL, Shi LM. Chapter V: Chemometrics: its methodology and application. in Frontiers of Modern Chemistry (Huaxue Qianyan Luntan) (J. Chen, ed.). Hunan Education Press, Changsha, 81-106 (1993).

69.   Shi LM Chapter XI: Applications of neural networks in chemistry. in Frontiers of Modern Chemistry (Huaxue Qianyan Luntan) (J. Chen, ed.). Hunan Education Press, Changsha, 204-227 (1993).

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).

76.   Shi 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 (UK) 8(1):1-12 (1991).

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).

80.   Shi L, Pan Z, Wang Q. Resolution of overlapped x-ray fluorescence spectra using the Kalman filter. Microcomputer Applications (USA) 10(3):113-116 (1991).

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. China (Zhongguo Kexue Jishu Daxue Xuebao) 20(4):428-436 (1990).

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).

93.   Li Z, Qiu X, Shi L, Qian F, Lin H. Inclusion chromatography and its application in pharmaceutical analysis. J. Pharmaceutical Sci. of China (Zhongguo Yaoxue Zazhi) 25(2):67-70 (1990).

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).

101.          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 Chinese Univ. (Gaodeng Xuexiao Huaxue Xuebao) 10(10):994-998 (1989).

102.          Shi L, Zhang M, Li Z. Expert system and its applications to chemistry. Nature J. (Ziran Zazhi) 11(6):412-416 (1988).

103.          Liu X, Lin A, Shi L, Zhang M. Simultaneous determination of seven organic compounds by Kalman filter-spectrophotometry. J. Univ. Sci. & Tech. China (Zhongguo Kexue Jishu Daxue Xuebao) 18(4):539-544 (1988).

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).

106.          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). J. Hunan Univ. (Hunan Daxue Xuebao) 13(3):94-100 (1986).

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).

 

 

RECENT PRESENTATION

 

1.      Shi L. QC metrics and thresholds for assessing the overall quality of a microarray study, The 44th Annual Meeting of the Society of Toxicology (www.toxicology.org), New Orleans, LA, March 6-10, 2005.

2.      Shi L. Pitfalls and challenges of microarray-based pharmacogenomic and toxicogenomic studies, International Forum on Biochip Technology 2004 (www.capitalbiochip.com/IFBT2004/), Beijing, October 21-24, 2004.

3.      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/), Shanghai, China, October 16-20, 2004.

4.      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 Hotel, Little Rock, Arkansas, October 7-9, 2004.

5.      Shi 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), Portland, OR, September 21-25, 2003. Invited oral presentation

6.      Shi L. Data mining in drug discovery, Symposium at Case Western Reserve University honoring the retirement of Prof. Gilles Klopman, Cleveland, OH, August 22-23, 2003.

7.      Shi L, ArrayTrack – Supporting toxicogenomic research at the FDA’s National Center for Toxicological Research (NCTR), Beyond Genome 2003 Conference, San Diego, CA, June 16-19, 2003.

8.      Lu 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, June 11-13, 2003, Boston MA, USA.

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, New Orleans, LA, March 23-27, 2003

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, New Orleans, LA, March 23-27, 2003

11.   Shi LM. An integrated biochemoinformatics system for drug discovery. Invited lecture at the International Forum on Biochip Technologies, November 9-13, 2002, Beijing, China.

12.   Shi 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 Procedures, November 21, 2001, Düsseldorf, Germany.

13.   Shi LM. DNA microarray and data mining. Invited lecture at the Chinese Biopharmaceutical Association (CBA) annual meeting, October 28, 2000, Bethesda, Maryland.

14.   Shi LM. Data mining: an integrated approach for drug discovery. Invited lecture at the International Forum on Biochip Technologies, October 11-14, 2000, Beijing, China.

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, April 13-17, 1997, San Francisco, California. Paper COMP 253.

21.   Shi 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, April 13-17, 1997, San Francisco, California. Paper COMP 214.

22.   Shi 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 Annual Meeting, April 12-16, 1997, San Diego, California.

 

 

PATENT APPLICATIONS

 

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 November 26, 2002. US60/429294.  WO04048338A1 (Publication date: June 10, 2004).

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 (Publication date: June 10, 2004).

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. China patent application number: 02152045.3

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.