March 2008 Wentian Li, Ph.D ---------------- Research Scientist, The Robert S Boas Center for Genomics and Human Genetics Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, NY 11030 email: wli@nslij-genetics.org, wli@nshs.edu web: http://www.nslij-genetics.org/wli/ FAX: 516-562-1153 RESEARCH FOCUS -------------- Computational/statistical biology/genetics/genomics, bioinformatics. EDUCATION --------- Oct 1989. Ph.D Physics Department, Columbia University, New York, NY Ph.D Thesis: "Problems in Complex Systems" Thesis advisors: Dr. Stephen Wolfram (founder of Wolfram Research Inc. and the author of Mathematica), Dr. Norman Packard (co-founder of Prediction Company). Jun 1984. M.A. Physics Department, Columbia University, New York, NY Jan 1982. B.A. Physics Department, Beijing University, Beijing, China EMPLOYMENTS ----------- 2008-now, Associate Professor, Elmezzi Graduate School of Molecular Medicine Feinstein Institute for Medical Research, North Shore LIJ Health System 2008-now, Associate Investigator, The Robert S Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System 2008-now, Associate Professor, Department of Epidemiology and Population Health , Albert Einstein College of Medicine 2001-2007, Research Scientist, The Robert S Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System 1997-2001, Assistant Professor, Statistical Genetics Lab, Rockefeller University 1996-1997, Research Associate, Statistical Genetics Lab, Rockefeller University 1995-1996, Associate Research Scientist, Psychiatric Department, Columbia University 1995-1996, Research Scientist, Statistical Genetics Department, New York State Psychiatric Institute, 1992-1994, Postdoc, Computational Molecular Biology Group, Cold Spring Harbor Lab. 1991-1992, Postdoc, Statistical Physics Lab, Rockefeller University. 1989-1991, Postdoctoral Fellow, Santa Fe Institute. 1989-1991, Collaborator, Center for Nonlinear Studies, Los Alamos National Lab. 1986-1989, Founding staff member, Center for Complex Systems Research, University of Illinois at Urbana-Champaign. 1986 spring, Teaching assistant, Physics Department, Columbia University. 1984-1985, Thesis contract student, Theoretical condensed matter physics group, Brookhaven National Lab. 1982-1984, Teaching assistant, Physics Department, Columbia University. HONORS/AWARDS ------------- 1997: Nominee of the James McDonnell Centennial Fellowship (nominated by Rockefeller University) 1997-2001: Special Emphasis Research Career Award (SERCA) in Genome Research, National Human Genome Research Institute, National Institute of Health. 1989-1991: Postdoctoral Fellow, Santa Fe Institute 1982-1983: Faculty Fellow, Columbia University 1981: CUSPEA Fellowship (CUSPEA, or China-US Physics Examination and Application, is a program organized by Nobel Laureate T.D. Lee which annually admits about 100 Chinese physics students nation-wide to study in US). FUNDINGS - ONGOING ------------------- NIH/NIAMS 08/1997-07/2008, PI: Peter Gregersen "Genetics Of Rheumatoid Arthritis" (NO1-AR-2-2263) NIH/NIAMS 10/2001-09/2008, PI: Peter Gregersen "Autoimmune Biomarkers Collaborative Network (ABCoN)" (NO1-AR-1-2256) NIH/NIAID 09/2005-02/2010, PI: Steve Hauser, co-PI: Peter Gregersen "International MHC Genetics Network (Imagen)" (U19) NIH/NIAMS 04/2007-03/2012, PI: Peter Gregersen "The Genetics of Rheumatoid Arthritis -NARAC" (RO1 AR44422) NIH/NIAID 07/2007-06/2012, PI: Peter Gregersen "Mapping Autoimmune Phenotypes in Multiplex families" (RO1-AI-68759) NIH/NIAMS 04/2008-03/2011, PI: Lou Bridges "Predictors of Rheumatoid Arthritis (RA) Severity in African Americans" (subcontract) FUNDINGS - COMPLETED ------------------- NIH/NHGRI, 4/30/1997 - 4/30/2001, $325,432, PI: Wentian Li "Training in Genomic Research for Complex Diseases", NIH/NIAMS, 06/2002-05/2006, PI: Peter Gregersen "Genetic analysis of rheumatoid arthritis sib pairs" (R01 AR44422) PROFESSIONAL ACTIVITIES - JOURNAL EDITOR ---------------------------------------- Guest Editor: Gene (2002) Editorial Board Member: 1. Computational Biology and Chemistry (2003 - now) 2. Journal of Theoretical Biology (2005- now) 3. Bioinformatics (2005- now) PROFESSIONAL ACTIVITIES - MANUSCRIPT REVIEWER --------------------------------------------- (total 66 journals) Advances in Complex Systems (1999,2001,2003,2006-2times,2007), American Journal of Epidemiology (2006) American Journal of Medical Genetics (2003) American Journal of Human Genetics(2002,2004,2007), Applied Bioinformatics (2001,2003,2004-2times), Artificial Intelligence in Medicine (2008), Artificial Life (2001), Arthritis & Rheumatism (2004-4times), BioEssays (2003), Bioinformatics (2001-2times,2002-4times,2004,2005-4times,2006-2times,2007-5times,2008), Biomarker Insights (2007) Biophysical Chemistry (2000), Biophysical Journal (1996), Biotechniques (2001), BMC Bioinformatics (2002,2005-3times,2006-2times,2007), BMC Genetics (2004,2005), BMC Medical Genetics (2006), BMC Proceedings(2007-2times), Cell Biochemistry and Biophysics (2002,2003), Chaos (1992), Comparative and Functional Genomics (2007), Complexity (1997,98,2000,2001), Complex Systems (1993,2000,2001,2007), Computational Biology and Chemistry (2002,2003-6times,2004-9times,2005-4times,2006-2times,2007), Computer Applications in Biosciences (1996-3times,97), Computers and Chemistry (bioinformatics special issue) (1993,1999,2000), EURASIP Journal on Applied Signal Processing (2003-2times), EURASIP Journal on Bioinformatics and System Biology (2006) European Physical Journal (2002), Europhysics Letters (1993,2005), FEBS Letters (2004,2005), Gene(2001,2002-4times,2003,2004,2006-2times), GenomeBiology (2002), Genomics (1996,2001,2003), Genome Research (1999,2001-2times,2004), Human Genetics (2008), Human Heredity (1999,2002), IEEE Signal Processing Letters (2005), IEEE Transactions on Computational Biology and Bioinformatics (2004,2005), IEEE Transactions on Systems, Man and Cybernetics (1998), Information Retrieval (2003), International Journal of Artificial Intelligence in Medicine (2003), Journal of Bioinformatics and Computational Biology (2003,2004,2007), Journal of Biomolecular Structure and Dynamics (2003,2005,2007-2times), Journal of Chemical Information and Computer Sciences (2004), Journal of Molecular Evolution (1997,2003-2times), Journal of Physics: Condensed Matter (2004), Journal of the Royal Society Interface (2007), Journal of Statistical Physics (1999), Journal of Theoretical Biology (1998-2times,2000,2001,2003,2004-4times,2006,2008), Mammalian Genome (2003), Mathematical Biosciences (2002), Metabolic Engineering (1999), Molecular Genetics and Metabolism (2004), Molecular Medicine (2006,2007), Nature (1992), Nucleic Acids Research (1998,2001,2002-2times,2004,2005-2times,2006), Physica A (2004,2005,2007) Physica D (1991,94,99,2002-2times,2008), Physical Review E (1997-3times,98-3times,99-3times,2000-2times,2001-3times, 2002-4times,2003-2times,2004-4times,2005,2006-2times, 2007), Physical Review Letters (1996,97-2times,98,99-3times,2000-2times,2001-3times, 2002, 2003-2times,2004-2times,2005-2times,2006), Physics Letters A (1991). PLoS Computational Biology (2006) Proceedings of National Academy of Sciences (2006) Seminars in Arthritis and Rheumatism (2007) Theory in Biociences (2006) Pacific Symposium on Biocomputing (2003) Research in Computational Biology (RECOMB) (2003) IEEE/EMBS Annual Conference (2006) Asia-Pacific Bioinformatics Conference (2007) Advances in Computational Intelligence in Bioinformatics (2007) PROFESSIONAL ACTIVITIES - GRANT PROPOSALS REVIEWER --------------------------------------------------- Action Thematique Incitative sur Programme et Equipes (ATIPE), Centre National de la Recherche Scientifique (CNRS), France (2000). David Phillips Fellowship, Biotechnology and Biological Sciences Research Council (BBSRC), UK (2005). Wellcome Trust, UK (2006-twice, 2007) Department of Biotechnology, Ministry of Science and Technology, India (2006) PROFESSIONAL ACTIVITIES - MEETING CHAIRS ---------------------------------------- IEEE Engineering in Medicine and Biology Society (EMBS) Annual International Conference: track co-chair for Bioinformatics and Computational Biology (2006) Asia-Pacific Bioinformatics Conference (APBC'2007): program committee Asia-Pacific Bioinformatics Conference (APBC'2009): program committee PROFESSIONAL ACTIVITIES - COMMITTEE ----------------------------------- Scientific Committee, Critical Assessment of Microarray Data Analysis (CAMDA) Workshop, October 2001 Academic Medicine Development Company (AMDEC) Bioinformatics Core Advisory Committee (2001- 2002). PROFESSIONAL ACTIVITIES - TRAININGS ----------------------------------- Human Disease Mapping (Statistics Department, North Carolina State University, June 1999). Quantitative genetic data analysis(Statistics Department, North Carolina State University, June 1998). Genetic approaches to biological problems(auditing, Genetics and Development Department, Columbia University, Fall, 1997). Theoretical Genetic Modeling Course (auditing, Department of Biostatistics, Columbia University, Spring, 1996). Genetic Epidemiologic Studies of Complex Diseases (auditing, Banbury Center, Cold Spring Harbor Lab, June 1994). 1994 Princeton Biophysics Lectures (NEC Institute, June 1994 and June 1992). Advanced Linkage Course (Columbia-Presbyterian Medical Center, Columbia University, January 1994). Training Course for IntelliGenetics Suite (given by IntelliGenetics Inc., at Cold Spring Harbor Lab, December 1993). SIMS Tutorial: Mathematical Sciences in Genomic Analysis (sponsored by Societal Institute of the Mathematical Sciences, at Rutgers University, July/August, 1992). Complex Systems Summer School (Santa Fe Institute, June/July 1988). PROFESSIONAL ACTIVITIES - RECENT CONFERENCE PRESENTATIONS --------------------------------------------------------- Annual Meeting of American Society of Human Genetics (1995,96,97,98,99,2000). Anton Dohrn Workshop on Natural Selection and Neutral Theory (2001, 2005). Aspen Workshop on Identifying Features in Biological Sequences (1990,93,96). Beijing Computational Biology Workshop (1999). Chinese Bioinformatics Conference (2002). Critical Assessment of Techniques for Microarray Data Mining (2000). Cold Spring Harbor Genome Meeting (1994,98,99,2000). Cold Spring Harbor Genome Sequence, Sequence Variation, and Gene Expression Meeting (2001) Institute of Mathematics and Applications (IMA) workshop on Statistical Methods for Gene Expression (2003) DNA in Chromatin (2002) Gene Discovery in silico (1997). Genetic Analysis Workshop (1996,98,2000). Research in Computational Molecular Biology (RECOMB) (1998,2001,2003). PROFESSIONAL ACTIVITIES - SUPERVISING STUDENTS/EDUCATION -------------------------------------------------------- David Kessler, pre-college science education program at Rockefeller University (1998,99,2000 summers) (an undergraduate at Harvard University (2000-2004) major: economics ). Eric van Nostrand, pre-college science education program at Rockefeller University (2000 summer). (an undergraduate at MIT (2001-2005) major: biology ) Young-Ju Suh, outside committee member for Ph.D Thesis, Dept of Applied Mathematics and Statistics, State Univ of New York at Stony Brook (2001). (currently a research professor at Sookmyung Women's University) Lecture: pre Chinese Bioinformatics Conference Course (2002). Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing. "Introduction of microarray data analysis". Lecturer and organizing committee: Theoretical and Practical Course: Pharmacogenomics - genetic epidemiology and web-based tools (2005). Guadalajara, Mexico. "Introduction to association analysis", "Practical issues in association analysis. I. indirect nature of disease genes", "Practical issues in association analysis. II. heterogeneity", "Family-based association analysis, interaction, and other topics", "Various statistical issues in association analysis". Lecture: Graduate Course on Genetics (2007), North Shore LIJ Graduate School of Molecular Medicine "Introduction of model-based linkage analysis" Ken Asher, Student Intern Research Program at Feinstein Institute for Medical Research (2006, 2007) Lisa Mao, Student Intern Research Program at Feinstein Institute for Medical Research (2007) COMPUTER EXPERIENCES -------------------- Programming: C (since 1986), Perl (since 1995), and others. Web: webmaster (since 1995). System administration: full-time UNIX administrator (1995-96). Scientific programming: S-plus (since 1998), Mathematica (since 1989), and others. PUBLICATIONS - JOURNAL ARTICLES, LETTERS, EDITORIAL --------------------------------------------------- (48 papers are first-author'ed) 81. G Zheng, M Meyer, W Li, Y Yang (2008) "Comparison of two-phase analyses for case-control genetic association studies" Statistics in Medicine, to appear. 80. HS Lee, AT Lee, LA Criswell, MF Seldin, CI Amos, JP Carulli, C Navarrete, EF Remmers, DL Kastner, RM Plenge, W Li, PK Gregersen (2008), "Several regions in the major histocompatibility complex confer risk for anti-CCP-antibody positive rheumatoid arthritis, independent of the DRB1 locus" Molecular Medicine, to appear. 79. W Li (2008), "Three lectures on case-control genetic association analysis", Briefings in Bioinformatics, 9:1-13. 79. RM Plenge, M Seielstad, L Padyukov, AT Lee, EF Remmers, B Ding, A Liew, H Khalili, A Chandrasekaran, LRL Davies, W Li, AKS Tan, C Bonnard, RTH Ong, A Thalamuthu, S Pettersson, C Liu, C Tian, WV Chen, JP Carulli, D Altschuler, L Alfredsson, LA Criswell, CI Amos, MF Seldin, DL Kastner, L Lareskog, PK Gregersen (2007), "TRAF1-C5 as a risk locus for rheumatoid arthritis -- a genomewide study", New England Journal of Medicine, 357(12):1199-1209. 77. EF Remmers, RM Plenge, AT Lee, RR Graham, G Hom, TW Behrens, PIW de Bakker, JM Le, HS Lee, F Batliwalla, W Li, SL Masters, MG Booty, JP Carulli, L Padyukov, L Alfredsson, L Klareskog, WV Chen, CI Amos, LA Criswell, MF Seldin, DL Kastner, PK Gregersen (2007), "STAT4 and risk of rheumatoid arthritis and systemic lupus erythematosus", New England Journal of Medicine, 357(10):977-986. 76. YJ Suh, HS Lee, F Batliwalla, W Li (2007), "A comparison of founder-only and all-pedigree-members genotype-expression association by regression analysis", BMC Proceedings, 1(suppl 1):S8. 75. YJ Suh, W Li (2007) "Genotype-based case-control analysis, violation of Hardy-Weinberg equilibrium, and phase diagram", Proceedings of the 5th Asia-Pacific Bioinformatics Conference, pp.185-194 (Imperial College Press). 74. PK Gregersen, E Kowalsky, W Li (2007) "Reply to Henthorn and Deutsch -- Ethnicity versus early environment: Comment on 'Early childhood music education and predisposition to absolute pitch: teasing apart genes and environment" (letters to the editor), American Journal of Medical Genetics, 143A:104-105. 73. W Fury, F Batliwalla, PK Gregersen, W Li (2006), "Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion", Conference proceedings of Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 5531-5541 (IEEE). 72. JW Bauer, EC Baechler, M Petri, FM Batliwalla, D Crawford, WA Ortmann, KJ Espe, W Li, DD Patel, PK Gregersen , TW Behrens (2006), "Elevated serum levels of interferon-regulated chemokines are biomarkers for active human systemic lupus erythematosus", PLoS Medicine, 3(12):e491. 71. HS Lee, W Li, A Lee, P Rodine, RR Graham, WA Ortmann, F Batliwalla, KW Lee, SC Bae, TW Behrens, PK Gregersen (2006), "Microsatellite typing for DRB1 alleles: application to the analysis of HLA associations with rheumatoid arthritis", Gene and Immunity, 7:533-543. 70. W Li, P Miramontes (2006), "Large-scale oscillation of structure-related DNA sequence features in human chromosome 21", Physical Review E, 74:021912. 69. CI Amos, WV Chen, AT Lee, W Li, M Kern, R Lundsten, F Batliwalla, M Wener, E Remmers, DA Kastner, LA Criswell, MF Seldin, PK Gregersen (2006), "High-density SNP analysis of 642 caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33", Gene and Immunity, 7(4):277-286. 68. E Shi, W Fury, W Li, W Mikulka, T Aldrich, A Rafique, G Chen, S Hoffenberg, TJ Daly, C Radziejewski (2006) "Monoclonal antibody classification based on epitope binding using differential antigen disruption", Journal of Immunological Methods, 314:9-20. 67. W Li (2006) "The-more-the-better and the-less-the-better", Bioinformatics, 22(18):2187-2188. 66. M Brenner, T Laragione, NC Yarlett, W Li, A Mello, PS Gulko (2006) "Cia27 is a novel non-MHC arthritis severity locus on rat chromosome 10 syntenic to the rheumatoid arthritis 17q22-q25 locus", Gene and Immunity, 7(5):335-341. 65. W Li, M Wang, P Irigoyen, PK gregersen (2006), "Inferring causal relationships among intermediate phenotypes and biomarkers: a case study of rheumatoid arthritis", Bioinformatics, 22(12):1503-1507. 64. FM Batliwalla, W Li, CT Ritchlin, X Xiao, M Brenner, T Laragione, T Shao, R Durham, S Kemshetti, E Schwarz, R Coe, M Kern, EC Baechler, TW Behrens, PK Gregersen, PS Gulko (2005), "Microarray analyses of peripheral blood cells identifies unique expression signature in psoriatic arthritis", Molecular Medicine, 11(1-12):21-29. 63. A Ulgen, W Li (2005), "Comparing single-nucleotide-polymorphism marker-based and microsatellite marker-based linkage analyses" BMC Genetics, 6(suppl 1):S13. 62. P Irigoyen, AT Lee, MH Wener, W Li, M Kern, F Batliwalla, RF Lum, E Massarotti, M Weisman, C Bombardier, EF Remmers, DL Kastner, MF Seldin, LA Criswell, PK Gregersen (2005), "Regulation of anti-cyclic citrullinated peptide antibodies in rheumatoid arthritis: contrasting effects of HLA-DR3 and the shared epitope alleles", Arthritis & Rheumatism, 52(12):3813-3818. 61. FB Batliwalla, EC Baechler, X Xiao, W Li, S Balasubramaniuan, H Khalili, A Damle, WA Ortmann, A Perrone, AB Kantor, PS Gulko, M Kern, R Furie, TW Behrens, PK Gregersen (2005), "Peripheral blood gene expression profiling in rheumatoid arthritis", Gene and Immunity, 6(5):388-397. 60. W Li, D Holste (2005), "Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome", Physical Review E, 71:041910. 59. LA Criswell, K Pfeiffer, RF Lum, B Gonzales, J Novitzke, M Kern, KL Moser, AB Begovich, VEH Carlton, W Li, AT Lee, W Ortmann, TW Behrens, PK Gregersen (2005), "Analysis of families in the Multiple Autoimmune Disease Genetics Consortium (MADGC): the PTPN22 620W allele associates with multiple autoimmune phenotypes", American Journal of Human Genetics, 76:561-571. 58. AT Lee, W Li, A Liew, C Bombardier, M Weisman, EM Massarotti, J Kent, F Wolfe, A Begovich, PK Gregersen (2005), "The PTPN22 R620W polymorphism associates with RF positive rheumatoid arthritis in a dose-dependent manner but not with HLA-SE status", Genes and Immunity, 6(2):129-133. 57. A Addo, J Le, W Li, I Aksentijevich, J Balow Jr, A Lee, PK Gregersen, DL Kastner, EF Remmers (2005), "Analysis of CARD15/NOD2 haplotypes fails to identify common variants associated with rheumatoid arthritis susceptibility", Scandinavian Journal of Rheumatology, 34(3):198-203. 56. W Li, D Holste (2004), "An unusual 500,000 bases long oscillation of guanine and cytosine content in human chromosome 21", Computational Biology and Chemistry, 28(5-6):393-399. 55. W Li, D Holste (2004), "Spectral analysis of guanine and cytosine fluctuations of mouse genomic DNA", Fluctuation and Noise Letters, 4(3):L453-L464. 54. JD Halley, AC Warden, S Sadedin, W Li (2004), "Rapid self-organized criticality: fractal evolution in extreme environments", Physical Review E, 70:036118. 53. HC Meng, MM Griffiths, EF Remmers, Y Kawahito, W Li, R Neisa, GW Cannon, RL Wilder, PS Gulko (2004), "Identification of two novel female-specific non-MHC loci regulating collagen-induced arthritis severity and chronicity, and evidence for epistasis", Arthritis & Rheumatism, 50(8):2695-2705. 52. W Li, FZ Sun, I Grosse (2004), "Extreme-value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression", Journal of Computational Biology, 11(2-3):215-226. 51. W Li, PK Gregersen (2004) "Reconstructing haplotypes in pedigrees: the importance of parental information", American Journal of Medical Genetics, 124A:107-109. 50. W Li, I Grosse (2004), "Comments on 'Linguistic features in eukaryotic genomes' " (letters to the editor), Complexity, 9(4):10-11. 49. A Ulgen, Z Han, W Li (2003) "Correlation between quantitative traits and correlation between corresponding LOD scores: detection of pleiotropic effects", BMC Genetics, 4(suppl 1):S60. 48. M Sanchez-Carbayo, N Socci, JJ Lozano, W Li, E Charytonowicz, T Belbin, M Preystowski, A Ortiz, G Childs, C Cordon-Cardo (2003) "Gene discovery in bladder cancer progression using cDNA microarrays", American Journal of Pathology, 163:505-516. 47. W Li, I Grosse (2003) "Gene selection criterion for discriminant microarray data analysis based on extreme value distributions", RECOMB2003: Proceedings of the Seventh Annual International Conference of Computational Molecular Biology, pages 217-223 (ACM Press). 46. W Li, JL Oliver, P Bernaola-Galvan, P Carpena (2003) "Isochores merit the prefix 'iso' ", Computational Biology and Chemistry, 27(1):5-10. and preprint: http://genomebiology.com/2002/3/11/preprint/0009, 45. W Li (2002) "Zipf's law everywhere", Glottometrics, 5:14-21. 44. W Li, Y Yang (2002) "Zipf's law in importance of genes for cancer classification", Journal of Theoretical Biology, 219(4):539-551. 43. W Li (2002) "Are isochore sequences homogeneous?" Gene, 300(1-2):129-139. 42. RK Azad, JS Rao, W Li, R Ramaswamy (2002), "Simplifying the mosaic description of DNA sequences", Physical Review E, 66:031913. 41. D Jawaheer, W Li , RR Graham, W Chen, A Damle, X Xiao, J Monteiro, H Khalili, A Lee, R Lundsten, A Begovich, T Bugawan, H Erlich, JT Elder, LA Criswell, MF Seldin, CI Amos, TW Behrens, PK Gregersen (2002), "Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis", American Journal of Human Genetics, 71:585-594. 40. Z Han, SC Heath, D Shmulewitz, W Li, SB Auerbach, ML Blundel, T Lehner, J Ott, M Stoffel, JM Friedman, JL Breslow (2002) "Candidate genes involved in cardiovascular risk factors in a family-based association study on the island of Kosrae, Federated States of Micronesia", American Journal of Medical Genetics, 110(3):234-242. 39. W Li, P Bernaola-Galvan, F Haghighi, I Grosse (2002) "Applications of recursive segmentation to the DNA sequence analysis", Computers & Chemistry (genome and informatics special issue), 26(5):491-510. 38. LJ Fang, W Li, N Chalhoub, J Feingold, J Ortenberg, J-P Thirion (2002) "Linkage disequilibrium and founder effect analysis of the NF1 gene in French Canadians from the Quebec population", Annales de Genetique, 45:39-44. 37. W Li, Y Yang (2002) "How many genes are needed for a discriminant microarray data analysis?", in "Methods of Microarray Data Analysis", eds. SM Lin and KF Johnson, pp.137-150 (Kluwer Academic) 36. LJ Fang, N Chalhoub, W Li, J Feingold, J Ortenberg, J-P Thirion (2001) "Genotyping analysis of the NF1 gene in the French Canadians from the Quebec population", American Journal of Medical Genetics, 104:189-198. 35. W Li (2001) "Delineating relative homogeneous G+C domains in DNA sequences", Gene, 276:57-72. 34. W Li, D Nyholt (2001) "Marker selection by Akaike information criterion and Bayesian information criterion", Genetic Epidemiology, 21(suppl 1):S272-S277. 33. D Gordon, J Hoh, SJ Finch, MA Levenstein, J Edington, W Li, J Majewski, J Ott (2001) "Two approaches for consolidating results from genome scans of complex traits: selection methods and scan statistics", Genetic Epidemiology, 21(suppl 1):S396-S342. 32. W Li (2001) "New stopping criteria for segmenting DNA sequences", Physical Review Letters, 86(25):5815-5818. 31. W Li (2001) "DNA segmentation as a model selection process", RECOMB2001: Proceedings of the Fifth Annual International Conference of Computational Molecular Biology, pages 204-210 (ACM Press). 30. W Li, J Reich (2000) "A complete enumeration and classification of two-locus disease models", Human Heredity, 50:334-349. 29. W Li, F Haghighi, CT Falk (1999) "Design of artificial neural network and its application to the analysis of alcoholism data", Genetic Epidemiology, 17(suppl 1):S223-S228. 28. W Li (1999) "Statistical properties of open reading frames in complete genome sequences", Computers & Chemistry (informatics and the genome issue), 23(3-4):283-301. 27. W Li, CSJ Fann, J Ott (1998) "Low order polynomial trends of female-to-male map distance ratios along human chromosomes", Human Heredity, 48(5):266-270. 26. W Li, G Stolvitzky, P Bernaola-Galvan, JL Oliver (1998) "Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes", Genome Research, 8(9):916-928. 25. JJ Higgins, I Litvan, LT Pho, W Li, LE Nee (1998) "Progressive supranuclear gaze palsy is in linkage disequilibrium with the tau and not the alpha-synuclein gene", Neurology, 50(1):270-273. 24. W Li (1998) "Comments on 'Simplicity and complexity in gene evolution' ", (letter to the editor), Complexity, 3(5):10. 23. W Li (1998) "Comments on 'Zipf's law and structures and evolution of natural languages' ", (letter to the editor), Complexity, 3(5):9-10. W Li (2003), "Reply to 'On words and genes' by A.A. Tsonis and P.A.Tsonis", (letters to the editor), Complexity, 8(5):13-14. 22. F Haghighi, W Li, CSJ Fann (1997) "Affected sibpair analysis of bipolar disorder using data on chromosome 18", Genetic Epidemiology, 14:641-646. 21. W Li (1997) "The complexity of DNA: the measure of compositional heterogeneity in DNA sequences and measures of complexity", Complexity, 3(2):33-37. 20. W Li (1997) "Study of correlation structure in DNA sequences: a critical review", Computers & Chemistry, 21(4):257-272. 19. AC Walsh, W Li, DR Rosen, DA Lawrence (1996) "Genetic mapping of GLCLC, the human gene encoding the catalytic subunit of gamma-glutamylcysteine synthetase, to chromosome 6p12 and characterization of a polymorphic trinucleotide repeat within its 5' untranslated region", Cytogenetics and Cell Genetics, 75(1):14-16. 18. W Li (1996) "Comments on 'Bell Curves and Monkey Languages'" (letter to the editor), Complexity, 1(6):6. 17. W Li, T Marr and K Kaneko (1994) "Understanding statistical long-range correlations in DNA sequences", Physica D, 75:392-416. 16. W Li and K Kaneko (1992) "DNA correlations" (scientific correspondence), Nature, 360:635-636. 15. W Li and K Kaneko (1992) "Long-range correlation and partial 1/f spectrum in a non-coding DNA sequence", Europhysics Letters, 17(7):655-660. [featured in Science magazine (Aug 7, 1992) and Scientific Americans (Sept 1992)] 14. W Li (1992) "Generating non-trivial long-range correlations and 1/f spectra by replication and mutation", International Journal of Bifurcation and Chaos, 2(1):137-154. 13. W Li (1992) "Random texts exhibit Zipf's-law-like word frequency distribution", IEEE Transactions on Information Theory, 38(6):1842-1845. 12. W Li (1992) "Phenomenology of non-local cellular automata", Journal of Statistical Physics, 68(5-6):829-882. 11. W Li and M Nordahl (1992) "Transient behavior of cellular automata rule 110", Physics Letters A, 166(5-6):335-339. 10. W Li (1991) "Absence of 1/f spectra in Dow Jones daily average", International Journal of Bifurcations and Chaos, 1(3):583-597. 9. W Li (1991) "Expansion-modification systems: a model for spatial 1/f spectra", Physical Review A, 43(10):5240-5260. 8. W Li (1991) "On the relationship between complexity and entropy for Markov chains and regular languages", Complex Systems, 5(4):381-399. 7. W Li (1990) "Mutual information functions versus correlation functions", Journal of Statistical Physics, 60(5-6):823-837. 6. W Li and N Packard (1990) "The structure of the elementary cellular automata rule space", Complex Systems, 4(3):281-298. 5. W Li, N Packard and C Langton (1990) "Transition phenomena in cellular automata rule space", Physica D (Nonlinearity), 45(1-3):77-94. 4. W Li (1989) "Spatial 1/f spectra in open dynamical systems", Europhysics Letters, 10(5):395-400. 3. W Li (1989) "Complex patterns generated by next nearest neighbors cellular automata", Computer & Graphics, 13(4):531-537. 2. W Li (1987) "Spectra of regular language and cellular automata", Complex Systems, 1(1):107-130. 1. W Li and P Bak (1986), "Fractal dimension of Cantori", Physical Review Letters, 57(6):655-658. PUBLICATIONS - ABSTRACTS ------------------------ YJ Suh, HS Lee, F Batliwalla, W Li (2006) Using pedigree founders only or using all pedigree members? -- A comparison of SNP-expression regression results Genetic Analysis Workshop 15, W Fury, F batliwalla, PK Gregersen, W Li (2006) Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterion IEEE Engineering in Medicine and Biology Society Annual Conference, Aug 30-Sept 3, New York, NY W Li, YJ Suh, J Zhang (2006) Does logarithm transformation of microarray data affect rank order of differentially expressed genes? IEEE Engineering in Medicine and Biology Society Annual Conference, Aug 30-Sept 3, New York, NY ZL Hu, JM Reecy, W Li (2006) A database for genetic analysis software, Plant and Animal Genome Conference, January 14-16, 2006, San Diego, CA F Batliwalla, C Ritchlin, W Li, X Xiao, M Brenner, T Laragione, T Shao, R Durham, S Kemshetti, E Schwarz, R Coe, M Kern, EC Baechler, TW Behrens, PK Gregersen, PS Gulko (2005), Microarray analyses of peripheral blood cells identifies unique gene expression signature that differentiates psoriatic arthritis from controls and from rheumatoid arthritis, American Congress of Rheumatology Annual Scientific Meeting, Nov 12-17, 2005, San Diego, CA FM Batliwalla, EC Baechler, W Li, X Xiao, AR Damle, W Ortmann, J Novitzke, S Carsons, D Fischer, R Schoen, JA Molitor, E Schned, R Furie, M Kern, TW Behrens, PK Gregersen (2005), Peripheral blood gene expression profiling in rheumatoid arthritis: potential utility for the prediction of response to anti-TNF therapy American Congress of Rheumatology Annual Scientific Meeting, Nov 12-17, 2005, San Diego, CA PK Gregersen, W Chen, AT Lee, MF Seldin, W Li, M Kern, EF Remmers, LA Criswell, DL Kastner, CI Amos (2005), Genome wide linkage scan of 748 affected sibling pair families with rheumatoid arthritis using the Illumina linkage IV set of ~5,600 SNP markers American Congress of Rheumatology Annual Scientific Meeting, Nov 12-17, 2005, San Diego, CA CC Chu, ST Reese, LO Goodwin, D Guzowski, A Chandrasekaran, C Gawel, W Li, PK Gregersen, XJ Yan, B Sherry, M Centola, SL Allen, KR Rai, N Chiorazzi (2005), Elevated serum interleukin-10 is not associated with promoter polymorphism (-1082, -819, -592) in B-cell chronic lymphocytic leukemia, International Workshop on CLL, Sept 16-18, 2005, Brooklyn NY. E Remmers, J Balow Jr, W Li, I Aksentijevich, A Lee, A Damle, W Chen, C Amos, P Gregersen, D Kastner (2004), Linkage disequilibrium structure and association analysis of candidate genes located within the rheumatoid arthritis susceptibility region on chromosome 18q, The Keystone symposium "Human Genome Sequence Variation and the Inherited Basis of Common Disease", Jan 8-13, 2004, Breckenridge, CO. E Remmers, J Balow Jr, W Li, I Aksentijevich, A Lee, A Damle, W Chen, C Amos, P Gregersen, D Kastner (2003), Possible association of a 14 kb haplotype block from the receptor mactivator of NF-kappa B (RANK) gene with susceptibility to rheumatoid arthritis American Journal of Human Genetics, ?. page ? D Jawaheer, W Li, R Graham, W Chen, A Damle, X Xiao, J Monteiro, H Khalili, A Lee, R Lundsten, A Begovich, T Bugawan, H Erlich, JT Elder, LA Criswell, MF Seldin, CI Amos, T Behrens, PK Gregersen (2002), Dissecting the genetic complexity of the HLA association with rheumatoid arthritis, American Congress of Rheumatology Annual Scientific Meeting, W Li, Y Yang, J Edington, F Haghighi (2001) Determination of the number of genes required for a discriminant microarray data analysis, Integrating Genome Sequence, Sequence Variation and Gene Expression (Cold Spring Harbor Lab) F Haghighi, WN Grundy, W Li (2001) An alternative method for computational detection of CpG island Genome Sequencing & Biology (Cold Spring Harbor Lab) W Li, A Sherriff, X Liu (2000) Assessing risk factors of human complex diseases by Akaike and Bayesian information criteria (AIC and BIC) American Journal of Human Genetics, s67. page 222. W Li (2000) A set of bioinformatics web resources Genome Sequencing & Biology (Cold Spring Harbor Lab), page 160. D Kessler, W Li (2000) Segmentation analysis of yeast telomere sequences Genome Sequencing & Biology (Cold Spring Harbor Lab), page 142. W Li, F Haghighi (1999) Perl as a tool for linkage analysis. American Journal of Human Genetics, s65, page A260. F Haghighi, P Banerjee, W Li (1999) Application of artificial neural networks in whole-genome analysis of complex diseases. Genome Sequencing & Biology (Cold Spring Harbor Lab), page 75. W Li (1998) An exact calculation of the probability of identity-by-descent in two-locus models using an extension of the Li-Sacks' method. American Journal of Human Genetics, s63, page A297. JL Oliver, W Li (1998) Quantitative analysis of compositional heterogeneity in long DNA sequences: the two-level segmentation test Genome Mapping, Sequencing & Biology (Cold Spring Harbor Lab), page 163. W Li (1997) A complete listing and classification of two-locus two-allele fully-penetrant disease model. American Journal of Human Genetics, s61, page A204. W Li, VFG Haghighi, TC Matise, J Ott (1996) Using web browsers as the graphical user interface for linkage analysis. American Journal of Human Genetics, s59, page A307. W Li, CSJ Fann, J Ott (1995) Positional difference of male-female genetic distances in all autosomal chromosomes using the computer program TREND. American Journal of Human Genetics, s57, page A197 W Li, TG Marr (1994) Theoretical studies of size distributions of inherited and identical-by-descent segments in pedigrees. Genome Mapping & Sequencing (Cold Spring Harbor Lab). UNPUBLISHED PAPERS ------------------ W Li (1999) Large-Scale Patterns in DNA Texts (unused manuscript prepared for Scientific American) JL Oliver, W Li (1998) Evaluating compositional homogeneity in DNA sequences: a two-level segmentation test W Li, M Zhang and T Marr (1994) The statistical distribution of the length of DNA segments that are identical-by-descent using a single crossover model, (Cold Spring Harbor Lab preprint) W Li (1989) Mutual information functions of natural language texts, (Santa Fe Institute working paper 89-008, November 1989). PUBLICATIONS - UNREFEREED BOOK CHAPTERS --------------------------------------- W Li (1995) Pattern 1170 in "Pattern Book: Fractals, Art, and Nature" by C. Pickover World Scientific, 1995) W Li (1992, 1997) Non-local cellular automata, in 1991 Lectures in Complex Systems, Santa Fe Institute Studies in the Sciences of Complexity, Vol IV, eds. L. Nadel and D. Stein, pp. 317-327 (Addison-Wesley). Reprinted in "Pattern Formation in the Physical and Biological Sciences" eds. D.L. Stein, L. Nadel, and F. Nijhout (Addison-Wesley, 1997). W Li (1991) Expansion-modification systems and spatial 1/f spectra, in Proceedings of the 1991 International Conference on Noise in Physical Systems and 1/f Fluctuations, eds. T. Musha, S. Sato, and M. Yamamoto, pp. 519-522 (Ohmsha). W Li (1989) Mutual information functions versus correlation functions in binary sequences, in Measures of Complexity and Chaos, eds. N.B. Abraham, A.M. Albano, A. Passamante, and P.E. Rapp (NATO ASI Series, Series B: Physics Vol. 208), 249-252 (Plenum). PUBLICATIONS - BOOKS -------------------- W Li, "Practical Human Genetic Analysis", Wiley & Sons, in preparation. AK Konopka, C Martingdale, W Li, "Yule Distribution and Zipf's Laws in Science and Culture", in preparation. ONLINE CREATIONS - BIOINFORMATICS AND GENOME RESEARCH ----------------------------------------------------- http://www.nslij-genetics.org/microarray/ Publications on microarray data analysis (1999-now). Selected as a "webpick of the day" by the BioMedNet Magazine, HMS Beagle, on April 20, 2000. Recommended in "Handbook of Bioinformatics" (Shanghai Science and Technology Press, 2000. in Chinese) Mirrored at the Centre of Bioinformatics at Beijing University (http://www.cbi.pku.edu.cn/mirror/microarray/microarray.html) http://www.nslij-genetics.org/gene/ bibliography on computational gene recognition (1995-now): A collection of publications for more than 21 years (1982-now) on computational gene recognition. Recommended by several books and review articles, including the 1997 Review Issue of Human Medical Genetics and "Genetics Databases" edited by Bishop (Academic Press, 1999). Mirrored at the Centre of Bioinformatics at Beijing University (http://www.cbi.pku.edu.cn/mirror/gene/gene.html) http://www.nslij-genetics.org/duplication/ Publications on gene and genome duplication (2001-now) http://www.nslij-genetics.org/dnacorr/ A bibliography on features, patterns, correlations in DNA and protein sequences (1995-now): A collection of publications for the last 11 years (1992-now) on correlation structures of DNA texts. http://www.nslij-genetics.org/seq/ A list of completely sequenced genome (1998-now) http://www.nslij-genetics.org/bioinfotraining/ A list of bioinformatics courses (1999-now): Mirrored at University of Nebraska Medical Center (http://molbio.unmc.edu/Other-tools/rock-page.html) and Centre of Bioinformatics at Beijing University (http://www.cbi.pku.edu.cn/binf_course) ONLINE CREATIONS - GENETICS --------------------------- http://linkage.rockefeller.edu/ Web resource of genetic linkage analysis (1995-now): comprehensive information on genetic linkage analysis. Selected as a "best of comp.infosystems.web.announce" in October 1996. Listed in (among others): Genome Mapping: A Practical Approach (Dear, ed. IRL Press, 1997), Approaches to Gene Mapping in Complex Human Diseases (Haines, Pericak-Vance, eds. Wiley-Liss, 1998), Genetics of Mental Disorder (Faraone, Tsuang, Tsuang, eds. Guilford Press, 1999). http://www.nslij-genetics.org/soft/ Mirrored at http://linkage.rockefeller.edu/soft/ An alphabetic list of genetic analysis software (1995-now): Comprehensive collection of more than 230 computer software on linkage analysis, marker mapping, and pedigree drawing. Recommended in December'96 issue of Trends in Genetics. http://linkage.rockefeller.edu/soft/perl/ Perl as a tool for linkage analysis (1999): Collection of Perl scripts for various tasks in linkage analysis, including automating genome-wide linkage analysis, handling data for complex diseases, etc. http://www.nslij-genetics.org/ld/ A bibliography on linkage disequilibrium analysis (1995-now). http://linkage.rockefeller.edu/bib/ibd/ A bibliography on allele-sharing linkage analysis (1995-now). http://linkage.rockefeller.edu/bib/algorithm/ A bibliography on algorithms in linkage analysis (1995-now). http://linkage.rockefeller.edu/bib/vc/ A bibliography on variance components analysis of human quantitative traits (1999). http://linkage.rockefeller.edu/gui/webpreplink.html web-preplink (1996): A CGI/perl program for online preparing input file for the LINKAGE programs. ONLINE CREATIONS - COMPLEX SYSTEMS ---------------------------------- http://www.nslij-genetics.org/wli/1fnoise/ A bibliography on 1/f spectra (1995-now): For the first time, a collection of publications on 1/f noise in diverse fields is brought together online. Recommended in the "Numerical Analysis and Associated Fields Resource Guide" (sci.math.num-analysis newsgroup). http://www.nslij-genetics.org/wli/zipf/ A page on Zipf's law (1997-now): Linked by, among others, ABC News online (science section, 1999).