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Keynote speaker, Conference on Engineering Technology and Application of Chinese and



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Keynote speaker, Conference on Engineering Technology and Application of Chinese and


Western Medicine. Taichung, Taiwan. Sept. 13.
Speaker, Genomics Days, University of Lausanne, Lausanne, Switzerland, Sept. 18-19.
2003 Xiangshan Science Symposium on Genomics and Evolution, Beijing, China. Oct. 27-30.
Seminar, Department of Ecology & Evolution, ETH Zurich, Switzerland, Nov. 6.
2004

Speaker, International Conference on "Evolutionary Genomics”, Tucson, Arizona. Jan. 16-17.

Speaker, Gordon Conference in Molecular Evolution. Ventura, California. February 1 – 6.


Speaker, GRC on “Structural, Functional & Evolutionary Genomics”. Ventura, Cal. Feb. 15 – 20.
Speaker and session co-chair, 2004 "Biology of Genomes", Cold Spring Harbor Laboratory. May 12 - 16.
Keynote Speaker, International Symposium on Statistical Physics: Biologically Motivated Statistical Physics and Related Problems. Taipei, Taiwan. June 22-26.
Speaker, Workshop on “Comparative genomics of vertebrates: concepts and bioinformatic tools”, La Londes Les Maures, France. May 27-28
Speaker, 2nd Functional Genomics Reunion Conference. Institute of Physics and Applied Mathematics, UCLA. June. 1-4.
Speaker, 3rd Wu Ta-You Science Camp, His-Tou, Taiwan. Aug. 9-13.
Keynote speaker, Symposium for Biomolecules, Medicine, Therapeutics, and Computation, University of Illinois at Chicago.  Oct. 8.
Seminar, Department of Biostatistics, University of Michigan. Oct. 11-12.
Seminar, Genetics Program, Texas A&M University. Nov. 3-5.

2005

Speaker, Florida Bioinformatics Workshop 2005. University of Florida. Feb. 21-22.




Speaker, International Society of Molecular Evolution meeting: “Genome and RNA: Expression and Functions”. Punta Leona, Costa Rica, Feb. 26-March 2.

Myra Samuels Lecture, Department of Statistics, Purdue University. April 21-22.


Speaker, System Biology and Bioinformatics Symposium 2005. March 29-31. Taipei, Taiwan.
Speaker, the Fourth Annual Department of Genome Sciences Symposium. University of Washington. Seattle. May 18.
Speaker, Symposium on Comparative and Functional Genomics, Penn State University. July 20-23.
Speaker, The 8th Chien-Shiung Wu Science Camp in 2005. Shi-tou, Nantou, Taiwan. August 9-11.
Speaker, International Workshop: "Complex biomolecular networks: structure, evolution, and function". The Montauk Yacht Club, Long Island. September 6-9.
Seminar, Department of Biological Sciences, University of Iowa. September 16.
Plenary speaker, Main Symposium, the 77th Annual Meeting of the Genetics Society of Japan. Tokyo, September 27-29.
Speaker, International Conference on Nonlinear Analysis, Institute of Mathematics, Taipei, Taiwan. December 17-20.
2006
Departmental Seminar, Dept of Ecology and Evolutionary Biology, UCLA, Feb. 8-10.
Keynote speaker, The Fourth Asian Pacific Bioinformatics Conference. Taipei, Taiwan. Feb. 13-16.

Plenary speaker and session organizer, HUGO-06, Taipei, Taiwan. March 6-10.

Huey Sun Lecture, National Chung-Hsing University, Tai-Chung, March 15.


Speaker, Symp. On “Teaching Evolution and the Nature of Science”. New York Academy of Sciences. New York City, April 21-22.
Seminar, University of Southern California, Los Angeles. March 20-22.
Seminar, Institute of Bioinformatics, University of Georgia, Athens. March 29-31.
Seminar, Evolution Seminar Series, University of Wisconsin, Madison, April 27.
Speaker and co-organizer, Symposium on "Mutation, selection and evolutionary genomics", Stockholm, Sweden. May 10-13.
Seminar, Dept of Genetics, University of Lund, March 14-15.
Speaker, “Genomes, Evolution, and Bioinformatics”, Annual Meeting of the Society for Molecular Biology and Evolution, Arizona State University. Tempe, Arizona. May 24 – 28.
Speaker and Co-Chair “Molecular Evolution”, 20th IUBMB International Congress of Biochemistry and Molecular Biology. Kyoto, Japan. June 18-23.
Speaker, Course on “DNA and Chromosomes: Physical and Biological Approaches”, Cargèse, Corsica, France. June 19 – July 1.
Seminar, Ochanomizu University, Tokyo, Japan, July 12-13.
Speaker, Evolutionary Genomics and Bioinformatics Symp., Taipei, August 15-16.
Seminar, Center for Cellular and Biomedical Research, University of Toronto, Toronto, Oct. 4-5.
Seminar, University of McMaster, Hamilton, Canada Oct. 6-7.
Keynote speaker, 2006 International Workshop on Medical and Bio Informatics and ICS 2006. Taipei, Dec. 4-6.
Plenary speaker, Annual Meeting, Taiwan Mathematics Society. Taipei, Dec. 8-10.

2007
Speaker, International Symp. “Genomics and Evolution”, Guangzhou, China, Jan. 3-5.
Speaker, KITP workshop on Evolution of Biological Networks, UCSB, Feb. 5 to 9.
Speaker, the 2007 Taipei International Statistical Symposium and ICSA

International Conference, Academia Sinica, June 25-27.


Seminar, Center for Systems Biology and Bioinformatics, National Taiwan University, June 27.

Seminar, Institute of Statistics, NCTU, Hsinchu, Taiwan, July 3.


Keynote speaker, The 5th Taiwan yeast annual meeting, Academia Sinica, Aug. 1.
Speaker, Symp. on “Evolution of unusual gene organization”, 11th European Congress of Evolutionary Biology. Uppsala, Sweden, Aug 20-25.
Seminar, University of Tromso, Norway, Aug. 24.
Seminar, University of Bergen, Norway, Aug. 27.
Speaker, “Evolution of Brain and Behaviour”, Cambridge UK, September 12-14.
Speaker, International Symposium on Influenza Virus, Taiwan. October 22-24.
The Clark Cockerham Lecture, North Carolina State University, Raleigh, North Carolina, Nov. 7-9.
Seminar, Institute for Cellular and Molecular Biology, UT Austin, Nov. 14-15.
Keynote Speaker, Symposium of Botanical Society of Taiwan. NTU, Nov. 24-25
Speaker, Symposium, Computational and Theoretical Biology, Rice University, Dec. 7-9.
Public lecture, National Museum of Natural History, TaiChung, Taiwan, Dec. 15.
2008
Seminar, Center for Integrative Genomics, University of Lausanne. Feb. 27-March 1.
Public lecture. “A genetic view of human evolution”. Academia Sinica. In honor of President Wang Shi-Jie. March 8
Keynote speech, Japan-Taiwan Young Computational Scientists. March 9-11.
Seminar, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. April 16.
Keynote speaker, Symposium on Applied Mathematics, National Chung-Hsing University, May 6.
Seminar, Chinese Science and Technology University, He Fei, Anhui, China. May 13.
Seminar, Anhui University, He Fei, Anhui, China. May 13.
Speaker, Chinese Academy of Sciences Symposium for Developmental Systems Biology. Beijing, May 18-20.
Speaker, International meeting of the Society for Molecular Biology and Evolution. Barcellona, Spain. June 5-8.
Public lecture: A genomic view of human evolution. Sao Paulo, Brazil. July 12.
Symp. On “Gene Regulation and Systems Biology”, Michigan State University, East Lansing, MI. July 18-20.
Keynote speaker, Plant Mol. Biol. Summer Camp. Chia-Yi, Aug. 7-9.
Keynote speaker, Biology Summer Camp. Hsi-Tou, Aug. 27-29
Student seminar, Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign. Date to be determined.
EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts. EMBL Heidelberg, Germany, Oct. 1-5.
Keynote speaker, Symp. Taiwanese Society of Molecular Medicine, Taipei, Oct. 18.
2009
S

eminar, Institute of Bioinformatics and Systems, National Central University, Chung-Li, Taiwan. Jan. 5.


Keynote speaker, 17th Symposium on Recent Advances in Cellular and Molecular Biology, Kenting, Ping-Tung, Taiwan. February 11-13.
Speaker, Darwin Bicentennial Series, National Taiwan University, Taipei, Taiwan. Feb. 27.
S

eminar, Department of Life Sciences, National Central University, Chung-Li, Tao-Yuan, March 3


Keynote speaker, Biodiversity Conference, Center for Biodiversity, Ji-Ji, Nantou, March 15-16.
Seminar, National Chung-Hsin University, Tai-Chung, Taiwan. March 20.
Seminar, China Medical University, Tai-Chung, Taiwan. March 20.
Keynote speaker, Taiwan Genomics Association. 14th Taiwan Joint Cancer Conference. Taipei, May 2~3.
Seminar, Institute of Genomics and Systems Biology, University of Chicago, May7.
Plenary speaker, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2009). Minneapolis, Minnesota. May 17-19.
Speaker, Symp. “Evolution of biological complexity, SMBE, Iowa City, Iowa. June 3-7.
Keynote speaker, Ta-You Wu Summer Science Camp, His-tou, Nan-Tou, Aug. 2-7.
Seminar, Dept of Life Sciences, Tung-Hai University. Sept. 30.
Speaker, the 100th International Titisee Conference on “Genome evolution and the origin of novel gene functions”. Titisee, Black Forest, Germany. October 14-18.
Public talk: “Genetics and Evolution”. Academia Sinica. Nov. 24.
Seminar, Dept of Boengineering, University of Illinois, Chapaign-Urbana, Nov. 5.
The Mendel Lecture. Discussion Meeting “Genetics and the Causes of Evolution: 150 Years of Progress since Darwin”, a joint annual meeting of Genetics Society of UK and Royal Society. London November 12-13.
Seminar, Modern sequencing technology and its applications, National Tsing-Hua University, Hsin-Chu. Dec. 25.
PUBLICATIONS:
Books
Li, W.-H. Ed. (1977) Stochastic Models in Population Genetics. Dowden, Hutchinson

Ross, Stroudsburg, Pa.


Li, W.-H. and D. Graur (1991) Fundamentals of Molecular Evolution, Sinauer Associates,

Sunderland, Massachusetts.


Li, W.-H. (1997) Molecular Evolution, Sinauer Associates, Sunderland, Massachusetts
Graur, D. And W.-H. Li (2000) Fundamentals of Molecular Evolution, 2nd Edition, Sinauer

Associates, Sunderland, Massachusetts.



Papers (refereed original papers; no abstracts and book reviews included):
1. Li, W.-H. and M. Nei (1972) Total number of individuals affected by a single deleterious mutation in a finite population. Amer. J. Hum. Genet. 24:667-679.
2. Li, W.-H. (1973) Total number of individuals affected by a single sex-linked deleterious mutation in a finite population. Amer. J. Hum. Genet. 25:598-603.
3. Nei, M. and W.-H. Li (1973) Linkage disequilibrium in subdivided populations. Genetics 75:213-219.
4. Li, W.-H. and M. Nei (1974) Stable linkage disequilibrium without epistasis in a subdivided population. Theor. Pop. Biol. 6:173-183.
5. Li, W.-H. (1975) Total number of individuals affected by deleterious mutant genes in a finite population. Ann. Hum. Genet. 38:333-340.
6. Li, W.-H. (1975) The first arrival time and mean age of a deleterious mutant gene in a finite population. Amer. J. Hum. Genet. 27:274-286.
7. Freire-Maia, A., W.-H. Li, and T. Maruyama (1975) Genetics of Acheiropodia (the handless and footless families of Brazil). VII. Population Dynamics. Amer. J. Hum. Genet. 27:665-675.
8. Li, W.-H. and M. Nei (1975) Drift variances of heterozygosity and genetic distance in transient states. Genet. Res. 25:229-248.
9. Nei, M. and W.-H. Li (1975) Probability of identical monomorphism in related species. Genet. Res. 26:31-43.
10. Li, W.-H. (1976) A note on the arrival probability, first arrival time and age of a mutant gene in a finite population. Ann. Hum. Genet. 39:435-440.
11. Li, W.-H. (1976) Growth of deleterious mutant genes in a large population. Ann. Hum. Genet. 39:441-446.
12. Li, W.-H. (1976) A mixed model of mutation for electrophoretic identity of proteins within and between populations. Genetics 83:423-432.
13. Li, W.-H. (1976) Effect of migration on genetic distance. Amer. Nat. 110:841-847.
14. Li, W.-H. (1976) Electrophoretic identity of proteins in a finite population and genetic distance between taxa. Genet. Res. 28:119-127.
15. Li, W.-H. (1976) Distribution of nucleotide differences between two randomly chosen cistrons in a subdivided population: the finite island model. Theor. Pop. Biol. 10:303-308.
16. Nei, M. and W.-H. Li (1976) The transient distribution of allele frequencies under mutation pressure. Genet. Res. 28:205-214.
17. Li, W.-H. (1977) Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics 85:331-337.
18. Li, W.-H. (1977) Maintenance of genetic variability under mutation and selection pressures in a finite population. Proc. Natl. Acad. Sci. U.S.A. 74:2509-2513.
19. Li, W.-H. and M. Nei (1977) Persistence of common alleles in two related populations or species. Genetics 86:901-914.
20. Li, W.-H. (1978) Maintenance of genetic variability under the joint effect of mutation, selection and random drift. Genetics 90:349-382.

21. Li, W.-H. (1979) Effect of changes in population size on the correlation between mutation rate and heterozygosity. J. Molec. Evol. 12:319-329.


22. Li, W.-H. (1979) Maintenance of genetic variability under the pressure of neutral and deleterious mutations in a finite population. Genetics 92: 647-667.
23. Li, W.-H. (1979) Variance of genetic distance and correlation of heterozygosity between populations under the pressure of stepwise mutation. Theor. Pop. Biol. 15:171-190.
24. Nei, M. and W.-H. Li (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
25. Ewens, W.J. and W.-H. Li (1980) Frequency spectra of neutral and deleterious alleles in a finite population. J. Math. Biol. 10:155-166.
26. Nei, M. and W.-H. Li (1980) Non-random association between electromorphs and inversion chromosomes in finite populations. Genet. Res. 35:65-83.
27. Li, W.-H. (1980) Rate of gene silencing at duplicate loci: A theoretical study and interpretation of data from tetraploid fishes. Genetics 95:237-258.
28. Li, W.-H. (1981) Simple method for constructing phylogenetic trees from distance matrices. Proc. Natl. Acad. Sci. USA 78:1085-1089.
29. Li, W.-H. (1981) A simulation study on Nei and Li's model for estimating DNA divergence from restriction enzyme maps. J. Mol. Evol. 17:251-255.
30. Li, W.-H., T. Gojobori and M. Nei (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292:237-239.
31. Nei, M., W.-H. Li, F. Tajima and P. Narrain (1981) Polymorphism and evolution of the Rh blood groups. Jap. J. Human Genet. 26:263-278.
32. Gojobori, T., W.-H. Li and D. Graur (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18: 360-369.
33. Griffiths, R.C. and W.-H. Li (1983) Simulating allele frequencies in a population and the genetic differentiation of populations under mutation pressure. Theor. Pop. Biol. 23:19-33.
34. Li, W.-H. and T. Gojobori (1983) Rapid evolution of goat and sheep globin genes following gene duplication. Mol. Biol. Evol. 1:94-108.
35. Li, W.-H. (1984) Retention of cryptic genes in microbial populations. Mol. Biol. Evol. 1:213-219.
36. Lopez, L.C., W.-H. Li, M.L. Frazier, C.-C. Luo and G.F. Saunders (1984) Evolution of glucagon genes. Mol. Biol. Evol. 1:335-344.
37. Li, W.-H., C.-I. Wu and C.-C. Luo (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21:58-71.
38. Li, W.-H., C.-I. Wu and C.-C. Luo (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
39. Wu, C.-I. and W.-H. Li (1985) Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82: 1741-1745.
40. Chan, L., C.-F. Wei, W.-H. Li, C.-Y. Yang, P. Ratner, H. Pawnall, A.M. Gotto, Jr., and L.C. Smith (1985) Human liver fatty acid binding protein cDNA and amino acid sequence: Functional and evolutonary implications. J. Biol. Chem. 260:2629-2632.
41. Wei, C.-F., S-H. Chen, C.-Y. Yang, Y.L. Marcel, R.W. Milne, W.-H. Li, J.T. Sparrow, A.M. Gotto Jr., and L. Chan (1985) Molecular cloning and expression of partial cDNAs and deduced amino acid sequence of a carboxyl-terminal fragment of human apolipoprotein B-100. Proc. Natl. Acad. Sci. USA 82:7265-7269.
42. Wu, C.-I., W.-H. Li, J.J. Shen, R.C. Scarpulla, K.J. Limbach, and R. Wu (1986) Evolution of Cytochrome c Genes and Pseudogenes. J. Mol Evol. 23:61-75.
43. Luo, C.-C., W.-H. Li, M.-N. Moore, and L. Chan (1986) Structure and evolution of the apolipoprotein multigene family. J. Mol. Biol. 187:325-340.
44. Li, W.-H. (1986) Evolutionary change of restriction cleavage sites and phylogenetic inference. Genetics. 113:187-213.
45. Fukasawa, K.M., W.-H. Li, K. Yagi, C.-C. Luo, and S.S.-L. Li (1986) Molecular evolution of mammalian lactate dehydrogenase-A genes and pseudogenes: Association of a mouse processed pseudogene with a B1 repetitive sequence. Mol. Biol. Evol. 3:330-342.
46. Li, W.-H. (1986) Evolutionary change of restriction sites under unequal rates of nucleotide substitution among the three positions of codons. J. Mol. Evol. 23:205-210
47. Chen, S.-H., C.-Y. Yang, P.-F. Chen, D. Setzer, M. Tanimura, W.-H. Li, A. M. Gotto, Jr. and L. Chan (1986) The complete cDNA and amino acid sequence of human apolipoprotein B-100. J. Biol. Chem. 261:12918-12921.
48. Yang, C.-Y., S.-H. Chen, J. T. Sparrow, S. H. Gianturco, W. A. Bradley, M. Tanimura, W.-H. Li, D. A. Sparrow, H. DeLoof, M. Rosseneu, F.-S. Lee, Z.- W. Gu, A. M. Gotto, Jr. and L. Chan (1986) Sequence, structure, receptor-binding domains and internal repeats of human apolipoprotein B-100. Nature 323:738-742
49. Sharp, P.M. and W.-H. Li (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for "rare" codons. Nucl. Acids Res. 14:7737-7749.
50. Sharp, P.M. and W.-H. Li (1986) An evolutionary perspective of synonymous codon usage in unicellular organisms. J. Mol. Evol. 24:28-38.
51. Byrness, L., C.-C. Luo, W.-H. Li, C.-Y. Yang, and L. Chan (1987) Chicken apolipoprotein A-I: cDNA sequence, tissue expression and evolution. Biochem. Biophys. Res. Comm., 148:485-492.
52. Chen, S.-H., G. Habib, C.-Y. Yang, Z.-W. Gu, B.R. Lee, S.-A. Weng, S. Silberman, S.-J. Cai, J.P. Deslypere, M. Rosseneu, A.M. Gotto, Jr., W.-H. Li and L. Chan (1987) Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science, 238:363-366.
53. Datta, S., W.-H. Li, I. Ghosh, C.-C. Luo, and L. Chan (1987) Structure and expression of dog apolipoprotein C-II and C-III mRNAs: Implications for the evolution and functional constraints of apolipoprotein structure. J. Biol. Chem., 262:10588-10593.
54. De Loof, H., M. Rosseneu, C.-Y Yang, W.-H. Li, A.M. Gotto, Jr. and L. Chan (1987) Human apolipoprotein B: analysis of internal repeats and homology with other apolipoproteins. J. Lipid Res., 28:1455-1465.
55. Li, W.-H. and M. Tanimura (1987) The molecular clock runs more slowly in man than in apes and monkeys. Nature 326:93-96.
56. Li, W.-H., (1987) Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J. Mol. Evol. 24:337-345.
57. Li, W.-H. and C.-I Wu (1987) Rates of nucleotide substitution are evidently higher in rodents than in man. Mol. Biol. Evol. 4:74-77.
58. Li, W.-H., M. Tanimura and P.M. Sharp (1987) An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J. Mol. Evol. 25:330-342.
59. Pamilo, P., M. Nei and W.-H. Li (1987) Accumulation of mutations in sexual and asexual populations. Genet. Res., 49:135-146.
60. Sharp, P.M. and W.-H. Li (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucl. Acids Res. 15:1281-1295.
61. Sharp, P.M. and W.-H. Li (1987) The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol., 4:222-230.
62. Sharp, P.M. and W.-H. Li (1987) Ubiquitin genes as a paradigm of concerted evolution of tandem repeats. J. Mol. Evol., 25:58-64.
63. Sharp, P.M. and W.-H. Li (1987) Molecular evolution of ubiquitin genes. Trends Ecol. Evol. 2:328-332.
64. Smouse, P.E. and W.-H. Li (1987) Likelihood analysis of mitochondrial restriction cleavage patterns for the human-chimpanzee-gorilla trichotomy. Evolution, 41:1162-1176.
65. Wolfe, K.H., W.-H. Li, and P.M. Sharp (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc. Natl. Acad. Sci. 84:9054-9058.
66. Li, W.-H., K.H. Wolfe, J. Sourdis, and P.M. Sharp (1987) Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution. In "Evolution of Catalytic Function", Cold Spring Harbor Symp. Quant. Biol. 52:847-856.
67. Datta, S., C.-C. Luo, W.-H. Li, P. VanTuinen, D.H. Ledbetter, M.A. Brown, S.-H. Chen, S.-W. Liu, and L. Chen (1988) Human hepatic lipase: Cloned cDNA sequence, restriction fragment polymorphisms, chromosomal localization and evolutionary relationships with lipoprotein lipase and pancreatic lipase. J. Biol. Chem., 263:1107-1110.
68. Li, W.-H., M. Tanimura, C.-C. Luo, S. Datta and L. Chan (1988) The apolipoprotein multigene family: biosynthesis, structure, structure-function relationships and evolution. J. Lipid Res. 29:245-271.
69. Su, C.-J., J.W. White, W.-H. Li, C.-C. Luo, M.L. Frazier, G.F. Saunders, and L. Chan (1988) Structure and evolution of somatostatin genes. Mol. Endocrinol. 2:209-216.
70. Li, W.-H., M. Tanimura, and P.M. Sharp (1988) Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5:313-330.
71. Graur, D., and W.-H. Li (1988) Evolution of protein inhibitors of serine proteinases: positive Darwinian selection or compositional effects? J. Mol. Evol. 28:131-135.
72. Sharp, P. M. and W.-H. Li (1988) Understanding the origins of AIDS viruses. Nature 336:315.
73. Yang, C.-y., Z.-W. Gu, S.-a. Weng, T. W. Kim, S.-H. Chen, H.J. Pownall, P.M. Sharp, S.-W. Liu, W.-H. Li, A.M. Gotto, Jr. and L. Chan (1989) Structure of apolipoprotein B-100 of human low density lipoproreins. Arteriosclerosis 9:96-108.
74. Semenkovich, C.F., S.-H. Chen, M. Wims, C.-C. Luo, W.-H. Li, and L. Chan (1989) Lipoprotein lipase and hepatic lipase mRNA tissue specific expression, developmental regulation and evolution. J. Lipid Res., 30:423-431.
75. Graur, D., Y. Shuali and W.-H. Li (1989) Deletions in processed pseudogenes accumulate faster in rodents than in humans. J. Mol. Evol. 28:279-285.
76. Wolfe, K.H., P.M. Sharp and W.-H. Li (1989) Mutation rates differ among regions of the mammalian genome. Nature 337:283-285.
77. Sharp, P. M. and W.-H. Li (1989) On the rate of DNA sequence evolution in Drosophila. J. Mol. Evol. 28:398-402.
78. Gouy, M. and W.-H. Li (1989) Molecular phylogeny of kingdoms Animalia, Plantae, and Fungi. Mol. Biol. Evol. 6:109-122.
79. Li, W.-H. (1989) A statistical test of phylogenies estimated from sequence data. Mol. Biol. Evol. 6: 424-435.
80. Wolfe, K.H., M. Gouy, Y.-W. Yang, P.M. Sharp and W.-H. Li (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA. 86:6201-6205.
81. Wolfe, K.H., P.M. Sharp and W.-H. Li (1989) Rates of synonymous substitution in plant nuclear genes. J. Mol. Evol. 29: 208-211.
82. Jenne, D.E., D. Masson, M. Zimmer, J.-A. Haefliger, W.-H. Li and J. Tschopp (1989) Isolation and complete structure of the lymphocyte serine protease granzyme G, a novel member of the granzyme multigene family in murine cytolytic T-lymphocytes. Evolutionary origin of lymphocyte proteases. Biochemistry 28:7953-7961.
83. Luo, C.-C, W.-H. Li and L. Chan (1989) Structure and expression of dog apolipoprotein A-I, E, and C-I mRNAs: Implications for the evolution and functional constraints of apolipoprotein structure. J. Lipid Res. 30:1735 -1746.
84. Gouy, M. and W.-H. Li (1989) Phylogenetic analysis based on rRNA sequences supports the archaebacterial tree rather than the eocyte tree. Nature 339:145-147.
85. Sharp, P.M., D.C. Shields, K.H. Wolfe and W.-H. Li (1989) Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246:808-810.
86. O'hUigin, C., L. Chan, and W.-H. Li (1990) Cloning and sequencing of bovine apolipoprotein A-I cDNA and molecular evolution of apoliproteins A-I and B-100. Mol. Biol. Evol. 7:327-339.
87. Hiraoka,B.Y., F.S. Sharief, Y.-W. Yang, W.-H. Li and S. S. Li (1990) The cDNA and protein sequences of mouse lactate dehydrogenase-B: Molecular evolution of vertebrate lactate dehydrogenase genes A (muscle), B (heart) and C (testis) Eur. J. Biochem.189:215-220.
88. Wu, J.H., C.F. Semenkovich, S.-H. Chen, W.-H. Li and L. Chan (1990) Apolipoprotein B editing: Validation of a sensitive assay and developmental biology of RNA editing in the rat. J. Biol. Chem. 265:12312-12316.
89. Li, W.-H., M. Gouy, P.M. Sharp, C. O'hUigin and Y.-W. Yang (1990) Molecular phylogeny of Rodentia, Lagmorpha, Primtes, Artiodactyla and Carnivora and molecular clocks. Proc. Natl. Acad. Sci. USA 87:6703-6707.
90. Xiong, W., W.-H. Li, I. Posner, T. Yamamura, A. Yamamoto, A.M. Gotto, Jr. and L. Chan (1991) No severe bottleneck during human evolution: evidence from two apolipoprotein deficiency alleles. Amer. J. Hum. Genet. 48:383-389.
91. Chan, L. and W.-H. Li (1991) Apolipoptrotein variation among different species. Current Opinion in Lipidology 2:96-103.
92. Li, W.-H. and L.A. Sadler (1991) Low nucleotide diversity in man. Genetics 129:513-523.
93. Graur, D., W.A. Hide and W.-H. Li (1991) Is the guinea pig a rodent? Nature 351:649 - 652.
94. Yang, Y.-W., L. Chan and W.-H. Li (1991) Cloning and sequencing of bovine apolipoprotein E cDNA and molecular evolution of apolipoproteins E, C-I and C-II. J. Mol. Evol. 32:469-475.
95. Fu, Y.X. and W.-H. Li (1991) Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree. Math. Biosci. 105:229-238.
96. Graur, D. and W.-H. Li (1991) Neutral mutation test. Nature 354:114-115.
97. Fu, Y.X. and W.-H. Li (1992) Necessary and sufficient conditions for the existence of linear invariants. Math. Biosci. 108:203-218.
98. Fu, Y.X. and W.-H. Li. (1992) Construction of linear invariants in phylogenetic inferenece. Math. Biosci. 109: 201-228.
99. Seino, S., G.I. Bell and W.-H. Li (1992) Sequences of primate insulin genes support the hypothesis of a slower rate of molecular evolution in humans and apes than in monkeys. Mol. Biol. Evol. 9:193-203.
100. Li, W.-H., W.A. Hide, A. Zharkikh, D.-P. Ma and D. Graur (1992) The molecular taxonomy and evolution of the guinea pig. J. Heredity, 83: 174-181.
101. Hide, W.A., L. Chan and W.-H. Li (1992) Structure and evolution of the lipase superfamily. J. Lipid Res. 33:167-178.
102. Zharkikh, A. and W.-H. Li (1992) Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: I. Four taxa with a molecular clock. Mol. Biol. Evol. 9:1119-1147.
103. Zharkikh, A. and W.-H. Li (1992) Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock. J. Mol. Evol. 35: 356-366.
104. O'hUigin, C. and W.-H. Li (1992) The molecular clock ticks regularly in muroid rodents. J. Mol. Evol. 35:377-384.
105. Fu, Y.-X and W.-H. Li (1992) Maximum likelihood estimation of population parameters. Genetics 134:1261-1270.
106. Gu, X. and W.-H. Li (1993) Higher rates of amino acid substitution in rodents than in humans. Mol. Phylogen. Evol. 1:211-214.
107. Li, W.-H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
108. Fu, Y.-X. and W.-H. Li (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709.
109. Ma, D.-P., A. Zharkikh, D. Graur, J. L. VandeBerg and W.-H. Li (1993) Structure and evolution of opossum, guinea pig, and porcupine cytochrome b genes. J. Mol. Evol. 36:327-334.
110. Shimmin, L. C., B. H.-J. Chang and W.-H. Li (1993) Male-driven evolution of DNA sequences. Nature 362:745-747.
111. Shimmin, L. C., H.-J. Chang, D. Hewett-Emmett and W.-H. Li (1993) Potential problems in estimating the male-to-female mutation rate ratio from DNA sequence data. J. Mol. Evol. 37:160-166.
112. Zharkikh, A. and W.-H. Li (1993) Inconsistency of the maximum-parsimony method: the case of five taxa with a molecular clock. Systematic Biol. 42:113-125.
113. Chaw, S.-M., H. Long, B.-S. Wang, A. Zharkikh and W.-H. Li (1993) The phylogenetic position of Taxaceae based on 18S rRNA sequences. J. Mol. Evol. 37:624-630.
114. Ellsworth, D., D. Hewett-Emmett and W.-H. Li (1993) Insulin-like growth factor II intron sequences support the Hominoid rate-slowdown hypothesis. Mol. Phylogen. Evol. 2:315-321.
115. Gu, Z.-W. Y.-H. Xie, W.-H. Li, M. Yang, K. Wang, Y. Li, A.M. Gotto, Jr., and C.Y. Yang (1993) Primary structure of Beijing duck apolipoprotein A-1. J. Protein Chem. 12:585-591.
116. Shyue, S.-K., L. Li, B. H.-J. Chang, D. Hewett-Emmett and W.-H. Li (1994) Intronic gene conversion in the evolution of human X-linked color vision genes. Mol. Biol. Evol. 11:548-551.
117. Chang, B. H.J., L.C. Shimmin, S.-K. Shyue, D. Hewett-Emmett, and W.-H. Li (1994) Weak male-driven evolution in rodents. Proc. Natl. Acad. Sci. USA, 91:827-831.
118. Gu, X. and W.-H. Li (1994) A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores. J. Mol. Evol. 38:468-475.
119. Shimmin, L. C., H.-J. Chang, and W.-H. Li (1994) Contrasting rates of nucleotide substitution in Y-linked and X-linked zinc finger genes. Mol. Biol. Evol. 39:569-578.
120. Ellsworth, D., D. Hewett-Emmett and W.-H. Li (1994) Evolution of base composition in the insulin and insulin-like growth factor genes. Mol. Biol. Evol. 11:875-885.

121. Li, W.-H. and A. Zharkikh (1994) What is the bootstrap technique? Syst. Biol. 43:424-430.


122. Oka, K., K. Ishimura-Oka, M.-j. Chu, M. Sullivan, J. Krushkal, W.-H. Li and L. Chan (1994) Mouse very low density lipoprotein receptor (VLDL) cDNA cloning, tissue-specific expression and evolutionary relationship with the low density liprotein receptor. Eur. J. Biochem. 224:975-982.
123. Chang, B. H.-J. and W.-H. Li (1995) Estimating the intensity of male-driven evolution in rodents by using X-linked and Y-linked Ube1 genes and pseudogenes. J. Mol. Evol. 40:70-77.
124. Gu, X., Y.-X Fu and W.-H. Li (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
125. Gu, X. and W.-H. Li (1995) The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J. Mol. Evol. 40:464-473.
126. Zharkikh, A. and W.-H. Li (1995) Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Mol. Phyl. Evol. 4:44-63.
127. Li, W.-H. and A. Zharkikh (1995) Statistical tests of DNA phylogenies. Syst. Biol. 44:49-63.
128. Nakamuta, M., K. Oka, J. Krushkal, K. Kobayashi, M. Yamamoto, W.-H. Li, and L. Chan (1995) Alternative mRNA splicing and differential promotor utilization determine tissue-specific expression of the apolipoprotein B mRNA-editing protein (Apobec1) gene in mice. J. Biol. Chem. 270: 13042-13056.
129. Chaw, S.-M., H.-M. Sung, H. Long, A. Zharkikh and W.-H. Li (1995) The phylogenetic positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia inferred from 18S rRNA sequences. J. Mol. Evol. 41:224-230.
130. Li, W.-H. and X. Gu (1995) Statistical models for studying DNA Sequence evolution. Physica A 221:159-167.
131. Krushkal, J. and W.-H. Li (1995) Substitution rates in the hepatis delta virus. J. Mol. Evol. 41:721-726.
132. Shyue, S.-K., D. Hewett-Emmett, H. G. Sperling, D.M. Hunt, J.K. Bowmaker, J.D. Mollon and W.-H. Li (1995) Adaptive evolution of colour vision genes in higher primates. Science 269:1265-1267
133. Li, W.-H., D.L. Ellsworth, J. Krushkal, Benny H.-J. Chang and D. Hewett-Emmett (1996) Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phyl. Evol. 5:182-187.
134. Chang, B. H.J., D. Hewett-Emmett, and W.-H. Li (1996) Male-to-female ratios of mutation rate in higher primates estimated from intron sequences. Zool. Study 35:64-48.
135. Zhou, Y.-H. and W.-H. Li (1996) Gene conversion and natural selection in the evolution of X-linked color vision genes in higher primates. Mol. Biol. Evol. 13:780-783.
136. Gu, X. and W.-H. Li (1996) A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc. Natl. Acad. Sci. USA 93:4671-4676.
137. Nakamuta, M., B.H.-J. Chang, R. Hoogeveen, W.-H. Li and L. Chan (1996) Mouse microsomal triglyceride transfer protein large subunit: cDNA cloning and deduced amino acid sequence, chromosomal localization of its gene, and tissue-specific mRNA expression. Genomics 33:313-316.
138. Fu, Y.-X. and W.-H. Li (1996) Estimating the age of the common ancestor of men from the ZFY intron. Science 272:1356-1357.
139. Gu, X. and W.-H. Li (1996) Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies. Mol. Biol. Evol. 13:1375-1383.
140. Huang, B. H.-J. Chang, X. Gu, D. Hewett-Emmett and W.- H. Li (1996) Sex differences in mutation rate in higher primates estimated from AMG intron sequences. J. Mol. Evol. 44:463-465.
141. Shimmin, L. C., P. Mai and W.- H. Li (1996) Sequences and evolution of human and squirrel monkey blue opsin genes. J. Mol. Evol. 44:378-382.
142. Chaw, S.-M., A. Zharkikh, H.-M. Sung, T.-C. Lau and W.-H. Li (1997) Molecular phylogeny of extant gymnosperms and seed plant evolution: Analysis of 18S rRNA sequences. Mol. Biol. Evol. 14:56-68.
143. Sun, H., A. Rodin, Y.-H. Zhou, D.P. Dickinson, D. E. Harper, D. Hewett-Emmett, and W.- H. Li (1997) Evolution of paired domains: Isolation and sequencing of jellyfish and hydra Pax genes related to Pax-5 and Pax-6. Proc. Natl. Acad. Sci. USA 94:5156-5161.
144. Mannen, H., S. C.-M. Tsoi, J. S. Krushkal, W.- H. Li, and S. S.-L. Li (1997) cDNA cloning and molecular evolution of reptile and pigeon lactate dehydrogenease isozymes. Mol. Biol. Evol. 14:1081-1087.
145. Fu, Y.-X. and W.-H. Li (1997) Estimating the age of the common ancestor of a sample of DNA sequences. Mol. Biol. Evol. 14:195-199.
146. Chan, L., Benny H.-J. Chang, M. Nakamuta, W.-H. Li and L.C. Smith (1997) Apobec-1 and apolipoprotein B mRNA editing. Biochim. Biophys. Acta 1345:11-26.
147. Casane, D., S. Boissinot, B. H.-J. Chang, L. Shimmin, and W.-H. Li (1997) Mutation pattern variation among regions of the primate genome. J. Mol. Evol. 45:216-226.
148. Boissinot, S., Y.-H. Zhou, L. Qiu, K.S. Dulai, K. Neiswanger, H. Schneider, I. Sampaio, D.M. Hunt, D. Hewett-Emmett, and W.-H. Li (1997) Origin and molecular evolution of the X-linked color vision genes in howler monkeys. Zool. Studies 36:360-369.
149. Huang, W., Y.-X. Fu, B. H.-J. Chang, X. Gu, L. B. Jorde, and W.-H. Li (1997) Sequence variation in ZFX introns in human populations. Mol. Biol. Evol. 15:138-142.
150. Zhou, Y.-H., D. Hewett-Emmett, J. P. Ward and W.-H. Li (1997) Unexpected conservation of the X-linked color vision gene in nocturnal prosimians: Evidence from two bush babies. J. Mol. Evol. 45: 610-618.
151. Shyue, S.-K., S. Boissinot, H. Schneider, I. Sampaio, M. P. Schneider, C.R. Abee, L. Williams, D. Hewett-Emmett, H. G. Sperling, J.A. Cowing, K. S. Dulai, D.M. Hunt, and W.-H. Li (1998) Molecular Genetics of spectral tuning in New World monkey colour vision. J. Mol. Evol. 46:697-702.
152. Gu, X., D. Hewett-Emmett and W.-H. Li (1998) Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica 102/103:383-391.
153. Shimmin, L.C., J. Miller, H.N. Tran, and W.-H. Li (1998) Contrasting levels of DNA polymorphism at the autosomal and X-linked visual color pigment loci in humans and squirrel monkeys. Mol. Biol. Evol. 15:449-455.
154. Zhao, Z., D. Hewett-Emmett, and W.-H. Li (1998) Frequent gene conversion between human red and green opsin genes. J. Mol. Evol. 46: 494-496.
155. Gu, X. and W.-H. Li (1998) Evolutionary distances under stationary and nonstationary models of nucleotide substitution. Proc. Natl. Acad. Sci. USA. 95: 5899-5905.
156. Hunt, D. K.S. Dulai, J.A. Cowing, J.D. Mollon, J.K Bowmaker, B.B. Lee, D. Hewett-Emmett, and W.-H. Li (1997) Molecular evolution of trichromacy in primates. Vision Res. 38:3299-3306.
157. Xia, X. and W.-H. Li (1998) What amino acid properties affect protein evolution? J. Mol. Evol. 47:557-564.
158. Boissinot, S., Y. Tan, S.K. Shyue, H. Schneider, I. Sampaio, K. Neiswanger, D. Hewett-Emmett, and W.-H. Li (1998) Origins and antiquity of the X-linked triallelic color vision systems in New World monkeys. Proc. Natl. Acad. Sci. USA 95:13749-13754.
159. Rana, B., D. Hewett-Emmett, L. Jin, B. H.-J. Chang, N. Sambuughin, M. Lin, S. Watkins, M. Bamshad, L. B. Jorde, M. Ramsay, T. Jenkins, and W.-H. Li (1999) High polymorphism at the human melanocortin 1 receptor locus.Genetics 151:1547-1557.
160. Yang, Y.-W., K.-N. Lai, P.-Y. Tai, and W.-H. Li (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J. Mol. Evol. 48:597-604.
161. Yang, Y.-W., K.-N. Lai, P.-Y. Tai, D.-P. Ma and W.-H. Li (1999) Molecular phylogenetic studies of Brassica, Rorippa, Arabidopsis, and allied genera based on the internal transcribed spacer region of 18S-25S rDNA. Mol. Phylog. Evol. 13:455-462.
162. Callaerts, P., A.M. Munoz-Marmol, S. Glardon, E. Castillo, H. Sun, W.H. Li, W.J. Gehring, and E. Salo. (1999) Isolation and expression of a Pax-6 gene in the regenerating and intact Planarian Dugesia (G) tigrina. Proc. Natl. Acd. Sci. USA. 96:558-563.
163. Tourasse, N. and W.-H. Li (1999) Performance of the relative rate test under nonstationary models of nucleotide substitution. Mol. Biol. Evol., 16:1068-1078.
164. Tan, Y. and W.-H. Li (1999) Trichromatic vision in prosimians. Nature 402:36.
165. Rodin, A. and W.-H. Li (1999) A rapid heuristic algorithm for finding minimum

evolution trees. Mol. Phylog. Evol. 16:173-179.


166. Tourasse, N. and W.-H. Li (1999) Selective constraints, amino acid composition and

the rate of protein evolution. Mol. Biol. Evol. 17:656-664.


167. Zhao, Z., L. Jin, Y-X Fu, M. Ramsay, T. Jenkins, E. Leskinen, P. Pamilo, M. Trexler,

L. Patthy, L. Jorde, N. Sambuughin, N. Yu, and W.-H. Li (2000) Worldwide DNA

sequence variation in a 10 kilobase noncoding region on chromosome 22. Proc. Natl.

Acad. Sci. USA 97: 11354-11358.

168. Yu, N., C. Zheng, Y.-P.Zhang, and W.-H. Li (2000) Molecular systematics of pikas

(genus Ochotona) inferred from mitochondrial DNA sequences. Mol. Phylog. Evol.,

16:85-95.


  1. Yu, N. and W.-H. Li (2000) No fixed difference between Africans and non-Africans at the pyruvate dehydrogenase E1 α-subunit locus. Genetics 155:1481-1483.




  1. Zhou, Y.-H., J. Zheng, G. Xun, W.-H. Li, and G. F. Saunders (2000) A novel Pax6

binding site in rodent B1 repetitive elements. Gene 245:319-328.


  1. Adkins, R.M., J. VandeBerg and W.-H. Li (2000) Molecular evolution of growth

hormone and receptor in the guinea pig, a mammal unresponsive to growth hormone.

Gene 246:357-363.





  1. Ota, S. and W.-H. Li (2000) NJML: A hybrid algorithm for the neighbor-joining and

maximum- likelihood methods. Mol. Biol. Evol. 17:1401-1409.


  1. Yao, Y.-G., X.-M. Lu, H.-R Luo, W.-H. Li, and Y.-P. Zhang (2000) Gene admixture in

the silkroad region of China – evidence from mtDNA and melanocortin 1 receptor

polymorphism. Genes Genet. Syst. 75:173-178.




  1. Nekrutenko, A. and W.-H. Li (2000) Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 10:1986-1995.




  1. Gu, Z., H. Wang, A. Nekrutenko and W.-H. Li (2000) Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequences. Gene 259:81-88.




  1. Adkins, R.M., A. Nekrutenko and W.-H. Li (2001) Bushbaby growth hormone is much

more similar to nonprimate growth hormones than to rhesus monkey and human

growth hormones. Mol. Biol. Evol. 18:55-60.




  1. Yu, N., Z. Zhao, Y-X Fu, M. Ramsay, T. Jenkins, E. Leskinen, L. Patthy, L. Jorde, N.

Sambuughin, and W.-H. Li (2001) Global Patterns of Human DNA Sequence

Variation in a 0-kb Region on Chromosome 1. Mol. Biol. Evol. 18:214-222.




  1. Liu, J.-C., K. Makova, R.M. Adkins, S. Gibson, and W.-H. Li (2001) Episodic

evolution of growth hormone in primates and emergence of the species specificity of

human growth hormone receptor. Mol. Biol. Evol. 18:945-953.




  1. Li, W.-H., Z. Gu, H. Wang, and A. Nekrutenko (2001) Evolutionary analyses of the human genome. Nature 409: 847-849.



  1. Chen, F-C and W.-H. Li (2001) Genomic divergences between human and other

hominoids and the effective population size of the common ancestor of human and

chimpanzee. Am. J. Hum. Genet. 68:444-456.



  1. Makova, K. D., M. Ramsay, T. Jenkins, and W.-H. Li. 2001. Human DNA sequence

variation in a 6.6-kilobase region containing the melanocortin 1 receptor promoter.

Genetics 158: 1253-1268.



  1. Ota, S. and W.-H. Li (2001) NJML+: An extension of the NJML method to handle

protein sequence data and computer software implementation. Mol. Biol. Evol.

8:1983-1992.





  1. Sun, H., D. P. Dickinson, J. Costello, and W.-H. Li (2001) Isolation of Cladonema

Pax-B genes and studies of the DNA binding properties of cnidarian Pax paired

domains. Mol. Biol. Evol. 18:1905-1918.



  1. Nekrutenko, A. and W.-H. Li (2001) Transposable elements are found in a large number of human protein coding regions. Trends in Genetics 17:619-621.




  1. Nekrutenko, A., K. D. Makova and W.-H. Li (2001) The KA/KS ratio test for assessing the protein-coding potential of genomic regions: An empirical and simulation study. Genome Res. 12:198-202.




  1. Chen, F.-C., E. J. Vallender, H. Wang, C.-S. Tzeng and W.-H. Li (2001) Genomic

divergence between human and chimpanzee estimated from large-scale alignments

of genomic sequences. J. Heredity 92:481-489.

187. Cropp, S., S. Boinski, and W.-H. Li (2001) Allelic variation in the squirrel monkey X-

linked color vision gene: Biogeographical and behavioral correlates. J. Mol. Evol. 54:

734-745.

188. Jacobs, G.H., J.F. Deegan, Y. Tan, and W.-H. Li (2002) Opsin gene and

Photopigment polymorphism in a prosimian primate. Vision Res. 42:11-18.
189. Gu, Z., A. Cavalcanti, F.-C. Chen, P. Bouman and W.-H. Li (2002) Extent of gene

duplication in the genomes of Drosophila, nematode and yeast. Mol. Biol. Evol. 19:256-262. PMID: 11861885
190. Yang, Y.-W., P.-Y. Tai, Y. Chen, and W.-H. Li (2002) A Study of the Phylogeny of

Brassica rapa, B. nigra, Raphanus sativus and Their Related Genera Using Non-

coding Regions of Chloroplast DNA. Mol. Phylogen. Evol. 23:268-275.

191. Yang, Y.-W., Y. Chen, and W.-H. Li (2002) The influence of adjacent nucleotides on



the pattern of nucleotide substitution in mitochondrial introns of angiosperms. J. Mol.

Evol. 55:111-15.
192. Makova, K. D. and W.-H. Li (2002) Strong male-driven evolution of DNA sequences

in humans and apes. Nature 416:624-626.

193. Yi, S., B. Bernat, G. Pál, A. Kossiakoff, and W.-H. Li (2002) Functional promiscuity of

squirrel monkey growth hormone receptor toward both primate and nonprimate

growth hormones. Mol. Biol. Evol. 19:1083-1092.
194. Sun, H., S. Merugu, X. Gu, D. P. Dickinson, P. Callaerts, and W.-H. Li (2002)

Identification of essential amino acid changes in paired domain evolution using a

combination of evolutionary analysis and in vitro and in vivo studies. Mol. Biol. Evol.

19:1490-1500.


195. Mu, J., J. Duan, K. Makova, D. A. Joy, C. Q. Huynh, O. H. Branch, W.-H. Li, and X.-z.

Su (2002) Chromosome-wide SNPs reveal an ancient origin for Plasmodium



falciparum. Nature 418: 323-326.
196. Yu, N., F.-C. Chen, S. Ota, L. B. Jorde, P. Pamilo, L. Patthy, M. Ramsay, T. Jenkins,

S.-K. Shyue and W.-H. Li (2002) Larger Genetic Differences within Africans than

between Africans and Eurasians. Genetics 161:269-274.
197. Yu, N., Y.-X. Fu, and W.-H. Li (2002) DNA Polymorphism in a world-wide sample of

human X chromosomes. Mol. Biol. Evol. 19:2131-2141.



198. Kaessmann, H., S. Zöllner, A. Nekrutenko and W.-H. Li (2002) Signatures of domain

shuffling in the human genome. Genome Res. 12: 1642-1650.



199. Gu, Z., D. Nicolae, H. H.-S Lu, and W.-H. Li (2002) Rapid divergence in expression

between duplicate genes inferred from microarray data. Trend Genet. 18:609-613.

PMID: 12446139

200. Yi, S., D. L. Ellsworth, and W.-H. Li (2002) Slow molecular clocks in Old World

monkeys, apes and humans. Mol. Biol. Evol. 19:2191-2198.
201. Gu, Z., L. M. Steinmetz, X. Gu, C. Scharfe, R. W. Davis, and W.-H. Li (2003) Role of

duplicate genes in genetic robustness against null mutations. Nature 421:63-66.

PMID: 12511954
202. Cavalcanti, A. R. O., Ricardo Ferreira, Z. Gu and W.-H. Li (2003) Patterns of gene

duplication in Saccharomyces cerevisiae and Caenorhabditis elegans. J. Mol. Evol.

56:28-37.
203. Xia, X., Z. Xie and W.-H. Li (2003) Effects of GC content and mutational pressure on

The lengths of exons and coding sequences. J. Mol. Evol. 56:362-370.


204. Dominy, N. J., J.-C. Svenning and W.-H. Li (2003) Historical contingency in the

evolution of primate color vision. J. Hum. Evol. 44:25-45.


205. Yang, J., Z. Gu and W.-H. Li (2003) Rate of protein evolution vs. fitness effect of

gene deletion. Mol. Biol. Evol. 20:772-774. PMID: 12679525


206. Makova, K. D. and W.-H. Li (2003) Divergence in the spatial pattern of gene

expression between human duplicate genes. Genome Res. 13: 1638-1645.


207. Jensen-Seaman, M. I. and W.-H. Li (2003) Evolution of the hominoid semenogelin

genes, the major proteins of ejaculated semen. J. Mol. Evol. 57:261-270.


208. Nekrutenko, A., W.-Y. Chung and W.-H. Li (2003) An evolutionary approach reveals

a high protein-coding capacity of the human genome. Trends Genet. 19: 306-310.


209. Yu, N., M. I. Jensen-Seaman, L. Chemnick, J. R. Kidd, A. S. Deinard, O. Ryder, K. K.

Kidd and W.-H. Li (2003) Low nucleotide diversity in chimpanzees and bonobos.

Genetics 164:1511-1518.
210. Shih, A. C.-C. and W.-H. Li (2003) Alignment of genomic sequences using bit-level

operations. Mol. Biol. Evol. 20:1299-1309.

211. John, PR, Makova, K, Li, WH, Jenkins, T, and Ramsay, M. (2003) DNA polymorphism

and selection at the melanocortin-1 receptor gene in normally pigmented southern

African individuals. Ann N Y Acad. Sci. 994:299-306.
212. Zhang, P. Z. Gu and W.-H. Li (2003) Different Evolutionary Patterns between Young

Duplicate Genes in the Human Genome. Genome Biology 4:R56.1-6.


213. Qin, H., H.H.S. Lu, W.B. Wu and W.-H. Li (2003) Evolution of the yeast protein

interaction network. Proc. Natl. Acad. Sci. USA. 100: 12820-12824. PMID: 14557537


214. Yang, J., R. Lusk and W.-H. Li (2003) Organismal complexity, protein complexity, and

gene duplicability. Proc. Natl. Acad. Sci. USA. 100: 15661-15665.


215. Yi, S., T. J. Summers, N. M. Pearson, and W.-H. Li (2004) Recombination has little

effect on the rate of sequence divergence in pseudoautosomal boundary 1 among

humans and great apes. Genome Res. 14:37-43.
216. Wang, D., T. Oakley, J. Mower, L. C. Shimmin, S.Yim, R. L. Honeycutt, H. Tsao and

W.-H. Li (2004) Molecular evolution of bat color vision genes. Mol. Biol. Evol. 21:

295-302.
217. Zhang, L. and W.-H. Li (2004) Mammalian housekeeping genes evolve more slowly

than tissue-specific genes. Mol. Biol. Evol. 21:236-239.


218. Chaw SM, Chang CC, Chen HL, and Li W-H (2004) Dating the monocot-dicot

divergence and the origin of core eudicots using whole chloroplast genomes. J. Mol.

Evol. 58:424-441.


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