Li Lab -- Publications (Full List)

Full list of publications (as of July 2008):

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 (1999) 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. Mol. 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, 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 porotein 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.

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

170. 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.

171. 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.

172. 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.

173. 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.

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

175. 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.

176. 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.

177. 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 10-kb Region on Chromosome 1. Mol. Biol. Evol. 18:214-222.

178. 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.

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

180. 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.

181. 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.

182. 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. 18:1983-1992.

183. 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.

184. 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.

185. 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.

186. 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.

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 Genetics 18:609-613.

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.

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.

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. Nekutenko, 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.

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.

219. Shiu, S.-H. and W.H. Li (2004) Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes. Mol. Biol. Evol. 21:828-840.

220. Yu, N., M. I. Jensen-Seaman, L. Chemnick, O. Ryder and W.-H. Li (2004) Nucleotide diversity in gorillas. Genetics 166:1375-1383.

221. Shiu, S.-H., W. M. Karlowski, R. Pan, Y.-H. Tzeng, K. F. X. Mayer, and W.H. Li (2004) Comparative analysis of the receptor-like kinase family. The Plant Cell 16: 1220-1234.

222. Gu, Z., S. A. Rifkin, K. P. White, and W.H. Li (2004) Duplicate genes increase gene expression diversity within and between Species. Nat. Genet. 36:577-579.

223. Chen, H.-C., H.-C. Lee, T.-Y. Lin, W.H. Li and B.- S. Chen (2004) Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 20:1914-1927.

224. Marland, E., A. Prachumwat, N. Maltsev, Z. Gu, and W.H. Li (2004) Higher gene duplicabilities for metabolic proteins than for non-metabolic proteins in yeast and E. coli. J. Mol. Evol. 59:806-814.

225. Yang, J. and W.H. Li (2004) Developmental constraint on gene duplicability in fruit flies and nematodes. Gene 340:237-240.

226. Zhang, P., W. Min and W.H. Li (2004) Different age distribution patterns of human, nematode and Arabidopsis duplicate genes. Gene 342: 263-268.

227. Tzeng, Y-H, R. Pan and W.H. Li (2004) Comparison of three methods for estimating rates of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 21:2290-2298.

228. Qin, H., W.-B Wu, J. M. Comeron, M. Kreitman and W.-H. Li (2004) Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics 168: 2245-2260.

229. Wang, D., M. Hsieh and W.H. Li (2005) A General tendency for conservation of protein length across eukaryotic kingdoms. Mol. Biol. Evol. 22:142-147.

230. Zhang, L., H. H.S. Lu, W.-Y. Chung, J. Yang and W.-H. Li (2005) Patterns of segmental duplications in the human genome. Mol. Biol. Evol. 22: 135-141.

231. Oakley, T. H., Z. Gu, E. Abouheif, N. H. Patel and W.-H. Li (2005) Comparative methods for the analysis of gene expression evolution: An example of using yeast functional genomic data. Mol. Biol. Evol. 22:40-50.

232. Chen, T.-M., C.-C. Lu and W.H. Li (2005) Prediction of splice sites with dependency graphs and their expanded Bayesian networks. Bioinformatics, 21:471-482.

233. Huang, S.-W., R. Friedman, N. Yu, A. Yu and W.-H. Li (2005) How strong is the mutagenicity of recombination in mammals? Mol. Biol. Evol. 22: 426-431.

234. Chen, B-S, Y-C Wang, W-S Wu and W.H. Li (2005) A new measure of the robustness of biochemical networks. Bioinformatics 21: 2698-2705.

235. Yi, S. and W.-H. Li (2005) Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Mol. Biol. Evol. 22:1223-1230.

236. Ponger, L. and W.-H. Li (2005) Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol. Biol. Evol. 22:1119-1128.

237. Yang, J., A. Su and W.H. Li (2005) Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol. Biol. Evol. 22:2113-2118.

238. Shiu, S.-H., M-C. Shih, and W.H. Li (2005) Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiology 139:18-26.

239. Tsai, H.K, H. H.-S. Lu and W.-H. Li (2005) Statistical methods for identifying yeast cell cycle transcription factors. Proc. Natl. Acad. Sci. USA. 102:13532-13537.

240. Zhang, L. and W.-H. Li (2005) Human SNPs reveal no evidence of frequent positive selection. Mol. Biol. Evol. 22:2504-2507.

241. Tan, Y., A. D. Yoder, N. Yamashita and W.-H. Li (2005) Evidence from opsin genes rejects nocturnality in ancestral primates. Proc. Natl. Acad. Sci. USA. 102: 14712-147.

242. Lin, L. H., H. C. Lee, W. H. Li and B. S. Chen (2005) Dynamic modeling and gene expression prediction for cis regulatory circuits via cross gene-identification. BMC Bioinformatics 6:258.

243. Prachumwat, A. and W.-H. Li (2006) Protein function, connectivity, and duplicability in yeast. Mol. Biol. Evol. 23:30-39.

244. Shiu, S.-H., J. K. Byrnes, R. Pan, P. Zhang and W.-H. Li (2006) Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc. Natl. Acad. Sci. USA. 103: 2232-2236.

245. Chen, F.-C., S.-S. Wang, C.-J. Chen, W.-H. Li and T.-J. Chuang (2006) Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol. Biol. Evol. 23:675-682.

246. Byrnes, J. K., G. P. Morris and W.-H. Li (2006) Reorganization of adjacent gene relationships in yeast genomes by whole genome duplication and gene deletion. Mol. Biol. Evol. 23:1136-1143.

247. Tsai, H.-K., G.T.-W. Huang, M.-Y. Chou, H. H.-S. Lu and W.-H. Li (2006) Method for identifying transcription factor binding sites in yeast. Bioinformatics 22:1675-1681.

248. Gu, J. and W.-H. Li (2006) Are GC-rich isochores vanishing in mammals? Gene 385:50-56.

249. Zhongming Zhao, Z. Y. Yu, Y.-X. Fu, and W.-H. Li (2006) Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics 174:399-409.

250. Hanada, K., T. Gojobori and W.-H. Li (2006) Radical amino acid change versus positive selection in the evolution of viral envelope proteins. Gene 385:83-88.

251. Lin, Y.-S., J. K. Byrnes, J.-K. Hwang, and W.-H. Li (2006) Codon usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc. Natl. Acad. Sci. USA. 103: 14412-14416.

252. Lin, Y.-S., J.-K. Hwang, and W.-H. Li (2006) Protein complexity, gene duplicability, and gene dispensability in the yeast genome. Gene 387: 109-117.

253. Wu, W.-S., W.-H. Li and Bor-Sen Chen (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7:421.

254. Saunders, M.A., J. M. Good, E. Lawrence, R. Ferrell, W.-H. Li, and M. W. Nachman (2006) Human adaptive evolution at Myostatin, a regulator of muscle growth. Am. J. Hum. Genet. 79:1089-1097.

255. Kim, J., S.-H. Shiu, S. Thoma, W.-H. Li and S. Patterson (2006) Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biology, 7:R87.

256. Chen, F.-C., C.-J. Chen, W.-H. Li and T.-J. Chuang (2007) Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res. 17:16-22.

257. Ha, M., W.-H. Li and Z. J. Chen (2007) External factors accelerate expression divergence between duplicate genes. Trends Genet. 23:162-166.

258. Chen, B.-S., Wan.-S. Wu, Wei.-S. Wu, and W.-H. Li (2007) On the adaptive design rules of biochemical networks in evolution. Evolutionary Bioinformatics 2: 27-39.

259. Hanada, K., X. Zhang, J. O. Borevitz, W.-H. Li , and S.-H. Shiu (2007) A large number of novel small open reading frames (sORFs) in the intergenic regions of the A. thaliana genome are transcribed or under purifying selection. Genome Res.17(5): 632-640.

260. Saunders, M.A., H. Liang, and W.-H. Li (2007) Human polymorphism at microRNAs and microRNA target sites. Proc. Natl. Acad. Sci. USA. 104: 3300-3305.

261. Tzeng, Y.-H. Li, and T.-J. Chuang (2007) Mathematical properties of some measures of evolutionary distance. J. Theoret. Biol. 245:790 - 792.

262. Lin, Y.-S., Wei-Lun Hsu, J.-K. Hwang, and W.-H. Li (2007) Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol. Biol. Evol. 24:1005-1011

263. Chen, C.C., W.-H. Li and H.M. Sung (2007) Patterns of internal gene duplication in the course of metazoan evolution. Gene 396:59-65.

264. Shih, A. C.-C., T.-C. Hsiao, M.-S. Ho and W.-H. Li (2007) Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc. Natl. Acad. Sci. USA. 104, 6283-6288.

265. Liang, H. and W.-H. Li (2007) Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet. 23(8):375-378.

266. Wang, D., H.-M. Sung, T.-Y. Wang, C.-J. Huang, P. Yang, T. Chang, Y.-C. Wang, D.-L. Tseng, J.-P Wu, T.-S. Lee, M.-C. Shih and W.-H. Li (2007) Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Res. 17(8): 1161-1169.

267. Tsai, H.-K., M.-Y. Chou, C.-H. Shih, G. Huang, T.-H. Chang and W.-H. Li (2007) MYBS: A comprehensive web server for mining transcription factor binding sites. Nucleic Acid Res. 35(Web Server Issue): W221-226.

268. Wu, W-S, W.-H. Li, and B.-S. Chen (2007) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7, 421.

269. Wu, W-S, W.-H. Li, and B.-S. Chen (2007) Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics 8, 188.

270. Liang, H. and W.-H. Li (2007) MicroRNA regulation of human protein-protein interaction network. RNA 14(9): 1402-1408.

271. Jiang, C., L. Han, B. Su, W.-H. Li, and Z. Zhao (2007) Features and trend of loss of promoter-associated CpG islands in the human and mouse Genomes. Mol. Biol. Evol. in press.

272. Hanada, K., S.-H. Shiu, and W.-H. Li (2007) Comparison of the nonsynonymous/synonymous substitution rate ratio and the radical/conservative replacement rate ratio in the evolution of mammalian genes. Mol. Biol. Evol. 24(10): 2235-2241

273. Lin YC, Hsieh LC, Kuo MW, Yu J, Kuo HH, Lo WL, Lin RJ, Yu AL, Li WH. (2007) Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol. 24(11):2525-2534.

274. Lin LH, Lee HC, Li WH, Chen BS. (2007) A systematic approach to detecting transcription factors in response to environmental stresses. BMC Bioinformatics. 8(1):473.

275. Prachumwat A, Li WH. (2007) Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. Genome Res. 18(2):221-32.

276. Liang H, Plazonic RK, Chen J, Li WH, Fernández A. (2008) Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet. 4(1): e11.

277. Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH. Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A. 2008 105(7):2527-32.

278. Liang H, Lin YS, Li WH. Fast evolution of core promoters in primate genomes. (2008) Mol Biol Evol. 25(6):1239-44.

279. Zhang C, Li WH, Krainer AR, Zhang MQ. (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A.105(15):5797-802.

280. Tzeng J, Lu HH, Li WH. (2008) Multidimensional scaling for large genomic data sets. BMC Bioinformatics. 9:179.

281. Sanna CR, Li WH, Zhang L. Overlapping genes in the human and mouse genomes. BMC Genomics. 9:169.

282. Han L, Su B, Li WH, Zhao Z. (2008) CpG island density and its correlations with genomic features in mammalian
genomes. Genome Biol. 9(5):R79.

283. Wang H, Tzeng YH, Li WH. Improved variance estimators for one- and two-parameter models of nucleotide
substitution. J Theor Biol. In press

284. Chang YW, Robert Liu FG, Yu N, Sung HM, Yang P, Wang D, Huang CJ, Shih MC, Li
WH. (2008) Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast.
Mol Biol Evol. In press

Reviews and Book Chapters

1. Li, W.-H. (1982) Evolutionary change of duplicate genes. In "Isozomes: Current Topics in Medical and Biological Research," M.C. Ratazzi, J.G. Scandalios, and G.S. Whitt (eds), New York: Alan R. Liss, Inc., Vol. VI, Pp. 55-92.

2. Li, W.-H. (1983) Evolution of duplicate genes and pseudogenes. In "Evolution of Genes and Proteins," M. Nei and R.K. Koehn (eds), Sinauer, Sunderland, Massachusetts, Pp. 14-37.

3. Li, W.-H. (1985) Accelerated evolution following gene duplication and its implication for the neutralist-selectionist controversy. In: "Population Genetics and Molecular Evolution," T. Ohta and K. Aoki (eds), Japan Scientific Societies Press, Tokyo, Pp 333-352.

4. Li, W.-H., C.-C. Luo and C.-I Wu (1985) Evolution of DNA sequences. In: "Molecular Evolutionary Genetics," R.J. MacIntyre (ed), Plenum, New York, Pp. 1 - 94.

5. Tsao, Y.K., C.C. Luo, W.-H. Li, M.N. Moore, F.T. Kao and L. Chan (1985) Apolopoprotein A-II gene structure: evolutionary implications. In: "Protides of the Biological Fluids," H. Peeters, Pergman Press, Oxford, Vol 33:35-38.

6. Li, W.-H. (1986) Estimation of the numbers of synonymous and nonsynonymous substitutions between protein coding genes. In: "Evolutionary Processes and Theory," S. Karlin and E. Nevo (eds), Academic Press, New York. Pp. 295-314.

7. Chan, L., W.-H. Li and M. Tanimura (1988) Hormonal control of gene expression. In: The Liver: Biology and Pathobiology, (eds) I. Arias, W.B. Jakoby, H. Popper, D. Schachter, and D.A. Shafritz. 2nd Ed. Raven Press, New York, Pp. 103-130.

8. Chan, L. and W.-H. Li (1989) Genetic background of human apolipoprotein structure and function. In: Biologie prospective. Comptes rendus du 7e Colloque de Pont-a-Mousson. Eds. M.-M. Galteau, G. Siest, J. Penny. John Libbey Eurotext, Paris. Pp127-134.

9. Li, W.-H. and M. Gouy (1990) Statistical tests of molecular phylogenies. in Methods of Enzymology, ed. R. Doolittle, Academic Press, Pp. 645-659.

10. Chan, L., E. Boerwinkle and W.-H. Li (1990) Molecular genetics of the plasma apolipoproteins. In "Molecular Biology of the Cardiovascular System", ed. S. Chien, Lea & Febiger, Philadelphia, Pp.183-219.

11. Gouy, M. and W.-H. Li (1990) Evolutionary relationships among primary lineages of life inferred from ribosomal RNA sequences. In "The Ribosome: Structure, Function, and Evolution", eds, W. E. Hill, A. Dahlberg, R.A. Garrett, P. Moore, D. Schlessinger and J.R. Warner, American Society for Microbiology, Washington, D.C. Pp. 573-578.

12. Li, W.-H. and M. Gouy (1991) Statistical methods for testing molecular phylogenies. In: Phylogenetic Analysis of DNA Sequences, Miyamoto, M. and J. Cracraft, eds. Oxford Press, Pp. 249-277.

13. Li, W.-H. and Y.X. Fu. (1992) Method of linear invariants for phylogenetic reconstruction. In " Modelling and Computer Methods in Molecular Biology and Genetics", pp. 379-389. Eds. V.A. Ratner and N.A. Kolchanov, Nova Science Publishers, New York.

14. Li, W.-H. and L.A. Sadler (1992) DNA variation in humans and its implications for human evolution. Oxford Surveys in Evolutionary Biology, 8:111 - 134.

15. Chan, L., W.A. Hide, Y.-W. Yang and W.-H. Li (1992) Structure and evolution of the apolipoprotein and lipase gene families. In: Cellular and Molecular Bilogy of Atherosclerosis, Gotto, Jr. A.M. (ed), Springer-Verlag, Pp93-107.

16. LI, W.-H., W. Xiong, S.-W Liu, and L. Chan (1993) Nucleotide diversity in humans and evidence for the absence of a severe bottleneck during human evolution. In Genetics of Cellular, Individual, Family, and Population Variability (eds. Sing, C. F. & Hanis, C. L.) 253-261. (Oxford University Press, New York, 1993).

17. Li, W.-H. and Y.-X. Fu (1994) Estimation of population parameters and detection of natural selection from DNA sequences. In: "Non-Neutral Evolution": Theories and Molecular Data, pp. 112-125. Ed. B. Golding, Chapman & Hall, New York.

18. Adkins, R.M. and W.-H. Li (1998) Dating the age of the last common ancestor of all living organisms with a protein clock. In: Horizontal Gene Transfer, pp. 380-391. Eds. M. Syvanen and C.I. Kado. Chapman & Hall, New York.

19. Li, W.-H., S. Boissinot, Y. Tan, S.-K. Shyue, and D. Hewett-Emmett (1999) Evolutionary genetics of primate color vision: recent progress and potential limits to knowledge. Evol. Biol. 32: 151-178.

20. Krushkal, J. and W.-H. Li (1999) Use of phylogenetic inference to test an HIV transmission hypothesis. In "The Evolution of HIV" ( K.A. Crandall, ed). The Johns Hopkins University Press, Baltimore, MD. Pp. 208-232.

21. Li, W.-H. and Y.-X. Fu (1999) Coalescent theory and its application in population genetics. In: Statistics in Genetics. (M.E. Halloran and S. Geisser, eds.). Springer Verlag, New York. Pp. 45-79.

22. Fu, Y.-X. and W.-H. Li (1999) Coalescing into the 21st century: An overview and prospects of coalescent theory. Theo. Popl. Biol. 56:1-10.

23. Li, W.-H., Y. Tan, S. Boissinot, S.-K. Shyue, and D. Hewett-Emmett (2000) Genetic diversity of color vision in primates. In: The Biology of Biodiversity. (M. Kato, ed.) Springer Verlag, New York. Pp. 259-274.

24. Li, W.-H, Z. Gu, A. R. O. Cavalcanti and A. Nekrutenko (2002) Detection of Gene Duplications and Block Duplications in Eukaryotic Genomes. J. Structural Functional Genomics. 3: 27-34.

25. Li, W.-H, S. Yi and K. Makova (2002) Male-driven evolution. Current Opinion in Genetics& Development 12:650-656.

26. Wolfe, K. and W.-H. Li (2003) Molecular evolution meets the genomics revolution. Nature Genetics Supplement 33: 255-265.

27. Nekrutenko, A., W.-Y. Chung and W.-H. Li (2003) ETOPE: Evolutionary Test of Predicted Exons. Nucleic Acid Res. 31:3564-3567.

28. Lu, J., W.H. Li, and C.I. Wu (2003) Comment on "Chromosomal Speciation and Molecular Divergence-Accelerated Evolution in Rearranged Chromosomes". Science 302:988b.

29. Li, W.H., J. Yang and X. Gu (2005) Expression divergence between duplicate genes. Trends Genet. 21:620-607.

30. Li, W.H. and M.A. Saunders (2005) The chimpanzee and us. Nature 437:50-51.

31. Yi, S. and W-H. Li (2006). Episodic molecular evolution of some protein hormones in primates and its implications for primate adaptation. In J. S. Ravosa and M. Dagosto (eds), Primate Origins: Adaptation and Evolution. Pp. 739-773. Springer, New York, NY, USA.