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CAS Members  
Name:
 CHUNG-I WU
Education:
Positions:
 Director
Academic title:
 Professor
Postal Code:
Subject categories:
 Cancer Genomics, Population Genetics
Mailing Address:
E-mail:
 wuci@big.ac.cn

Resume:

Professor CHUNG-I WU was born in 1954, Taipei, Taiwan. He obtained his bachelor degree in Biology from Tunghai University, Taiwan, in 1976, and Ph.D degree in Population Genetics from the University of British Columbia, Canada, in 1982. Between 1982 and 1984, he joined the University of Taxes, Houston Medical Center, as a senior research associate. In 1985 and 1986, he was an NIH fellow at the University of Wiscosin, Madison.

Between 1986 - 1991, he was an assistant and then associate professor in the Department of Biology, University of Rochester. In 1991, he moved to the University of Chicago as an associate professor in the Department Ecology and Evolution. In 1998, he became a professor and served as the chair of the department until 2006. In 2008, he was appointed the director of Beijing Institute of Genomics, Chinese Academy of Sciences.

Prof. Wu’s research activities are mainly involved in the following four areas: 1) Molecular and population genetics of speciation in Drosophila. 2) Evolutionary genomics in Drosophila, especially microRNAs. 3) Evolutionary genomics in human and higher primates. 4) Theories of natural selection for application to human and Drosophila. Over the past several years, he and his laboratory have successfully led the trend of molecular evolution research in United States, his department has played a very important role in transforming the classic evolution research into molecular time. Professor Wu has published about 50 scientific papers and many of them are in high impact international journals such as Nature, Science and Cell.

Professor Wu has won many awards, including Research Career Development Award from NIH (1990 - 1995), National Down Syndrome Society Awards(1989 - 1991), and Distinguished Alumnus, Tunghai University, Taiwan(2004). He was elected member of Academia Sinica in 2004. In the same year, he was elected as fellow of American Association for the Advancement of Science.

Summary of academic and scholastic contributions of Chung-I Wu

Speciation and natural selection, which Darwin integrated into one field in his “Origin of Species”, are two most fundamental issues in evolution and the main subjects of Chung-I Wu's molecular evolutionary work. He has also significantly contributed to selfish genetic elements, molecular clock, evolution of X-inactivation, microRNA evolution and evolutionary genomics. The breadth and depth of his work in both theory and experiments have helped him transform a premiere department of Ecology and Evolution from the classical to the molecular era.

1) Speciation -

Speciation is a most difficult area in evolution. Even up to 1990, there was little rigorous genetic, let alone molecular, analysis on speciation. Wu’s 1992 paper was a breakthrough in genetic analysis. Since then, Wu's laboratory has transformed the field and become a foremost group in the genetics of species formation. His major publications were often noted by commentaries in Nature/Science. Between 1990-2000, Wu's lab worked out the broad genetic architecture underlying species divergence in a series of 30 papers, all in the highest caliber journals. This work established that interspecific genetic differences are extensive, in the hundreds of genes between even morphologically-indistinguishable species. The results, highlighted in 2000, concluded that species formation is a prolonged process with numerous genetic changes, driven by natural and sexual selection. This body of work contributed to the Renaissance of speciation study in the last decade and paved the way for the molecular analysis of speciation.

With the genetic results firmly in place, Wu's group became the first laboratory to clone genes of speciation. Their 1998 paper is a milestone marking the transition into the molecular era. An extreme acceleration in genic evolution was shown to accompany speciation. This was followed by a second case which is remarkable in that speciation is still in progress. His group is the first one to introduce the advanced technology of gene replacement to answer the most classical ecological questions --- in this case, how species became different (e.g., cold tolerance via pheromonal change). A connection between the formation of new genes and the formation of new species has also been shown, adding a new dimension to the field. In short, speciation at the molecular level represents a major departure from the neo-Darwinian view of the last 50 years. In his “genic view of speciation”, which attracted 10 commentaries in the same issue, Wu outlined the conceptual revolution that molecular analysis has brought, and will continue to bring, to the question of speciation. The concept has opened a new door to using genomic tools to test and develop hypotheses of speciation.

Since 2006, Wu has developed a new research project on the microevolutionary consequences of microRNA evolution. The project is an extension of his speciation research but, instead of going from phenotype to genes, it goes from genes (i.e., miRNAs) to phenotype. Their papers in this new area has started appearing in the beginning of 2008 with one in Nature Genetics and one in Molecular Biology and Evolution.

2) Natural selection -

The importance of selection at the molecular level was disputed by the neutral theory of molecular evolution, which has dominated the field for more than 20 years (Kimura 1983). His 2000 Nature paper capped their long string of studies showing that selection in relation to sex is prevalent. They subsequently generalized the trend and suggested that positive selection may in fact be pervasive. If this challenge to the neutral theory prevails, it will reverse a trend of molecular evolutionary studies. The return of the view that natural selection is the main driving force of evolution, even at the molecular level, will have far-reaching consequences in evolution and human genetics.

3) Other areas -

Wu's papers published in Cell and Nature on the involvement of satellite DNA in meiotic drive was a true feat. The Responder (or target) site was biologically inexplicable as its existence appeared suicidal; it was also deemed unclonable because of its proximity to the centromere. The involvement of satellite DNA resolved the whole mystery. The 1985 PNAS paper with WH Li opened a floodgate of research on molecular clock. Wu and Maeda (1985) published in Nature opened the avenue for recent research on strand asymmetry of mutation. Wu and Xu (2004) may revolutionize how we see the evolution of X-inactivation.

Direction:

Cancer Genomics, Population Genetics.

Achievements:

Article:
  1. Wu, C.-I. The fate of autosomal modifiers of the Sex-Ratio trait in Drosophila and other sex-linked meiotic drive systems. Theor. Pop. Biol. 24(2)(1983):107-120.
  2. Wu, C.-I. Virility selection and the Sex-Ratio trait in Drosophila pseudoobscura: I. Sperm displacement and sexual selection. Genetics 105(3) (1983):651-662.
  3. Wu, C.-I. Virility selection and the Sex-Ratio trait in Drosophila pseudoobscura: II. Multiple insemination and overall virility selection. Genetics 105(3) (1983):663-679.
  4. Wu, C.-I and A.T. Beckenbach. Evidence for extensive genetic differentiation between the Sex-Ratio and the standard arrangement of Drosophila pseudoobscura and D. persimilis and identification of hybrid sterility factors. Genetics 105(1) (1983):71-86.
  5. Nei, M., T. Maruyama and C.-I Wu. Models of evolution of reproductive isolation. Genetics 103（1983）:557-579.
  6. Li, W.H., C.-I Wu and C.C. Luo. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21(1984):58-71.
  7. Wu, C.-I. A stochastic simulation study on speciation by sexual selection. Evolution 39(1985):66-82.
  8. Wu, C.-I and W.H. Li. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. 82(1985):1741-1745.
  9. Li, W.H., C.-I Wu and C.C. Luo. 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(1985):150-174.
  10. Li, W.H., C.C. Luo and C.-I Wu. Evolution of DNA sequences. In: Molecular Evolutionary Genetics. R. J. McIntyre (ed.) Plenum, 1985, New York. 1-94.
  11. Wu, C.-I, W.H. Li, J.J. Shen, R.C. Scarpulla, K.J. Limbach and R. Wu. Evolution of cytochrome c genes and pseudogenes. J. Mol. Evol. 23(1)( 1986):61-75.
  12. Li, W.H. and C.-I Wu.. Rates of nucleotide substitution are evidently higher in rodents than in man. Mol. Biol. Evol. 4(1)( 1987):74-77.
  13. Wu, C.-I and N. Maeda. Inequality in mutation rates of the two strands of DNA. Nature 327(1987):169-170.
  14. Maeda, N., J. B., C.-I Wu, J. Reneke and J. Bliska. Molecular evolution of higher primates: Intergenic structure, rate and pattern of DNA changes and origin of simple sequences. Mol. Biol. Evol. 5(1)( 1988): 1-20.
  15. Wu, C.-I, T. W. Lyttle, M.-L. Wu and G. Lin. Association between a satellite DNA sequence and the Responder of Segregation Distorter in D. melanogaster. Cell 54(1988):179-189.
  16. Werren, J. H., U. Nur and C.-I Wu. Selfish genetic elements. Trends in Ecol. and Evol. 3(1988):297-302.
  17. Wu, C.-I, J. R. True and N. Johnson. Fitness reduction associated with the deletion of a satellite DNA array. Nature. 341(1989):248-251.
  18. Wu, C.-I and M. F. Hammer. Molecular evolution of ultraselfish genes of meiotic drive systems. In: Evolution at the Molecular Level, Selander, Whittam and Clark (eds.) Sinaur Press. 1990, p. 177-203.
  19. Wu, C.-I . Inference of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127(2)( 1991): 429-435.
  20. Wu, C.-I . Segregation Distorter in Drosophila melanogaster : Responder at the molecular level. Amer. Natur. 137(1991):314-322.
  21. Lyttle, T. W., C.-I Wu. and S. Howley . Molecular analysis of insect meiosis and sex ratio distortion. In "Molecular approaches to pure and applied entomology", M. J. Whitten and J. G. Oakeshott. Springer-Verlag ,1991, Berlin.
  22. Doshi, P., S. Kaushal, C. Benyajati and C.-I Wu. Molecular analysis of the Responder satellite DNA in Drosophila melanogaster. I. DNA bending, nucleosome spacing, and Rsp-binding proteins. Mol. Biol. Evol. 8(5)( 1991): 721 - 741.
  23. Johnson, N. A. and C-I Wu. An empirical test of the meiotic drive models of hybrid sterility: Sex-ratio data from hybrids between Drosophila simulans and D. sechellia. Genetics 130(1992):507-511.(University of Chicago affiliation below)
  24. Johnson, N. A., D. E. Perez, E. L. Cabot, H. Hollocher and C.-I Wu. A test of reciprocal X-Y interactions as a cause of hybrid sterility in Drosophila. Nature 358(1992):751-753.
  25. Wu, C-I. A note on Haldane’s ruel: Hybrid inviability versus hybrid sterility. Evolution 46(5)( 1992): 1584-1587.
  26. Wu, C-I, Daniel E. Perez, Andrew W. Davis, Norman A. Johnson, Eric. L. Cabot, Michael F. Palopoli and M.-L. Wu. Molecular genetics of reproductive isolation in Drosophila. In: “Mechanisms of Molecular Evolution” by N. Takahata and A. G. clark (ed.), Sinauer Press, 1993.
  27. Wu, C-I. and A. W. Davis. Evolution of postmating reproductive isolation: The composite nature of Haldane’s rule and its genetic bases. Amer. Natur. 142(1993):187-212.
  28. Johnson, N. A. and C.-I Wu. Evolution of postmating reproductive isolation: measuring the pleiotropic fitness effects associated with hybrid male sterility factors. Amer. Natur. 142(1993):213-223.
  29. Perez, D. E., C.-I Wu, N. A. Johnson and M.-L. Wu. Genetics of reproductive isolation in the Drosophila simulans clade: DNA marker-assisted mapping and characterization of a hybrid-male sterility gene, Odysseus (Ods). Genetics 134(1993):261-275.
  30. Johnson, N. J., H. Hollocher, E. Noonberg and C.-I Wu. The effects of iterspecific Y chromosome replacements on hybrid sterility within the Drosophila simulans clade: A comprehensive study. Genetics 135(1993): 443-453.
  31. Cabot, E. L., P. Doshi, M.-L. Wu and C.-I Wu. Population genetics of tandem repeats in centromeric heterochromatin: unequal crossing over and interchromosomal divergence at the Responder locus. Genetics 135(1993): 477-487.
  32. Palopoli, M., P. Doshi and C.-I Wu. Characterization of two Segregation distorter revertants: Evidence that the tandem duplication is necessary for the SD phenotype in Drosophila melanogaster. Genetics 136(1994): 209-215.
  33. Cabot, E. L., A. W. Davis, N. A. Johnson and C.-I Wu. Genetics of reproductive isolation in the Drosophila simulans clade: Complex epistasis underlying hybrid sterility. Genetics 137(1994): 175-189.
  34. Davis, A. W., E. Noonberg and C.-I Wu. Complex genic interactions between conspecific chromosomes underlying hybrid female serility in the Drosophila simulans clade. Genetics 137(1994): 191-199.
  35. Palopoli, M. and C.-I Wu. Genetics of hybrid male sterility between Drosophila sibling species: A complex web of epistasis is revealed in interspecific studies. Genetics138(1994):329-341.
  36. Wu, C.-I and M. F. Palopoli. Genetics of postmating reproductive isolation in animals. Ann. Rev. Genetics 28(1994):283-308.
  37. Perez, D. P. and C-I Wu. Further characterization of the hybrid sterility gene, Odysseus (Ods), in the Drosophila simulans clade: one gene is not enough. Genetics 140(1995):201-206.
  38. Wu, C.-I, H. Hollocher, D. Begun, C. F. Aquadro, Y. Xu and M.-L. Wu. Sexual isolation in Drosophila melanogaster: A possible case of incipient speciation. Proc. Natl. Acad. Sci. 92(1995):2519-2523.
  39. Davis, A. W., and C.-I. Wu, The broom of Sorcerer's apprentice: The fine structure of a chromosomal region causing reproductive isolation between two sibling species of Drosophila. Genetics 143(1996):1287-1298.
  40. Hollocher, H., and C.-I. Wu., The genetics of reproductive isolation in the Drosophila simulans clade: X vs. autosomal effects and male vs. female effects. Genetics 143(1996):1243-1255.
  41. Wu, C.-I., N. A. Johnson, and M. F. Palopoli, Haldane's rule and its legacy: why are there so many sterile males? Trends in Ecol. Evol. 11(1996):281-284.
  42. Palopoli, M. F., and C.-I. Wu, Rapid evolution of a coadapted gene complex: Evidence from the Segregation Distorter system of meiotic drive in Drosophila melanogaster. Genetics 143(1996): 1675-1688.
  43. Palopoli, M. F., A. W. Davis, and C.-I. Wu, Discord between the phylogenies inferred from molecular vs. functional data: uneven rates of functional evolution or low levels of gene flow? Genetics 144(1996):1321-1328.
  44. Tsaur, S. C., and C.-I Wu, Positive selection and the molecular evolution of a gene of male reproduction. Molec. Biol. Evol. 14(1997):544-549.
  45. Hollocher, H., C.-T. Ting, F. Pollack and C.-I Wu, Incipient speciation by sexual isolation in Drosophila melanogaster : Variation in mating preference among antural isolates. Evolution 51(1997): 1175-1181.
  46. Hollocher, H., C.-T. Ting, M.-L. Wu and C.-I Wu, Incipient speciation by sexual isolation in Drosophila melanogaster : Extensive divergence without reinforcement. Genetics 147(1997): 1191-1201.
  47. Tsaur, S. C., C.-T. Ting and C.-I Wu, Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila: II. Divergence vs. polymorphism. Molec. Biol. Evol. 15(1998):1040 - 1046.
  48. Wu, C.-I., and H. Hollocher, Subtle is nature: the genetics of species differentiation and speciation, pp.339-351 in Endless forms: species and speciation, edited by D. Howard and S. Berlocher. Oxford University Press, 1998.
  49. Ting, C.-T., S.-C. Tsaur, M.-L. Wu and C.-I Wu, A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282(1998): 1501-1504.
  50. Fay, J. C. and C.-I Wu, A human population bottleneck is not incompatible with the discordance between patterns of mitochondrial vs. nuclear DNA variation. Molec. Biol. Evol. 16(1999):1003 - 1006.
  51. Wyckoff, G. J., W. Wang and C.-I Wu, Rapid evolution of male reproductive genes in the descent of man. Nature 403(2000): 304 - 309.
  52. Sawamura, K., A. W. Davis and C.-I Wu, Genetic analysis by means of introgression into Drosophila melanogaster. Proc. Natl. Acad. Sci. 97(2000):2652-2655.
  53. Ting, T.-C., S. C. Tsaur, S.-C., and C.-I Wu, The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc. Natl. Acad. Sci. 97(2000):5313 - 5316.
  54. Fay, J. C. and C.-I Wu, Hitchhiking under positive Darwinian selection. Genetics 155(2000): 1405-1413.
  55. Wu, C.-I, Genetics of species differentiation: What is unknown and what will be unknowable? Evol. Biol. 32(2000): 239 - 248. (M. T. Clegg, M. K. Hecht and R. J. MacIntyre, eds.)
  56. Tsaur, S. C., C.-T. Ting and C.-I Wu, Sex in Drosophila mauritiana: Extremely high level of replacement polymorphism in a male reproductive gene. Molec. Biol. Evol. 18(2001):22-26
  57. Alipaz, J. A., C-I Wu and T. L. Karr, Sperm-egg incompatibility between races of Drosophila. Proc. Roy. Soc. 268(2001):789-795.
  58. Takahashi, A, S.C. Tsaur, J. A. Coyne and C.-I Wu, The nucleotide changes governing pheromonal variation in Drosophila and their evolution. Proc. Natl. Acad. Sci. 98(2001):3920-3925.
  59. Fay, J. C., G. J. Wyckoff and C.-I Wu, Positive and negative selection on the human genome. Genetics 158(2001):1227-1234.
  60. Ting, C.T., A. Takahashi and C.-I Wu, Incipient speciation by sexual selection: concurrent evolution at multiple loci. Proc. Natl. Acad. Sci. 98(2001): 6709-6713 (see also Nature 412:31-32)
  61. Luo, Z.W. and C.-I Wu, Modeling linkage disequilibrium between a polymorphic marker locus and a locus affecting dichotomous disease traits in natural populations. Genetics 158(2001): 1785-1800.
  62. Wu, C.-I The genic view of the process of speciation. J. Evol. Biol. 14(2001): 851-865..
  63. Wu, C.-I Genes and Speciation - A reply. J. Evol. Biol. 14(2001):889-891.
  64. Fay, J. C. and C.-I Wu, The neutral theory in the genomic era. Curr. Opinion Gen. Dev. 11(2001):642-646.
  65. Fay, J. C., G. J. Wyckoff and C.-I Wu, Testing the neutral theory of molecular evolution with genomic data. Nature 415(2002): 1024 - 1026.
  66. Luo, Z.W., C.-I Wu, and M. J. Kearsey, Precision and high-resolution mapping of quantitative trait loci by use of recurrent selection, backcross or intercross schemes. Genetics 161(2002): 915-929.
  67. Wyckoff, G. J., J. Li and C.-I Wu, Molecular evolution of functional genes on the mammalian Y chromosome. Molec. Biol. Evol. 19(2002): 1633-1636
  68. Fang, S., A. Takahashi, and C.-I Wu, A mutation in the promoter of desaturase 2 is correlated with sexual isolation between Drosophila behavioral races. Genetics 168 (2002): 781-784.
  69. Wu, C.-I and E. Y. Xu, Sexual antagonism and X-inactivation - The SAXI hypothesis. Trends in Genetics 19(2003):243-247.
  70. Fay, J. C., and C.-I. Wu, Sequence divergence, selective constraint and selection in protein evolution. Ann. Rev. Genomics Hum. Genet. 4(2003a):213-235.
  71. Fay, J. C., and C.-I. Wu, Detecting hitchhiking from patterns of DNA polymorphisms in Selective sweeps, edited by D. I. Nurminsky. Landes Bioscience. 2003b.
  72. Wang, H-Y., H. Tang, C. K. Shen and C.-I Wu Rapidly evolving genes in human ?C I. The glycophorins and their possible role in evading malaria parasites. Mol. Biol. Evol. 20(2003):1795-1804.
  73. Greenberg, A. J., J. R. Moran, J. A. Coyne, and Chung-I Wu Ecological adaptation during incipient speciation as revealed by precise gene replacement. Science 302(2003): 1754-1757.
  74. Lu, J., W.-H. Li and C.-I Wu. Chromosomal speciation and gene flow. Science 302(2003):988c.
  75. Wu, C.-I, S. Shi and Y. Zhang. A case for conservation. Nature 428(2004):213-214. (A commentary in a supplementary issue).
  76. Wu, C.-I and C.-T. Ting. Genes and speciation. Nature Review Genetics 5(2004): 114-122.
  77. He, J et al. (51 authors). Molecuar evolution of the SARS-conronavirus during the course of SARS-epidemic in China. Science 303(2004): 1666-1669 (C.-I Wu is a communicating author for the data analysis section).
  78. Kohn, M. H., S. Fang and C.-I Wu. Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes. Mol. Biol. Evol. 21(2004):374-383.
  79. Kyoichi Sawamura, John Roote, Chung-I Wu, and Masa-Toshi Yamamoto. Extreme Genetic Complexity Underlying Hybrid Male Sterility in Drosophila. Genetics 166(2004): 789-796.
  80. Tang, H. , G. J. Wyckoff, J Lu, and C.-I Wu, A Universal Evolutionary Index for Amino Acid Changes. Mol. Biol. Evol. 21(2004): 1548-1556.
  81. Ting, C., S. Tsuar, S. Sun, W. Browne, N. Patel and C.-I Wu. Gene duplication and speciation in Drosophila ?C Evidence from the Odysseus locus. Proc. Natl. Acad. Sci.101(2004): 12232-12235.
  82. Sun, S, C. Ting, and C.-I Wu. The normal function of a speciation gene, Odysseus, and its hybrid sterility effect. Science 305(2004): 81-83.
  83. Osada, N. and C.-I Wu. Testing the mode of speciation with genomic data - Examples from the great apes. Genetics 169(2005): 259-264.
  84. Song, H.-D. et al. C.-I Wu and G.-P. Zhao. Cross-host evolution of SARS coronavirus in palm civet and human. Proc. Natl. Acad. Sci.102(2005): 2430-2435
  85. Alipaz, J. A., S. Fang and C.-I Wu. Evolution of sexual isolation in laboratory populations: I. Genotypic vs. phenotypic changes during secondary contact. Amer. Natur. 165(2005):420-428.
  86. Alipaz, J. A., T. Karr and C.-I Wu. Evolution of sexual isolation in laboratory populations: II. Fitness effects of mating traits and the associated hybrid incompatibilities. Amer. Natur. 165(2005):429-438.
  87. Lu, Jian and C.-I Wu. Weak selection revealed by the whole-genome comparison between the X and autosomes of human and chimpanzee. Proc. Natl. Acad. Sci. 102(2005): 4063-4067.
  88. Zhou, R., S. Shi and C-I Wu. Molecular criteria for determining new hybrid species - an application to the Sonneratia hybrids. Molec. Phy. Evol. 35(2005):595-601.
  89. Lee, S., et al. C-I Wu, X. Zhang and S. Wang. Detecting novel low-abundant transcripts in Drosophila. RNA 11(2005):939-946.
  90. Osada, N. et al. C.-I Wu and K. Hashimoto. Substitution rate and structural divergence of 5’UTR evolution: Comparative analysis between human and cynomolgus monkey cDNAs. Molec. Biol. Evol. 22(2005):1976-1982.
  91. Tang, H and C.-I Wu. A new method for estimating nonsynonymous substitutions and its applications to detecting positive selection. Molec. Biol. Evol. 23(2006):372-379.
  92. Greenberg, A. J., J. R. Moran, S. Fang and C.-I Wu. Adaptive loss of an old duplicate gene during incipient speciation. Mol. Biol. Evol., 23(2006):401--410.
  93. Greenberg, A. J., J. R. Moran and C.-I Wu. Proper control of genetic background with precise allele substitution: A comment on Coyne and Elwyn. Evolution 60(2006): 623-625.
  94. Greenberg, A. J. and C.-I Wu. Molecular genetics of natural populations. Mol. Biol. Evol. 23(2006):883-886.
  95. Lu, J., T. Tang, J. Huang, S. Shi, and C.-I Wu. The accumulation of deleterious mutations in the rice genomes: a hypothesis on the cost of domestication. Trends in Genetics 22(2006): 126 - 131.
  96. Liu, X., Y. Fu, (9 other authors), C.-I Wu, and A. Xu. An ancient balanced polymorphism in a regulatory region of human Major Histocompatibility Comlex is retained in Chinese minorities but lost worldwide. Amer. J. Hum. Genet. 78(2006): 393 - 400.
  97. Osada, N., M. H. Kohn, and C.-I Wu. Genomic Inference of cis-regulatory nucleotide polymorphism underlying gene expression differences between Drosophila melanogaster mating races. Molec. Biol. Evol. 23(8)( 2006):1585-1591.
  98. Zeng, Kai, S.H., Shi, Y.X. Fu, and C.-I Wu. Statistical Tests for Detecting Positive Selection by Utilizing High Frequency SNPs. Genetics 174(2006):1431-1439.
  99. Tang, T., J. Lu, J. Huang, J. He, Y. Shen, K. Zeng, S. R. McCouch, M. D. Purugganan, S. Shi and C.-I Wu. Genomic variation in rice - Genesis of highly polymorphic linkdage blocks during domestication. PlosGenetics 2(2006):1824-1833.
  100. Wang, Huan-Chieh Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, Chen-Kung Chou, Shih-Feng Tsai, Chung-I Wu, C.-K. James Shen. Rate of evolution in brain-expressed genes in humans. PlosBiology 5(2007): 335-342.
  101. Shapiro, J. A. et al. C.-I Wu. Adaptive Genic evolution in the Drosophila genomes. Proc. Natl. Acad. Sci. 104(2007):2271-2276.
  102. Gojobori, J., H. Tang, J. Akey and C.-I Wu. Negative correlation between the two phases of molecular evolution - constraint and adaptation in the human genomes. Proc. Natl. Acad. Sci. 104(2007):3907-3912.
  103. Zeng, K., S. Mano, S. Shi and C.-I Wu. Comparisons of site- and Haplotype-Frequency methods for detecting positive selection. Molec. Biol. Evol. 24(7)( 2007): 1562-1574.
  104. Zeng, K., S. Shi and C.-I Wu. Compound tests for the detection of hitchhiking under positive selection. Molec. Biol. Evol. 24(8)( 2007):1898-1908.
  105. Wang HY, Chang HT, Pai TW, Wu CI, Lee YH, Chang YH, Tai HL, Tang CY, Chou WY, Chang MD. Transcriptional Regulation of Human Eosinophil RNases by an Evolutionary- Conserved Sequence Motif in Primate Genome. BMC Mol Biol. 8(1)( 2007):89-107.
  106. Zhou, R, K. Zeng, W. Wu, X. Chen, Z. Yang, S. Shi and C.-I Wu. Population genetics of speciation in non-model organisms: I. Ancestral polymorphism in mangroves. Molec. Biol. Evol. 24(2007): 2746-2754.
  107. Lu, J., Y. Fu, S. Kumar, Y. Shen, R. W. Carthew and C.-I Wu. Adaptive evolution of newly-ermged microRNA genes in Drosophila. Molec. Biol. Evol. 25(2008):929-938.
  108. Lu, J., Y. Shen, Q. Wu, S. Kumar, B. He, S. Shi, R. W. Carthew, S. Wang and C.-I Wu. The birth and death of microRNA genes in Drosophila. Nature Genetics 40(2008):351-355.
  109. Wang, H., Y Fu, M. McPeek, X. Lu, S. Nuzhdin, A. Xu, M. Wu and C.-I Wu. Complex genetic interactions underlying expression differences between Drosophila races - Analysis of chromosome substitutions. Proc. Natl. Acad. Sci. 105(2008): 6362-6367.
  110. Zhou, R., X. Gong, D. Boufford, C.-I Wu and S. Shi. Testing the Hypothesis on Unidirectional Hybridization in Plants: Observations on Sonneratia, Bruguiera and Ligularia. BMC Evolutionary Biology 8(2008): 149-157.
  111. Yu, Y., T. Tang, Q, Qian, Y. Wang, M. Yan, D. Zeng, B. Han, C.-I Wu, S. Shi and J. Li. Independent Losses of Function in a Polyphenol Oxidase in Rice - Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection in Domestication. Plant Cell 20(2008): 2946-2959.
  112. Kohn, M. H., J. Shapiro and C.-I Wu. Decoupled differentiation of gene expression and coding sequence among Drosophila populations. Gene and Genetic Systems 83(2008):265-273.
  113. Wu, Q, Y. C. Kim, J. Lu, et al. M. Q. Zhang, C.-I Wu and S. M. Wang. Poly A- transcripts expressed in HeLa cells. PLoSOne 3(7) (2008):e2803.
  114. Wu, C.-I, Y. Shen and T. Tang. Evolution under canalization and the dual functions of microRNAs ?C A Hypothesis. Genome Research (2009, in press).
 

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