Hideki Innan

Summary

Affiliation: Texas Medical Center
Country: USA

Publications

  1. ncbi request reprint The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, USA
    Mol Biol Evol 23:1040-7. 2006
  2. pmc Pattern of polymorphism after strong artificial selection in a domestication event
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 101:10667-72. 2004
  3. ncbi request reprint Theories for analyzing polymorphism data in duplicated genes
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Genes Genet Syst 79:65-75. 2004
  4. pmc Distinguishing the hitchhiking and background selection models
    Hideki Innan
    Human Genetics Center, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 165:2307-12. 2003
  5. ncbi request reprint Selection for more of the same product as a force to enhance concerted evolution of duplicated genes
    Ryuichi P Sugino
    University of Texas Health Science Center at Houston School of Public Health, Human Genetics Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Trends Genet 22:642-4. 2006
  6. pmc Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast
    Ryuichi P Sugino
    Human Genetics Center, School of Public Health, Unversity of Texas Health Science Center, Houston 77030, USA
    Genetics 171:63-9. 2005
  7. pmc Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, 77030, USA
    Genetics 169:1763-77. 2005
  8. pmc Modified Hudson-Kreitman-Aguade test and two-dimensional evaluation of neutrality tests
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 173:1725-33. 2006
  9. ncbi request reprint Very low gene duplication rate in the yeast genome
    Li Zhi Gao
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Science 306:1367-70. 2004
  10. pmc The pattern of polymorphism on human chromosome 21
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Genome Res 13:1158-68. 2003

Detail Information

Publications30

  1. ncbi request reprint The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, USA
    Mol Biol Evol 23:1040-7. 2006
    ..The result is discussed in the view of the mode of speciation. Another ML method is developed to estimate the male-female ratio (alpha) of mutation rate, in which the coalescent process in the ancestral population is taken into account...
  2. pmc Pattern of polymorphism after strong artificial selection in a domestication event
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 101:10667-72. 2004
    ..These theoretical results are discussed in light of data collected from maize. Although the main focus of this article is on domestication, this model can also be generalized to describe selective sweeps from standing genetic variation...
  3. ncbi request reprint Theories for analyzing polymorphism data in duplicated genes
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Genes Genet Syst 79:65-75. 2004
    ..The theoretical results are well in agreement with polymorphism data in duplicated genes. The effect of selection on the pattern of polymorphism is also considered...
  4. pmc Distinguishing the hitchhiking and background selection models
    Hideki Innan
    Human Genetics Center, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 165:2307-12. 2003
    ..The method is applied to data from Drosophila melanogaster and two highly selfing tomato species...
  5. ncbi request reprint Selection for more of the same product as a force to enhance concerted evolution of duplicated genes
    Ryuichi P Sugino
    University of Texas Health Science Center at Houston School of Public Health, Human Genetics Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Trends Genet 22:642-4. 2006
    ..This observation can be explained by selection favoring more of the same product, which could enhance concerted evolution in dosage-sensitive genes...
  6. pmc Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast
    Ryuichi P Sugino
    Human Genetics Center, School of Public Health, Unversity of Texas Health Science Center, Houston 77030, USA
    Genetics 171:63-9. 2005
    ..cerevisiae and Kluyveromyces waltii, suggesting that the WGD occurred in very early stages after speciation or the WGD might have been involved in the speciation event...
  7. pmc Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, 77030, USA
    Genetics 169:1763-77. 2005
    ..For larger samples, we consider simulation-based approaches. The utility of the HCT is demonstrated in simulations of alternative models and in application to data from Drosophila melanogaster...
  8. pmc Modified Hudson-Kreitman-Aguade test and two-dimensional evaluation of neutrality tests
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030, USA
    Genetics 173:1725-33. 2006
    ....
  9. ncbi request reprint Very low gene duplication rate in the yeast genome
    Li Zhi Gao
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030, USA
    Science 306:1367-70. 2004
    ..The average length of the period of concerted evolution and the gene conversion rate are estimated to be approximately 25 million years and approximately 28 times the mutation rate, respectively...
  10. pmc The pattern of polymorphism on human chromosome 21
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Genome Res 13:1158-68. 2003
    ....
  11. pmc The coalescent and infinite-site model of a small multigene family
    Hideki Innan
    Department of Biological Science, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 163:803-10. 2003
    ..Using the coalescent simulation of duplicated genes, the applicability of statistical tests of neutrality to multigene families is considered...
  12. pmc The extent of linkage disequilibrium and haplotype sharing around a polymorphic site
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 165:437-44. 2003
    ..The implications of our results for data analysis, and in particular for detecting selection, are discussed...
  13. ncbi request reprint Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions
    Cuong Than
    Department of Computer Science, Rice University, Houston, Texas 77005, USA
    J Comput Biol 14:517-35. 2007
    ..Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios...
  14. doi request reprint Evolution of complexity in miRNA-mediated gene regulation systems
    Shohei Takuno
    Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
    Trends Genet 24:56-9. 2008
    ..Furthermore, we show that the mode of selection to maintain the systems depend on their complexity levels...
  15. pmc A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes
    Hideki Innan
    Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 100:8793-8. 2003
    ..The selection intensity is estimated on the basis of the theoretical result...
  16. pmc Neofunctionalization of duplicated genes under the pressure of gene conversion
    Kosuke M Teshima
    The Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 178:1385-98. 2008
    ....
  17. pmc The direction of linkage disequilibrium: a new measure based on the ancestral-derived status of segregating alleles
    K Ryo Takahasi
    Population and Quantitative Genomics Team, Genomic Sciences Center, RIKEN, Yokohama 230 0045, Japan
    Genetics 179:1705-12. 2008
    ....
  18. pmc The evolutionary rate of duplicated genes under concerted evolution
    Shuhei Mano
    Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
    Genetics 180:493-505. 2008
    ..We also argue about the applicability of the theoretical results to models of multigene families with more than two loci...
  19. ncbi request reprint Molecular population genetics
    Magnus Nordborg
    Department of Biological Sciences, University of Southern California, 835 W 37th St, SHS 172, Los Angeles, California 90089 1340, USA
    Curr Opin Plant Biol 5:69-73. 2002
    ..Furthermore, population genetics is becoming increasingly relevant to other fields of biology, for example to genetic epidemiology, because of disease gene mapping in general populations...
  20. pmc A method for estimating the mutation, gene conversion and recombination parameters in small multigene families
    Hideki Innan
    Department of Biological Science, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 161:865-72. 2002
    ..The gene conversion rate is estimated to be approximately 60-165 times higher than the mutation rate for synonymous sites...
  21. ncbi request reprint Recombination or mutational hot spots in human mtDNA?
    Hideki Innan
    Molecular and Computational Biology, University of Southern California, CA 90089 1340, USA
    Mol Biol Evol 19:1122-7. 2002
    ..Thus, there appears to be no evidence for recombination in the mtDNA polymorphism data. In conclusion, we discuss the possibility of detecting recombination in mtDNA and the implications of its existence...
  22. pmc Preservation of a pseudogene by gene conversion and diversifying selection
    Shohei Takuno
    Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
    Genetics 180:517-31. 2008
    ....
  23. pmc Relaxed selective pressure on an essential component of pheromone transduction in primate evolution
    Emily R Liman
    Department of Biological Sciences and Program in Neurosciences, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 100:3328-32. 2003
    ..We propose that, at this point in evolution, other modalities, notably the development of color vision, may have largely replaced signaling by pheromones...
  24. pmc The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089 1340, USA
    Genetics 163:1201-13. 2003
    ..We focus in particular on the statistical power to detect balancing selection when it is present...
  25. pmc The effect of gene conversion on the divergence between duplicated genes
    Kosuke M Teshima
    Center for Genome Information, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, USA
    Genetics 166:1553-60. 2004
    ..Finally, we discuss potential problems in genomic data analysis of duplicated genes when it is based on the molecular clock but concerted evolution is common...
  26. pmc The probability and chromosomal extent of trans-specific polymorphism
    Carsten Wiuf
    Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
    Genetics 168:2363-72. 2004
    ..When trans-specific polymorphism is obvious, on the other hand, it may be reasonable to argue that selection must be acting on multiple sites or that recombination is suppressed in the surrounding region...
  27. pmc Molecular evolution of pathogenicity-island genes in Pseudomonas viridiflava
    Hitoshi Araki
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Genetics 177:1031-41. 2007
    ..Evolutionarily stable PAIs may be preferable in this species because preexisting genetic variation enables P. viridiflava to respond rapidly to natural selection...
  28. pmc Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites
    Li Zhi Gao
    Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, People s Republic of China
    Genetics 179:965-76. 2008
    ..The results suggest that completely independent domestication of indica and japonica subspecies may not explain our data and that there is at least partial sharing of their ancestral populations and/or recent gene flow between them...
  29. pmc Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations
    Hideki Innan
    Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
    Genetics 179:1713-20. 2008
    ..Therefore, for detecting the signature of local adaptation in polymorphism data, it is important to evaluate the data from both parental and derived populations simultaneously...
  30. ncbi request reprint A statistical test for the difference in the amounts of DNA variation between two populations
    Hideki Innan
    Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7 3 1, Tokyo 113 0033, Japan
    Genet Res 80:15-25. 2002
    ..crassa and L. uniflora. The results of our test show that the level of variation in L. stylosa is significantly higher than those in the other species...