Research Topics
| Hideki InnanSummaryAffiliation: Baylor College of Medicine Country: USA Publications
|
Detail Information
Publications
The effect of gene flow on the coalescent time in the human-chimpanzee ancestral populationHideki 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...
Pattern of polymorphism after strong artificial selection in a domestication eventHideki 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...- Theories for analyzing polymorphism data in duplicated genesHideki 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... - Distinguishing the hitchhiking and background selection modelsHideki 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... - Selection for more of the same product as a force to enhance concerted evolution of duplicated genesRyuichi 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... - Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeastRyuichi 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... - Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sitesHideki 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... - Modified Hudson-Kreitman-Aguade test and two-dimensional evaluation of neutrality testsHideki Innan
Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030, USA
Genetics 173:1725-33. 2006.... - Very low gene duplication rate in the yeast genomeLi-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... - The pattern of polymorphism on human chromosome 21Hideki Innan
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Genome Res 13:1158-68. 2003.... - The coalescent and infinite-site model of a small multigene familyHideki 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... - The extent of linkage disequilibrium and haplotype sharing around a polymorphic siteHideki 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... - Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutionsCuong 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... - Evolution of complexity in miRNA-mediated gene regulation systemsShohei 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... - A two-locus gene conversion model with selection and its application to the human RHCE and RHD genesHideki 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... - Neofunctionalization of duplicated genes under the pressure of gene conversionKosuke M Teshima
The Graduate University for Advanced Studies, Hayama, Kanagawa 240 0193, Japan
Genetics 178:1385-98. 2008.... - The direction of linkage disequilibrium: a new measure based on the ancestral-derived status of segregating allelesK Ryo Takahasi
Population and Quantitative Genomics Team, Genomic Sciences Center, RIKEN, Yokohama 230 0045, Japan
Genetics 179:1705-12. 2008.... - The evolutionary rate of duplicated genes under concerted evolutionShuhei 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... - Molecular population geneticsMagnus 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... - A method for estimating the mutation, gene conversion and recombination parameters in small multigene familiesHideki 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... - 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... - Preservation of a pseudogene by gene conversion and diversifying selectionShohei Takuno
Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
Genetics 180:517-31. 2008.... - Relaxed selective pressure on an essential component of pheromone transduction in primate evolutionEmily 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... - The genealogy of sequences containing multiple sites subject to strong selection in a subdivided populationMagnus 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... - The effect of gene conversion on the divergence between duplicated genesKosuke 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... - The probability and chromosomal extent of trans-specific polymorphismCarsten 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... - Molecular evolution of pathogenicity-island genes in Pseudomonas viridiflavaHitoshi 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... - Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellitesLi 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... - Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populationsHideki 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... - A statistical test for the difference in the amounts of DNA variation between two populationsHideki 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...