Naruya Saitou

Summary

Affiliation: National Institute of Genetics
Country: Japan

Publications

  1. ncbi The PNarec method for detection of ancient recombinations through phylogenetic network analysis
    Naruya Saitou
    Division of Population Genetics, National Institute of Genetics, Mishima 411 8540, Japan
    Mol Phylogenet Evol 66:507-14. 2013
  2. ncbi MISHIMA--a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data
    Kirill Kryukov
    Division of Population Genetics, National Institute of Genetics 1111 Yata, Mishima, 411 8540, Japan
    BMC Bioinformatics 11:142. 2010
  3. ncbi Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies
    Yu Hua Liu
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Genes Genet Syst 83:77-88. 2008
  4. ncbi Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis
    Takashi Kitano
    Division of Population Genetics, National Institute of Genetics, Yata, Mishima, Japan
    Mol Phylogenet Evol 51:465-71. 2009
  5. ncbi Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis
    Masatoshi Matsunami
    Department of Genetics, School of Life Science, The Graduate University for Advanced Studies Sokendai, Mishima, 411 8540, Japan
    J Mol Evol 71:427-36. 2010
  6. ncbi Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes
    Takashi Kitano
    Division of Population Genetics, National Institute of Genetics Mishima, Japan
    Genes Genet Syst 80:225-32. 2005
  7. ncbi Evolutionary pattern of gene homogenization between primate-specific paralogs after human and macaque speciation using the 4-2-4 method
    Kiyoshi Ezawa
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 27:2152-71. 2010
  8. ncbi Evolutionary patterns of recently emerged animal duplogs
    Kiyoshi Ezawa
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Genome Biol Evol 3:1119-35. 2011
  9. ncbi Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat
    Kiyoshi Ezawa
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 23:927-40. 2006
  10. ncbi Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1
    Kenta Sumiyama
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 28:3005-7. 2011

Collaborators

Detail Information

Publications11

  1. ncbi The PNarec method for detection of ancient recombinations through phylogenetic network analysis
    Naruya Saitou
    Division of Population Genetics, National Institute of Genetics, Mishima 411 8540, Japan
    Mol Phylogenet Evol 66:507-14. 2013
    ..2009. Mol. Phylogenet. Evol., 51, 465-471]. We present applications of this method, now named as "PNarec", to various virus sequences as well as HLA genes...
  2. ncbi MISHIMA--a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data
    Kirill Kryukov
    Division of Population Genetics, National Institute of Genetics 1111 Yata, Mishima, 411 8540, Japan
    BMC Bioinformatics 11:142. 2010
    ..These approaches have performance problems when the number of sequences is large and when dealing with genome scale sequences...
  3. ncbi Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies
    Yu Hua Liu
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Genes Genet Syst 83:77-88. 2008
    ..Gene genealogies of Fut4 and Dfy loci also suggested existence of the gene flow between M. musculus and M. spicilegus or other distant species...
  4. ncbi Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis
    Takashi Kitano
    Division of Population Genetics, National Institute of Genetics, Yata, Mishima, Japan
    Mol Phylogenet Evol 51:465-71. 2009
    ..This establishes the coexistence of divergent allelic lineages of the ABO blood group gene for a long period in the ancestral gibbon species, and strengthens the non-neutral evolution for this gene...
  5. ncbi Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis
    Masatoshi Matsunami
    Department of Genetics, School of Life Science, The Graduate University for Advanced Studies Sokendai, Mishima, 411 8540, Japan
    J Mol Evol 71:427-36. 2010
    ..The authors also compared vertebrate CNSs with amphioxus CNSs within the Hox cluster, and found that two CNSs in the HoxA and HoxB clusters retain homology with amphioxus CNSs through the two-round whole genome duplications...
  6. ncbi Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes
    Takashi Kitano
    Division of Population Genetics, National Institute of Genetics Mishima, Japan
    Genes Genet Syst 80:225-32. 2005
    ..17-1.76 x 10(-9)) of nucleotide substitutions for the corresponding 5' upstream regions in rodents (mouse/rat comparison). Thus the primate rate was lower than rodent rate also for the 5' upstream regions...
  7. ncbi Evolutionary pattern of gene homogenization between primate-specific paralogs after human and macaque speciation using the 4-2-4 method
    Kiyoshi Ezawa
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 27:2152-71. 2010
    ..Patterns of the homogenization in the genomic alignments of human-macaque quartets indicate that gene conversion, rather than unequal crossing-over, is the major cause of the homogenization...
  8. ncbi Evolutionary patterns of recently emerged animal duplogs
    Kiyoshi Ezawa
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Genome Biol Evol 3:1119-35. 2011
    ..The drift duplication has been producing duplicate copies at paces comparable with tandem duplications since the common ancestor of vertebrates, and it may have already operated in the common ancestor of bilateral animals...
  9. ncbi Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat
    Kiyoshi Ezawa
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 23:927-40. 2006
    ..These findings will be useful to deepen the understanding of the roles of gene conversion...
  10. ncbi Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1
    Kenta Sumiyama
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 28:3005-7. 2011
    ..This result infers that loss of function in the HACNS1 81-bp region, possibly via a BGC, played an important role in human-specific evolution...
  11. ncbi Mitochondrial DNA genealogy of chimpanzees in the Nimba mountains and Bossou, West Africa
    Makoto K Shimada
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Am J Primatol 64:261-75. 2004
    ..This suggests that the Bossou-Nimba populations derived only recently from the common ancestral population of the West African chimpanzees, and did not pass through a bottleneck...