Naruya Saitou

Summary

Affiliation: National Institute of Genetics
Country: Japan

Publications

  1. doi request reprint 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 request reprint 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
  3. doi request reprint 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
  4. pmc A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses
    Kirill Kryukov
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Genome Biol Evol 4:501-12. 2012
  5. pmc 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
  6. ncbi request reprint 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. doi request reprint 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
  8. pmc 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
  9. ncbi request reprint 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
  10. ncbi request reprint 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

Collaborators

Detail Information

Publications16

  1. doi request reprint 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 request reprint 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...
  3. doi request reprint 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...
  4. pmc A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses
    Kirill Kryukov
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Genome Biol Evol 4:501-12. 2012
    ..Mammalian genomes showed the largest deviation among animals. The results of comparison are available online at http://esper.lab.nig.ac.jp/genome-composition-database/...
  5. pmc 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...
  6. ncbi request reprint 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. doi request reprint 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...
  8. pmc 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...
  9. ncbi request reprint 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...
  10. ncbi request reprint 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...
  11. doi request reprint 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...
  12. doi request reprint Estimation of bacterial species phylogeny through oligonucleotide frequency distances
    Mahoko Takahashi
    Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411 8540, Japan
    Genomics 93:525-33. 2009
    ..Our results suggest that oligonucleotide frequency is useful not only for classification of bacteria, but also for estimation of their phylogenetic relationships for closely related species...
  13. doi request reprint 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...
  14. ncbi request reprint Phylogenetic analysis of proteins associated in the four major energy metabolism systems: photosynthesis, aerobic respiration, denitrification, and sulfur respiration
    Takeshi Tomiki
    Division of Population Genetics, National Institute of Genetics, and Department of Genetics, School of Life Sciences, Graduate University for Advanced Studies, Mishima, Japan
    J Mol Evol 59:158-76. 2004
    ....
  15. pmc Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes
    Rumiko Suzuki
    Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411 8540, Japan
    DNA Res 18:177-87. 2011
    ..These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution...
  16. ncbi request reprint Human-specific amino acid changes found in 103 protein-coding genes
    Takashi Kitano
    Division of Population Genetics, National Institute of Genetics, Mishima, Japan
    Mol Biol Evol 21:936-44. 2004
    ..These results suggest that a small proportion of protein-coding genes started to evolve differently in the human lineage after it diverged from the ape lineage...