List of Main Publications of Saitou Lab

Last updated: June 12, A.S. 0008 (2008 A.D.)
Note. Bold letterd names are people in Saitou Laboratory.
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Saitou's publication
  1. Sasaki T., Nishihara H., Hirakawa M., Fujimura K., Tanaka M., Kokubo N., Kimura-Yoshida C., Matsuo I., Sumiyama K., Saitou N. Shimogori T. and Okada N.(2008) Possible involvement of SINEs in mammalian-specific brain formation. Proceedings of the National Academy of Sciences of the United States of America vol. 105, no. 11, pp. 4220-4225.
  2. Blancher A., Bonhomme M., Crouau-Roy B., Terao K., Kitano T., , and Saitou N. (2008) Mitochondrial DNA sequence phylogeny of four populations of the widely distributed cynomolgus macaque (Macaca fascicularis fascicularis). Journal of Heredity vol.99, no.3, pp.254-264. Epub 2008 Mar 11.PMID: 18334507 [PubMed - in process]
  3. Liu Y.-H., Takahashi A., Kitano T., Koide T., Shiroishi T., Moriwaki K., and Saitou N. (2008) Mosaic genealogy of the Mus musculus genome revealed by 21 nuclear genes from its three subspecies. Genes and Genetic Systems vol. 83, pp. 77-88.
  4. Kitano T., Umetsu K., Tian W., Yamazaki K., and Saitou N. (2007) Tempo and mode of evolution of the Rh blood group genes before and after gene duplication. Immunogenetics, vol. 59, pp. 427-431.
  5. Yoshiura K., Kinoshita A., Ishida T., Ninokata A., Ishikawa T., Kaname T., Bannai M., Tokunaga K., Sonoda S., Komaki R., Ihara M., Saenko V.A., Alipov G.K., Sekine I., Komatsu K., Takahashi H., Nakashima M., Sosonkina N., Mapendano C.K., Ghadami M., Nomura M., Liang D.S., Miwa N., Kim D.K., Garidkhuu A., Natsume N., Ohta T., Tomita H., Kaneko A., Kikuchi M., Russomando G., Hirayama K., Ishibashi M., Takahashi A., Saitou N., Murray J.C., Saito S., Nakamura Y., and Niikawa N. (2006) A SNP in the ABCC11 gene is the determinant of human earwax type. Nature Genetics vol. 38, no. 3, pp. 324-330.
  6. Ezawa K., OOta S., and Saitou N. (2006) Genomewide search of gene conversions in duplicated genes of mouse and rat. Molecular Biology and Evolution, (Published online: January 11, 2006)
  7. Yoko Kuroki, Atsushi Toyoda, Hideki Noguchi, Todd D Taylor, Takehiko Itoh, Dae-Soo Kim, Dae-Won Kim, Sang-Haeng Choi, Il-Chul Kim, Han Ho Choi, Yong Sung Kim, Yoko Satta, Naruya Saitou, Tomoyuki Yamada, Shinichi Morishita, Masahira Hattori, Yoshiyuki Sakaki, Hong-Seog Park, and Asao Fujiyama (2006) Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nature Genetics, vol. 38, no. 2, pp. 158-167.
  8. Li S. L., Yamamoto T., Yoshimoto T., Uchihi R., Mizutani M., Kurimoto Y., Tokunaga K., Jin F., Katsumata Y., and Saitou N. (2005) hylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci. Human Genetics, , vol. 118, no. 6, pp. 695-707.
  9. Kitano T. and Saitou N. (2005) Evolutionary conservation of 5' upstream sequence of nine genes between human and great apes. Genes and Genetic Systems, vol. 80, No. 3, pp. 225-232.
  10. Saitou N. (2005) Evolution of hominoids and the search for a genetic basis for creating humanness. Cytogenetic and Genome Research, vol. 108, pp. 16-21.
  11. Shimada M., Kim C.-G, Kitano T., Ferell R.E., Kohara Y., and Saitou N. (2005) Nucleotide sequence comparison of a chromosome rearrangement on the human chromosome 12 and corresponding ape chromosomes. Cytogenetic and Genome Research, vol. 108, pp. 83-90.
  12. Abe K., Noguchi H., Tagawa K., Yuzuriha M., Toyoda A., Kojima T., Ezawa K., Saitou N., Hattori M., Sakaki Y., Moriwaki K., and Shiroishi T. (2004) Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC end sequence-SNP analysis. Genome Research, vol. 14, pp. 2239-2247.
  13. Shimada M., Hayakawa S., Hamle T., Fujita S., Hirata S., Sugiyama Y. , and Saitou N. (2004) Mitochondrial DNA Genealogy of Chimpanzees in Nimba Mountains and Bossou, West Africa. American Journal of Primatology, vol. 64, pp. 261-275.
  14. Tomiki T. and Saitou N. (2004) Phylogenetic analysis of proteins associated in four major energy metabolism systems: photosynthesis, oxidative phosphorylation, nitrogen metabolism and sulfur metabolism. Journal of Molecular Evolution, vol. 59, pp. 158-176.
  15. The International Chimpanzee Chromosome 22 Consortium [H.Watanabe, A.Fujiyama, M.Hattori, T. D.Taylor, A.Toyoda, Y.Kuroki, H.Noguchi, A.BenKahla, H.Lehrach, R.Sudbrak, M.Kube,S.Taenzer, P.Galgoczy, M.Platzer, M.Scharfe, G.Nordsiek, H.Blocker, I.Hellmann, P.Khaitovich, S.Paabo, R.Reinhardt, H.-J.Zheng,X.-L.Zhang, G.-F.Zhu, B.-F.Wang, G.Fu, S.-X.Ren9, G.-P.Zhao, Z.Chen, Y.-S.Lee, J.-E.Cheong, S.-H.Choi, K.-M.Wu, T.-T.Liu, K.-J.Hsiao, S.-F.Tsai, C.-G.Kim, S.Oota, T.Kitano, Y.Kohara, N.Saitou, H.-S.Park, S.-Y.Wang, M.-L.Yaspo, and Y.Sakaki] (2004) DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature, vol. 429, No. 6990, pp. 382-388.
  16. Roubinet F.,Despiau S.-P., Calafell F.,Jin F., Bertanpetit J., Saitou N., and Blancher A.(2004) Evolution of O alleles of the human ABO blood group gene. Transfusion, vol. 44, no. 5, pp. 707-715.
  17. Kitano T., Liu Y.-H., Ueda S., and Saitou N. (2004) Human specific amino acid changes found in 103 protein coding genes. Molecular Biology and Evolution, vol. 21, no. 5, pp. 936-944.
  18. Takahashi A., Liu Y.-H., and Saitou N. (2004) Genetic variation versus recombination rate in a structured population of mice. Molecular Biology and Evolution, vol. 21, pp. 404-409.
  19. Tachikui H., Saitou N., Nakajima T.,Hayasaka I., Ishida T., and Inoue I. (2004) Lineage specific homogenization of the polyubiquitin gene among human and great apes. Journal of Molecular Evolution, vol. 57, pp. 737-744.
  20. Kryukov K., Saitou N. (2003) Netview: application software for constructing and visually exploring phylogenetic networks. Genome Informatics, 14, 280-281.
  21. Kim C.-G, Fujiyama A., and Saitou N. (2003) Construction of a gorilla fosmid library and its PCR screening system. Genomics, vol. 82, pp. 571-574.
  22. Sumiyama K., and Ruddle F.H. (2003) Regulation of Dlx3 gene expression in visceral arches by evolutionarily conserved enhancer elements. Proc. Natl. Acad. Sci. U.S.A. 100, 4030-4034.
  23. Sumiyama K., Irvine, S.Q., and Ruddle F.H. (2003) The role of gene duplication in the evolution and function of the vertebrate distal-less/Dlx bigene cluster. J. Struct. Funct. Genomics 3, 151-159.
  24. Kim, C.B., Shashikant, C.S., Sumiyama K., Amemiya C.T., Wang W.C., and Ruddle F.H. (2003) Phylogenetic Analysis of the Mammalian Hoxc8 Non-coding Region. J. Struct. Funct. Genomics 3, 195-199.
  25. Sumiyama K., Saitou N., and Ueda S. (2002) Adaptive evolution of the IgA hinge region in primates. Molecular Biology and Evolution, vol. 19, no. 7, pp. 1093-1099.
  26. OOta S. and Saitou N. (2002). NJML+P: A Hybrid Algorithm of The Maximum Likelihood and Neighbor-Joining Methods Using Parallel Computing. Proceedings of Genome Informatics, vol. 13, pp. 434-435.
  27. Sumiyama K. Irvine S.Q., Stock D.W., Weiss K.M., Kawasaki K., Shimizu N., Shashikant C.S., Miller W. and Ruddle F.H. (2002) Genomic Structure and Functional Control of the Dlx3-7 Bigene Cluster. Proc. Natl.Acad. Sci. U. S. A. 99, 780-785.
  28. Oota H., Kitano T., Jin F., Yuasa I., Wang L., Ueda S., Saitou N., and Stoneking M. (2002) Extreme mtDNA homogeneity in continental Asian populations. American Journal of Physical Anthropology, vol. 118, no. 2, pp. 146-53.
  29. Noda R., Kim C.-G., Takenaka O., Ferrell R. E., Tanoue T., Hayasaka I., Ueda S., Ishida T., and Saitou N. (2001) Mitochondrial 16S rRNA sequence diversity of hominoids. Journal of Heredity, vol. 92, pp. 490-496.
  30. Miyako Yamamoto, Xiao-Hong Lin, Yoshihiko Kominato, Yukiko Hata , Reiko Noda, Naruya Saitou, and Fumiichiro Yamamoto. (2001) Murine equivalent of the human histo-blood group ABO gene is a cis-AB gene and encodes a glycosyltransferase with both A and B transferase activity. Journal of Biological Chemmistry, vol. 276, no. 17, pp. 13701-13708.
  31. Osawa M., Yuasa I., Kitano T., Heinke J., Kaneko M., Saitou N., and Umetsu K. (2001) Haplotype analysis of human alpha2-HS glycoprotein (fetuin). Annals of Human Genetics, vol. 65, no. 1, pp. 27-34.
  32. Alan R. Sanders, Qiuhe Cao, Jennifer Taylor, Tamara E. Levin, Judith A. Badner, Anibal Cravchik, Josep M. Comeron, Naruya Saitou, Amado Del Rosario, Debra A. Salvi, Katherine A. Walczyk, Lynn R. Goldin, Bryan J. Mowry, Douglas F. Levinson, Raymond R. Crowe, Jeremy M. Silverman, and Pablo V. Gejman (2001) Genetic Diversity of the Human Serotonin Receptor 1B (HTR1B) Gene. Genomics, vol. 72, pp. 1-14.
  33. Sumiyama K., Kitano T., Noda R., Ueda S., Ferrell R., and Saitou N. (2000) Sequence variation in the ABO blood group gene exon 7 of chimpanzee and bonobo. Gene, vol. 259, pp. 75-79.
  34. Wang L., Oota H., Saitou N., Jin F., Matsushita T., and Ueda S. (2000) Genetic structure of a 2500-year-old human population in China and its spatiotemporal changes. Molecular Biology and Evolution, vol. 17, no. 9, pp. 1396-1400.

    35. Abstract in Mol. Biol. Evol. homepage
  35. Kitano T. and Saitou N. (2000) Evolutionary history of the Rh blood group-related genes in vertebrates. Immunogenetics, vol. 51, no. 7, pp. 856-862.

    36. Full text in Immunogenetics homepage
  36. Noda R., Kitano T., Takenaka O., and Saitou N. (2000) Evolution of the ABO blood group gene in Japanese macaque. Genes and Genetic Systems, vol. 75, no. 3, pp. 141-147.
  37. Kitano T., Noda R., Sumiyama K., Ferrell R. E., and Saitou N. (2000) Gene diversity of chimpanzee ABO blood group elucidated from intron 6 sequences. Journal of Heredity, vol. 91, no. 3, pp. 211-214.

  38. Kitano T., OOta S., and Saitou N. (1999) Molecular evolutionary analyses of the Rh blood group genes and Rh50 genes in mammales. Zoological Studies, vol. 38 (in press).
  39. Kaneko M., Kudo T., Iwasaki H., Shiina T., Inoko H., Kozaki T., Saitou N., and Narimatsu H. (1999) Assignment of the human alpha 1,3-fucosyltransferase IX (FUT9) gene to chromosome band 6q16 by in situ hybridization. Cytogenetics and Cell Genetics, vol. 86, pp. 329-330.
  40. Kitano T. and Saitou N. (1999) Evolution of Rh blood group genes have experienced gene conversions and positive selection. Journal of Molecular Evolution, vol. 49, no. 5, pp. 615-626.
  41. Sawada H., Suzuki F., Matsuda I, and Saitou N. (1999) Phylogenetic analysis of Pseudomonas syringe pathovar suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster. Journal of Molecular Evolution, vo. 49, no. 5, pp. 627-644.
  42. Kaneko M., Kudo T., Iwasaki H., Ikehara Y., Nishihara S., Nakagawa S., Sasaki K., Shiina T., Inoko H., Saitou N., and Narimatsu H. (1999) alpha1-3-Fucosyltransferase IX (Fuc-TIX) is very highly conserved between human and mouse; molecular cloning, characterization and tissue distribution of human Fuc-TIX. FEBS Letters, vol. 452, pp. 237-242.

    43. *** NCBI/Entrez Abstract ***
  43. OOta S. and Saitou N. (1999) Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Molecular Biology and Evolution, vol. 16, no. 6, pp. 856-867.

    44. *** NCBI/Entrez Abstract ***
  44. Kitano T., Sumiyama K., Shiroishi T., and Saitou N. (1998) Conserved evolution of the Rh50 gene compared to its homologous Rh blood group gene. Biochemical and Biophysical Research Communications, vol. 249, No. 1, pp. 78-85.

    45. *** NCBI/Entrez Abstract ***
  45. Saitou N. and Yamamoto F.-I. (1997) Evolution of primate ABO blood group genes and their homologous genes. Molecular Biology and Evolution, Vol. 14, No. 4, pp. 399-411.

    46. *** NCBI/Entrez Abstract ***
  46. Omoto K. and Saitou N. (1997) Genetic origins of the Japanese: A partial support for the "dual structure hypothesis". American Journal of Physical Anthropology, Vol. 102, No. 4, pp. 437-446.

    47. *** NCBI/Entrez Abstract ***
  47. OOta S. and Saitou N. (1997) Reconstruction of maximum likelihood phylogenetic trees in parallel enviromnent using logic programming. In Miyano S. and Takagi T. (eds.), Genome Informatics 1997, Universal Academy Press, Tokyo, pp. 326-327.

  48. Saitou N. (1996) Reconstruction of gene trees from sequence data. In Doolittle R. (ed.), Methods in Enzymology, Vol. 266, Academic Press, Inc., Orlando, pp. 427-449.

    49. *** NCBI/Entrez Abstract ***
  49. Ohtsuka H., Oyanagi M., Mafune Y., Miyashita N., Shiroishi T., Moriwaki K., Kominami R., and Saitou N. (1996) The presence/absence polymorphism and evolution of p53 pseudogene within the genus Mus. Molecular Phylogenetics and Evolution, Vol. 5, No. 3, pp.548-556.

    50. *** NCBI/Entrez Abstract ***
  50. Saitou N. (1996) Contrasting gene trees and population trees on the evolution of modern humans. In Boyce A. J. and Mascie-Taylor C.G.N. (eds.), Society for the Study of Human Biology Symposium Series: Molecular Biology and Human Diversity, Cambridge University Press, Cambridge, pp. 265-282.

  51. OOta S., Saitou N., and Kunifuji S. (1995) Application of a parallel logic programming for reconstruction of molecular phylogenetic trees using the maximum likelihood method. In Chikawama T., Nakashima H., and Tick E. (eds.), ICLP'95 Workshop on Parallel Logic Programming, Department of Electronic Engineering, University of Tokyo, pp. 61-72.

    52. *** Abstract ***
  52. Saitou N. (1995) A genetic affinity analysis of human populations. Human Evolution, Vol. 10, No. 1, pp. 17-33.

    53. *** Abstract ***
  53. Ishida N., Oyunsuren T., Mashima S., Mukoyama H., and Saitou N. (1995) Mitochondrial DNA sequences of various species of the genus Equus with a special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse. Journal of Molecular Evolution, Vol. 41, pp. 180-188.

    54. *** NCBI/Entrez Abstract ***
  54. Saitou N. (1995) Methods for building phylogenetic trees of genes and species. In Griffin H. and Griffin A. (eds.), Molecular Biology: Current Innovations and Future Trends Part 2 , Horizon Scientific Press, Wymondham, U.K., pp. 115-135.

    55. *** Abstract ***
  55. Saitou N., Omoto K., Du C., and Du R. (1994) Population genetic study in Hainan Island, China. II. Genetic affinity analyses. Anthropological Science, Vol. 102, No. 2, pp. 129-147.

    56. *** Abstract ***
  56. Saitou N. and Ueda S. (1994) Evolutionary rate of insertions and deletions in non-coding nucleotide sequences of primates. Molecular Biology and Evolution, Vol. 11, No. 3, pp. 504-512.

    57. *** NCBI/Entrez Abstract ***
  57. Saitou N., Tokunaga K., and Omoto K. (1992) Genetic affinities of human populations. In Roberts D.L., Fujiki N., and Torizuka K. (eds.), Society for the Study of Human Biology Symposium Series 33: Isolation and Migration, Cambridge University Press, Cambridge, pp. 118- 129.

    58. *** Abstract ***
  58. Saitou N. (1992) Evolutionary rate of insertions and deletions. In Takahata N. ed., Population Paleo-Genetics: Proceedings of the Seventeenth Taniguchi Symposium, Japan Science Society Press, Tokyo, pp. 335-343.

  59. Saitou N. (1991) Reconstruction of molecular phylogeny of extant hominoids from DNA sequence data. American Journal of Physical Anthropology, Vol. 84, No. 1, pp. 75-85.

    60. *** NCBI/Entrez Abstract ***
  60. Saitou N. (1991) Statistical methods for phylogenetic tree reconstruction. In Rao C.R. and Chakraborty R. (eds.), Handbook of Statistics, Volume 8: Statistical Methods for Biological and Medical Sciences, Elsevier Science Publishers B.V., Amsterdam, pp. 317-346.
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