1. Kato K., Hayashizaki Y., Takahashi Y., Himeno S. and Matsubara K., Molecular cloning of the human gastrin gene, Nucl. Acids Res., 11, 8197-8203, 1983
  2. Takahashi Y., Kato K., Hayashizaki Y., Wakabayashi T., Ohtsuka E., Matsuki S., Ikehara M. and Matsubara K., Molecular cloning of the human cholecystokinin gene by use of a synthetic probe containing deoxyinosine, Proc. Natl. Acad. Sci. USA, 82, 1931-1935, 1985
  3. Hayashizaki Y., Miyai K., Kato K. and Matsubara K., Molecular cloning of the human thyrotropin - subunit gene, FEBS letters, 188, 394-400, 1985
  4. Hayashizaki Y., Miyai K., Onishi T. and Kumahara Y., Effects of corticotropin releasing factor and growth hormone releasing factor on pituitary hormone secretion in patients with congenital thyrotropin deficiency, Horm. Metab. Res., 18, 849-853, 1986
  5. Kariya Y., Kato K., Hayashizaki Y., Himeno S., Tarui S. and Matsubara K., Expression of human gastrin gene in normal and gastrinoma tissues, Gene, 50, 345-352, 1986
  6. Kariya Y., Kato K., Hayashizaki Y., Himeno S., Tarui S. and Matsubara K., Revision of consensus sequence of human Alu repeats-a review, Gene, 53, 1-10, 1987
  7. Watanabe S., Hayashizaki Y., Endo Y., Hirono M., Takimoto N., Tamaki M., Teraoka H., Miyai K. and Matsubara, K., Production of human thyroid-stimulating hormone in Chinese Hamster Ovary cells, Biochem. Biophys. Res. Commun., 149, 1149-1155, 1987
  8. Hayashizaki Y., Endo Y., Miyai K. and Matsubara K., The production of active human thyroid-stimulating hormone from and mRNAs in Xenopus laevis oocytes, Biochem. Biophys. Res. Commun., 152, 703-710, 1988
  9. Miyai K., Endo Y., Iijima Y., Kabutomori O. and Hayashizaki, Y., Serum free thyrotropin subunit in congenital isolated thyrotropin deficiency, Endocrinol. Japon., 35, 517-521, 1988
  10. Tatsumi K., Hayashizaki Y., Hiraoka Y., Miyai K. and Matsubara K., The structure of the human thyrotropin - subunit gene, Gene, 73, 489-497, 1988
  11. Hayashizaki Y., Hiraoka Y., Endo Y. and Matsubara K., Thyroid-stimulating hormone (TSH) deficiency caused by a single base substitution in the CAGYC region of the -subunit, EMBO J., 8, 2291-2296, 1989
  12. Takata K., Watanabe S., Hirono M., Tamaki M., Teraoka H. and Hayashizaki, Y., The role of the carboxyl-terminal 6 amino acid extention of human TSH subunit, Biochem. Biophys. Res. Commun., 165, 1035-1042, 1989
  13. Tokino T., Hayashizaki Y., Takata K., Yoshida M. C. and Matsubara K., Chromosome regional mapping for the human thyroid stimulating hormone subunit (TSHB) gene, Cytogenet. Cell Genet., 53, 140-143, 1990
  14. Hayashizaki Y., Hiraoka Y., Tatsumi K., Hashimoto T., Furuyama J., Miyai K., Nishijo K., Matsuura M., Kohno H., Labbe A. and Matsubara K., Deoxyribonucleic acid analyses of five families with familial inherited thyroid stimulating hormone deficiency, J. Clin. Endocrinol. Metab., 71, 792-796, 1990
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  17. Hirotsune S., Hatada I., Komatsubara H., Nagai H., Kuma K., Kobayakawa K., Kawara T., Nakagawara A., Fujii K., Mukai T. and Hayashizaki Y., New approach for detection of amplification in cancer DNA using restriction landmark genomic scanning, Cancer Research, 52, 3642-3647, 1992
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  19. Hayashizaki Y., Hirotsune S., Okazaki Y., Hatada I., Shibata H., Kawai J., Hirose K., Watanabe S., Fushiki S., Wada S., Sugimoto T., Kobayakawa K., Kawara T., Katsuki M., Sibuya T. and Mukai T., Restriction landmark genomic scanning method and its various applications, Electrophoresis, 14, 251-258, 1993
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  21. Nagai H., Hirotsune S., Komatubara H., Hatada I., Mukai T., Hayashizaki Y. and Matsubara K., Genomic analysis of human hepatocellular carcinomas using restriction landmark genomic scanning., Cancer Detection and Prevention, 17, 399-404, 1993
  22. Sasaki N., Hayashizaki Y., Kasai N., Absence of linkage between the retinoblastoma gene and hts gene in the LEC Rat: A model of human Wilson's disease., Jpn. J. Cancer Res., 84, 1019-1022, 1993
  23. Kawai J., Hirotsune S, Hirose K., Fushiki S., Watanabe S. and Hayashizaki Y., Methylation profiles of genomic DNA of mouse developmental brain detected by restriction landmark genomic scanning (RLGS) method, Nucl. Acid. Res., 21, 5604-5608, 1993
  24. Hayashizaki Y., Shibata H., Hirotsune S., Sugino H., Okazaki Y., Sasaki N., Hirose K., Imoto H., Okuizumi H., Muramatsu M., Komatsubara H., Shiroishi T., Moriwaki K., Katsuki M., Hatano N., Sasaki H., Ueda T., Mise N., Takagi N., Plass C. and Chapman V.M., Identification of an imprinted U2af binding protein related sequence on mouse chromosome 11 using the RLGS method., Nature Genetics, 6, 33-40, 1994
  25. Okuizumi H., Okazaki Y., Sasaki N., Muramatsu M., Nakashima K., Fan K., Tano H., Ohba K and Hayashizaki Y,, Application of the RLGS method to large-size genomes using a restriction trapper., DNA Res., 1, 99-102, 1994
  26. Sasaki N., Hayashizaki Y., Muramatsu M., Matsuda Y., Ando Y., Kuramoto T., Serikawa T., Azuma T., Naito A., Agui T., Yamashita T., Miyoshi I., Takeichi N. and Kasai N., The gene responsible for LEC hepatitis, located on rat chromosome 16, is the homolog to the human Wilson disease gene., Biochem Biophys. Res. Comm., 202, 512-518, 1994
  27. Maki K., Miyoshi I., Kon Y., Yamashita T., Sasaki N., Aoyama S., Takahashi E., Namioka S., Hayashizaki Y. and Kasai N., Targeted pituitary tumorigenesis using the human thyrotropin b-subunit chain promoter in transgenic mice., Mol. Cell. Endocrinol., 105, 147-154, 1994
  28. Kawai J., Hirose K., Fushiki S., Hirotsune S., Ozawa N., Hara A., Hayashizaki Y. and Watanabe S, Comparison of DNA methylation patterns among mouse cell lines by restriction landmark genomic scanning., Mol. Cell Biol., 14, 7421-7427, 1994
  29. Imoto H., Hirotsune S., Muramatsu M., Okuda K., Sugimoto O., Chapman V.M. and Hayashizaki Y., Direct determination of NotI cleavage sites in the genomic DNA of adult mouse kidney and human trophoblast using whole-range restriction landmark genomic scanning., DNA Res., 1, 239-243, 1994
  30. Hayashizaki Y., Hirotsune S., Okazaki Y., Shibata H., Akasako A., Muramatsu M., Kawai J., Hirasawa T., Watanabe S., Shiroishi T., Moriwaki K., Taylor B. A., Matsuda Y., Elliott R. W., Manly K. F. and Chapman V.M., A genetic linkage map of the mouse using restriction landmark genomic scanning (RLGS), Genetics, 138, 1207-1238, 1994
  31. Tada M., Tada T., Takagi N., Hayashizaki Y., Shibata H., Hirotsune S., Okazaki Y. Muramatsu M., Sasaki H., Ueda T. and Chapman V.M., Localization of mouse imprinted gene U2af1-rs1 to A3.2-4 band of chromosome 11 by FISH, Mammalian Genome, 5, 655, 1994
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  37. Ohsumi T, Okazaki Y, Shibata H., Hirotsune S., Muramatsu M, Suzuki H., Taga C., Watanabe S. and Hayashizaki Y., A spot cloning method for restriction landmark genomic scanning, Electrophoresis, 16, 203-209, 1995
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  39. Watanabe S., Kawai J., Hirotsune S., Suzuki H., Hirose K., Taga C, Ozawa N., Fushiki S. and Hayashizaki Y., Accessibility to tissue-specific genes from methylation profiles of mouse brain genomic DNA, Electrophoresis, 16, 218-226, 1995
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  41. Okuizumi H., Okazaki Y., Ohsumi T., Hanami T., Mizuno Y., Muramatsu M., Hayashizaki Y., Plass C and Chapman V.M., A single gel analysis of 575 dominant and codominant restriction landmark genomic scanning loci in mice interspecific backcross progeny, Electrophoresis, 16, 253-260, 1995
  42. Plass C., Kawai J., Kalcheva I., Davis L., Watanabe S., Hayashizaki Y. and Chapman V.M., Comparative analysis of mouse NotI linking clones with mouse and human genomic sequences and transcripts, DNA Res., 2, 27-35, 1995
  43. Hirotsune S., Takahara T., Sasaki N., Hirose K., Yoshiki A., Ohashi T., Kusakabe M., Murakami Y., Muramatsu M., Watanabe S., Nakao K., Katsuki M. and Hayashizaki Y. The reeler gene encodes a protein with an EGF-like motif expressed by pioneer neurons, Nature Genetics, 10, 77-83, 1995
  44. Latham K.E., Rambhatla L., Hayashizaki Y. and Chapman V.M., Stage-specific induction and regulation by genomic imprinitng of the mouse U2afbp-rs gene during preimplantation development, Developmental Biology, 168, 670-676, 1995
  45. Okazaki Y., Hirose K., Hirotsune S., Okuizumi H., Sasaki N., Ohsumi T., Yoshiki A., Kusakabe M., Muramatsu M., Kawai J., Watanabe S., Plass C., Chapman V.M., Nakao K., Katsuki M. and Hayashizaki Y., Direct detection and isolation of restriction landmark genomic scanning (RLGS) spot DNA markers tightly linked to a specific trait by using the RLGS spot-bombing method, Proc. Natl. Acad. Sci. USA., 92, 5610-5614, 1995
  46. Ohsumi T., Okazaki Y., Okuizumi H., Shibata K., Hanami T., Mizuno Y., Takahara T., Sasaki N., Ueda M., Muramatsu M., Kerns K. A., Chapman V.M., Held W.A. and Hayashizaki Y., Loss of hetrozygosity in chromosome 1, 5, 7 and 13 in mouse hepatoma detected by systematic genome-wide scanning using RLGS genetic map, Biochem. Biophys. Res. Comm., 212, 632-639, 1995
  47. Kuromitsu J., Kataoka H., Yamashita H., Muramatsu M., Furuichi Y., Sekine T and Hayashizaki Y., Reproducible alterations of DNA methylation at a specific population of CpG islands during blast formation of peripheral blood lymphocytes, DNA Research, 2, 263-267, 1995
  48. Aruga J., Nagai T., Tokuyama T., Hayashizaki Y., Okazaki Y., Chapman V.M. and Mikoshiba K., The Mouse Zic Gene Family, J. Biol. Chem., 271, 1043-1047, 1996
  49. Okazaki Y., Okuizumi H., Ohsumi T., Nomura O., Takada S., Kamiya M., Sasaki N., Matsuda Y., Nishimura M., Tagaya O., Muramatsu M. and Hayashizaki Y., A genetic linkage map of the syrian hamster and localization of cardiomyopathy locus on chromosome 9qa2.1-b1 using RLGS spot-mapping, Nature Genetics, 13, 87-90, 1996
  50. Pearsall R.S., Shibata H., Brozowska A., Yoshino K., Okuda K., deJong P.J., Plass C., Chapman V.M., Hayashizaki Y. and Held W.A., Absence of imprinting in U2AFBPL, a human homologue of the imprinted mouse gene U2afbp-rs, Biochem. Biophys. Res. Comm., 222, 171-177, 1996
  51. Takahara T., Ohsumi T., Kuromitsu J., Shibata K., Sasaki N., Okazaki Y., Shibata H., Sato S., Yoshiki A., Kusakabe M., Muramatsu M., Ueki M., Okuda K. and Hayashizaki Y., Dysfunction of the Orleans reeler gene arising from exon skipping due to transposition of a full-length copy of an active L1 sequence into the skipped exon, Hum. Mol. Genet., 5, 989-993, 1996
  52. Shibata H., Yoshino K., Sunahara S., Gondo Y., Katsuki M., Ueda T., Kamiya M., Muramatsu M., Murakami Y., Kalcheva I., Plass C., Chapman V.M. and Hayashizaki Y., Inactive allele-specific methylation and chromatin structure of the imprinted gene U2af1-rs1 on mouse chromosome 11, Genomics, 35, 248-252, 1996
  53. Aruga J., Yozu A., Hayashizaki Y.,Okazaki Y., Chapman V.M. and Mikoshiba K., Identification and characterization of Zic4, a new member of the mouse Zic gene family, .Gene ,172, 291-294, 1996
  54. Matsuda Y., Takahara T., Kusakabe M. and Hayashizaki Y., Comparative mapping of the reeler gene on human chromosome 7q22, rat chromosome 4q11.2, and mouse chromosome 5 A3-B1, Mammalian Genome, 7, 468-469, 1996
  55. Plass C., Shibata H., Kalcheva I, Mullins L., Kotelevtseva N., Mullins J., Kato R., Sasaki H., Hirotsune S., Okazaki Y., Held W.A., Hayashizaki Y. and Chapman V.M., Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M, Nature Genetics, 14, 106-109, 1996
  56. Takada S., Okazaki Y., Kamiya M., Ohsumi T., Nomura O., Okuizumi H., Sasaki N., Shibata H., Mori M., Nishimura M., Muramatsu M., Hayashizaki Y. and Matsuda Y., Five candidate genes for hamster cardiomyopathy did not map to the cardiomyopathy locus by FISH analysis, DNA Res., 3, 273-276, 1996
  57. Miwa W., Yasuda J., Murakami Y., Yashima K., Sugano K., Sekine T., Kono A., Egawa S., Yamaguchi K., Hayashizaki Y. and Sekiya T., Isolation of DNA sequences amplified at chromosome 19q13.1-q13.2 including the AKT2 locus in human pancreatic cancer, Biochem. Biophys. Res. Comm., 225, 968-974, 1996
  58. Suzuki H., Kawai J., Taga C., Yaoi T., Hara A., Hirose K., Hayashizaki Y., and Watanabe S., Stac, a novel neuron-specific protein with cysteine-rich and SH3 domains, Biochem. Biophys. Res. Commun.,, 229, 902-909, 1996
  59. Hirotsune S., Takahara T., Sasaki N., Imoto H., Okazaki Y., Eki T., Murakami Y., Abe M., Furuya K., Muramatsu M., Eto Y., Chapman V.M. and Hayashizaki Y., Construction of high-resolution physical maps from yeast artificial chromosomes using restriction landmark genomic scanning (RLGS), Genomics, 37, 87-95, 1996
  60. Carninci P., Kvam C., Kitamura A., Ohsumi T., Okazaki Y., Itoh M., Kamiya M., Shibata K, Sasaki N., Izawa M., Muramatsu M., Hayashizaki1 Y. and Schneider C., High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37,327-336, 1996
  61. Kuromitsu J., Yamashita H., Kataoka H., Takahara T., Muramatsu M., Sekine T., Okamoto N., Furuichi Y and Hayashizaki Y., A unique downregulation of h2-calponin gene expression in down syndrome : a possible attenuation mechanism for fetal survival by methylation at the CpG island in the trisomic chromosome 21, Mol. and Cell. Biol., 17, 707-712, 1997
  62. Okuizumi H., Ohsumi T., Sasaki N., Imoto H., Mizuno Y., Hanami T., Yamashita H., Kamiya M., Takada S., Kitamura A., Muramatsu M., Nishimura M., Mori M., Matsuda Y., Tagaya O., Okazaki Y. and Hayashizaki Y., Linkage map of Syrian hamster with restriction landmark genomic scanning, Mammalian Genome, 8, 121-128, 1997
  63. Ito M., Carninci P., Nagaoka S., Sasaki N., Okazaki Y., Ohsumi T., Muramatsu M.and Hayashizaki Y., Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates, Nucleic Acides Res., 25, 1315-1316, 1997
  64. Nigro V., Okazaki Y., Belsito A., Piluso G., Matsuda Y., Politano L., Nigro G., Ventura C., Abbondanza C., Molinari A. M., Acampora D., Nishimura M., Hayashizaki Y. and Puca G. A., Identification of the Syrian hamster cardiomyopathy gene., Hum. Mol. Genet. 6, 601-607, 1997
  65. Carninci P., Westover A., Nishiyama Y., Ohsumi T., Itoh M., Nagaoka S., Sasaki N., Okazaki Y., Muramatsu M., Schneider C. and Hayashizaki Y., High efficiency selection of full-length cDNA by improved biotinylated cap trapper, DNA Res., 4, 61-66, 1997
  66. Akama T. O., Okazaki Y., Itoh M., Okuizumi H., Konno H., Muramatsu M., Plass C., Held W.A. and Hayashizaki Y., Restriction landmark genomic scanning (RLGS-M)-based genome-wide scanning of mouse liver tumors for alterations in DNA methylation status, Cancer Res., 57, 3294-3299, 1997
  67. Shibata H., Ueda T., Kamiya M., Yoshiki A., Kusakabe M., Plass C., Held W.A., Sunahara S., Katsuki M., Muramatsu M. and Hayashizaki Y., An oocyte-specific methylation imprint center in the mouse U2afbp-rs/U2af1-rs1 gene marks the establishment of allele-specific methylation during preimplantation development, Genomics, 44, 171-178, 1997
  68. Sasaki N., Izawa M., Shimojo M., Shibata K., Akiyama J., Itoh M., Nagaoka S., Carninci P., Okazaki Y., Moriuchi T., Muramatsu M., Watanabe S. and Hayashizaki Y., A novel control system for polymerase chain reaction using a RIKEN GS384 thermalcycler, DNA Res., 4, 387-391, 1997
  69. Sugahara Y., Hayashizaki Y., Tanihata I., An automatic image analysis system for RLGS films, Genome Informatics Series, No.8, 340-341, 1997
  70. Kato M.V., Ikawa Y., Hayashizaki Y. and Shibata H. Paternal imprinting of mouse serotonin receptor 2A gene Htr2 in embryonic eye; A conserved imprinting regulation on the RB/Rb locus, Genomics, 47, 146-148, 1998
  71. Naas, T.P., DeBerardinis R.J., Moran J.V., Ostertag E.M., Kingsmore S.F., Seldin M.F., Hayashizaki Y., Martin S.L. and Kazazian, Jr. H.H., An actively retrotransposing, novel subfamily of mouse L1 elements, EMBO, 17, 590-597, 1998
  72. Sasaki N., Izawa M., Watahiki M., Ozawa K., Tanaka T., YonedaY., Matsuura S., Carninci P., Muramatsu M., Okazaki Y. and Hayashizaki Y., Transcriptional sequencing: A method for DNA sequencing using RNA polymerase, Proc. Natl. Acad. Sci. USA., 95. 3455-3460, 1998
  73. Sasaki N., Nagaoka S., Itoh M., Izawa M., Konno H., Carninci P., Yoshiki A., Kusakabe M., Moriuchi T., Muramatsu M., Okazaki Y. and Hayashizaki Y., Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones, Genomics, 49, 167-179, 1998
  74. Carninci P., Nishiyama Y., Westover A., Itoh M., Nagaoka S., Sasaki N., Okazaki Y., Muramatsu M. and Hayashizaki Y.,Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA, Proc. Natl. Acad. Sci. USA. 95, 520-524, 1998
  75. Shibata H., Yoda Y., Kato R., Ueda T., Kamiya M., Haraiwa N., Yoshiki A., Plass C., Pearsall R. S., Held W.A., Muramatsu M., Sasaki H., Kusakabe M. and Hayashizaki Y., A methylation imprint mark in the mouse imprinted gene Grf1/Cdc25 Mm locus shares a common feature with the U2afbp-rs gene; An association with a short tandem repeat and a hypermethylated region, Genomics, 49, 30-37, 1998
  76. Pearsall R.S., Imai K., Shibata H., Hayashizaki Y., Chapman V.M., Held W.A. and Plass C., The Rasgrf1-repeat sequence (D9Ncvs53) maps between Mod1 and Rbp1 on mouse chromosome 9 and may define a putative imprinted region, Mammal. Genome , 9, 261-262, 1998
  77. Izawa M.,Sasaki N., Watahiki M., Ohara E., Yoneda Y., Muramatsu M., Okazaki Y. and Hayashizaki Y., Recognition sites of 3'-OH group by T7 RNA polymerase and its application to transcriptional sequencing, J.Biol. Chem. 273, 14242-14246, 1998
  78. Sugahara Y., Akiyoshi S., Okazaki Y., Hayashizaki Y. and Tanihata I., An automatic image analysis system for RLGS films, Mammal. Genome , 9, 643-651, 1998
  79. Hayward B.E., Kamiya M., Strain L., Moran V., Campbell R., Hayashizaki Y. and Bonthron D.T., The human GNAS1 gene is imprinted, and encodes distinct paternally and biallelically expressed G proteins, Proc. Natl. Acad. Sci. USA., 95, 10038-10043, 1998
  80. Sasaki N., Izawa M., Sugahara Y., Tanaka T., Watahiki M., Ozawa K., Ohrara E., Funaki H., Yoneda Y., Matsuura S., Muramatsu M., Okazaki Y. and Hayashizaki Y., Identification of stable RNA hairpins causing band compression in transcriptional sequencing and their elimination by use of inosine triphosphate, GENE , 222, 17-24, 1998
  81. Seki M., Carninci P., Nishiyama Y., Hayashizaki Y. and Shinozaki K., High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper, Plant Journal, 15C707-720, 1998
  82. Mori M., Akiyoshi S., Mizuno Y., Okuizumi H., Okazaki Y., Hayashizaki Y. and Nishimura M., Genetic profile of the SMXA recombinant inbred mouse strains revealed with restriction landmark genomic scanning, Mammalian Genome, 9, 695-709, 1998
  83. Tateno M. and Hayashizaki Y., Construction of large-insert BAC library from C57BL/6J mouse, Bioimages, 6, 117-125, 1998
  84. Fukunishi Y., Konno H. and Hayashizaki Y., Automatic cDNA classification system for mouse genome project, Genome Informaticcs Series, No.9, 321-323, 1998
  85. Konno H., Sugahara Y., Fukunishi Y., Shibata K. and Hayashizaki Y., Automated cDNA informaiton system for large scale cDNA project, Genome Informatics Series, No.9, 324-325, 1998
  86. Sugahara Y. and Hayashizaki Y., Application of the RLGS image analysis tool (RAT) to the construction of a genetic linkage map of recombinant inbred strain SMXA, Genome Informatics Series, No.9, 326-327, 1998
  87. Cattanach B.M., Shibata H., Hayashizaki Y., Townsend K.M., Ball S. and Beechey C.V., Association of a redefined proximal mouse chromosome 11 imprinting region and U2afbp-rs/U2af1-rs1 expression, Cytogenet. Cell Genet., 80, 41-47, 1998
  88. Sugahara Y., Akiyoshi S., Okazaki Y., Tanihata I. Nishimura M. and Hayashizaki Y., Application of RLGS image analysis tool (RAT) to the construction of a genetic linkage map of recombinant inbred strain SMXA, Mammal. Genome, 10, 611-616, 1999
  89. Mizuno Y., Carninci P., Okazaki Y., Tateno M., Kawai J., Amanuma H., Muramatsu M. and Hayashizaki Y., Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display, Nucleic Acides Res., 27, 1345-1349, 1999
  90. Itoh M., Kitsunai T., Akiyama J., Shibata K., Izawa M., Kawai J., Tomaru Y., Carninci P., Shibata Y., Ozawa Y., Muramatsu M., Okazaki Y. and Hayashizaki Y., Automated filtration-based high-throughput plasmid preparation system, Genome Res., 9, 463-470, 1999
  91. Pearsall R.S., Plass C., Romano M.A., Garrick M.D., Shibata H., Hayashizaki Y. and Held W.A., A direct repeat sequence at the Rasgrf1 locus and imprinted expression, Genomics, 55, 194-201, 1999
  92. Fukunishi Y., Suzuki H., Yoshino M., Konno H. and Hayashizaki Y., Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database, FEBS Lett., 464, 129-132, 1999
  93. Takada S., Kamiya M., Arima T., Kagebayashi H., Shibata H., Muramatsu M., Chapman V.M., Wake N., Hayashizaki Y. and Takagi N.,Detection and cloning of an X-linked locus associated with a NotI site that is not methylated on mouse inactivated X chromosome by the RLGS-M method, Genomics, 61, 92-100, 1999
  94. Kadota K., Miki R., Okazaki Y., Shimizu K. and Hayashizaki Y., Development of an efficient data processing method for cDNA microarray and its application to tissue expression profiling, Genome Informatics Series, No.10, 221-222, 1999
  95. Konno H., Fukunishi Y., Endo T. and Hayashizaki Y., Construction and application of mouse full-length cDNA database, Genome Informatics Series, No.10, 288-289, 1999
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  189. Ravasi T., Huber T., Zavolan M., Forrest A., Gaasterland T., Grimmond S., RIKEN GER Group Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Hume D.A., Systematic characterization of the zinc finger containing proteins in the mouse transcriptome, Genome Research, 13, 1430-1442, 2003
  190. Forrest A.A., Ravasi T., Taylor D., Huber T., Hume D.A., RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Grimmond S., Phosphoregulators: protein kinases and protein phosphatases of mouse, Genome Research, 13, 1443-1454, 2003
  191. Miki H., Setou M., RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Hirokawa N., Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome, Genome Research, 13, 1455-1465, 2003
  192. Kawasawa Y., McKenzie L.M., Hill D.P., Bono H., RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Yanagisawa M., The comparative proteomics of ubiquitination in mouse, Genome Research, 13, 1466-1477, 2003
  193. Furuno M., Kasukawa T., Saito R., Adachi J., Suzuki H., Baldarelli R., Hayashizaki Y. and Okazaki Y., CDS annotation in full length cDNA sequence, Genome Research, 13, 1478-1487, 2003
  194. Kawai J. and Hayashizaki Y., DNA Book, Genome Research, 13, 1488-1495, 2003
  195. Schriml L.M., Hill D.P., Blake J.A., Bono H., Wynshaw-Boris A., Pavan W.J., Ring B.Z., Beisel K., Setou M., RIKEN GER Group Members (Arakawa T., Carninci P., Kawai J.), Okazaki Y. and Hayashizaki Y., Human Disease Genes and Their Cloned Mouse Orthologs: Exploration of the FANTOM2 cDNA Sequence Data Set, Genome Research, 13, 1496-1500, 2003
  196. Baldarelli R., Hill D.P., Blake J.A., Adachi J., Furuno M., Bradt D., Corbani L.E., Cousins S., Frazer K.S., Qi D., Yang L., Ramachandran S., Reed D., Zhu Y., Kasukawa T., Ringwald M., King B.L., Maltais L.J., McKenzie L.M., Schriml L.M., Maglott D., Church D.M., Pruitt K., Eppig J.T., Richardson J.E., Kadin J.A. and Bult C., Connecting sequence and biology in the laboratory mouse, Genome Research, 13, 1505-1519, 2003
  197. Nagashima T., Silva D.G., Petrovsky N., Socha L.A., Suzuki H., Saito R., Kasukawa T., Kurochkin I.V., Konagaya A., and Schonbach C., Interring higher functional information for RIKEN mouse full-length cDNA clones with FACTS, Genome Research, 13, 1520-1533
  198. Suzuki H., R. Saito, Kanamori M., Kai C., Schonbach C., Nagashima T., Hosaka J, and Hayashizaki Y., The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer, Genome Research, 13, 1534-1541, 2003
  199. Kasukawa T., Furuno M., Nikaido I., Bono H., Hume D.A., Bult C., Hill D.P., Baldarelli R., Gough J., Kanapin A., Matsuda H., Schriml L.M., Hayashizaki Y., Okazaki Y. and Quackenbush J., Development and evaluation of an automated annotation pipeline and cDNA annotation system, Genome Research, 13, 1542-1551, 2003
  200. Kiyosawa H., Kawashima T., Hasegawa Y., Yamanaka I, Sakai K., Kondo S., RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J.) and Hayashizaki Y., Positional candidate cloning approach to identify human disease-related genes using the FANTOM2 clone set and Riken-GenoMapper mapping viewer system, Genome Research, 13, 1554-1555, 2003
  201. Silva D.G., Schonbach C., Brusic V., Socha L.A., Nagashima T., RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Petrovsky N., Identification of novel gPathologsh (Human disease-related gene candidates) from the RIKEN full-length mouse cDNA data set, Genome Research, 13, 1559, 2003
  202. Kurochkin I.V., RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Schonbach C., Identification of potential peroxisomal proteins in mouse, Genome Research, 13, 1560, 2003
  203. Watanabe Y., Nishiguchi S., Watanabe M., Shimada K, RIKEN GER Group and GSL Members (Arakawa T., Carninci P., Kawai J., Hayashizaki Y.) and Koyama K.., Yamanishi H, The mouse neuronal protein 15.6 gene family, Genome Research, 13, 1561, 2003
  204. Shibata K., Izawa M., Hyashizaki Y., and Watahiki M., Pratctical application of transcriptional sequencing for GC-rich temples., Journal of Structural and Functional Genomics, 4, 35-39, 2003
  205. Nishiyama T., Fujita T., Shin-I., Seki M., Nishide H., Uchiyama I., Kamiya A., Carninci P., Hayashizaki Y., Shinozaki K., Kohara Y., Hasebe M., Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis Thaliana: Implication for land plant evolution. Proceedings of the Natinal Academy of Science of the USA., Vol.100, No.13, 8007-8012, 2003
  206. Hirozane-Kishikawa H., Shiraki T., Waki K., Nakamura M., Arakawa T., Kawai J., Fagiolini M., Hensch T.K., Hayashizaki Y., Carninci P., Subtraction of cap-trapped full length cDNA libraries to select rare transcripts., Bio Techniques, 35, 510-518, 2003
  207. National Institute of Aerobiological Science Rice Full-Length cDNA Project Team: Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashidume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y., Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice, science, 301, 376-379, 2003
  208. Shimizu H, Taniguchi H, Hippo Y, Hayashizaki Y, Aburatani H, Ishikawa T.., Characterization of the mouse Abcc12 gene and its transcript encoding an ATP-binding cassette transporter, an orthologue of human ABCC12, GENE, 310, 17-28, 2003
  209. Kanamori M, Sandy P, Marzinotto S, Benetti R, Kai C, Hayashizaki Y, Schneider C, Suzuki H., The PDZ protein TIP-1 inhibits beta-catenin transcriptional activity and growth of colorectal cancer cells, J Biol Chem., 278(40), 38758-38764, 2003
  210. Gariboldi M, Spinola M, Milani S, Pignatiello C, Kadota K, Bono H, Hayashizaki Y, Dragani TA, Okazaki Y., Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice, Carcinogenesis, still online only
  211. Wells C.A., Ravasi T., Faulkner G.J., Carninci P., Okazaki Y., Hayashizaki Y., Sweet M., Wainwright B.J., and Hume D.A., Genetic control of the innate immune response, BMC, still online only
  212. Futaki S, Hayashi Y, Yamashita M, Yagi K, Bono H, Hayashizaki Y, Okazaki Y, Sekiguchi K.., Molecular basis of constitutive production of basement membrane components: Gene expression profiles of Engelbreth-Holm-Swarm tumor and F9 embryonal carcinoma cells, J Biol Chem, still online only
  213. Fujimoto S., Washio T., Higo K., Ohtomo Y., Murakawa K., Matsubara K., Kawai J., Carninci P., Hayashizaki Y., Kikuchi S., and Tomita M, Anovel feature of microsatelite in plants: a distribution gradient along the direction of transcription, FEBS Letters, 554, 17-22, 2003
  214. Tomaru Y., Kondo s., Suzuki M., Hayashizaki Y., Acomprehensive search for HNF-3--regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis, BBRC, 310(2), 667-674, 2003
  215. Evidence for Tissue-specific Transcription Regulated by Alteranative First Exons in O.sativa, Genome Research, 13, 1318-23 (2003)
  216. Juan Hou, Kenta Yashiro, Yasushi Okazaki, Yukio Saijoh, Yoshihide Hayashizaki, and Hiroshi Hamada. Identification of a Novel Left-Right Asymmetrically Expressed Gene in the Mouse Belonging to the BPI/PLUNC Superfamily, Developmental Dynamics, 229, 373?379(2004)
  217. Nikaido I., Saito C., Wakamoto A. Tomaru Y. Arakawa T., Hayashizaki Y., Okazaki Y., REICO (Expression-based Imprint Candidate Organizer): Finding disease-related imprinted genes Nucleic Acid Research 23, 548-551, 2003
  218. Shiraki T., Kondo S., Katayama S., Waki K., Kasukawa T., Kawaji H., Kodzius R., Watahiki A., Nakamura M., Arakawa T., Fukuda S., Sasaki D., Podhajska A., Harbers M., Kawai J., Carninci P., Hayashizaki Y., Cap Anaalysis Gene Expression (CAGE) for high throughput analysis of tanscriptiona atarting point and identification of promoter usage, PNAS 100(26), 15776-15781, 2003
  219. Naoki Osato, Hitomi Yamada, Kouji Satoh, Hisako Ooka, Makoto Yamamoto, Kohji Suzuki, Jun Kawai, Piero Carninci, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Shoshi Kikuchi and Yoshihide Hayashizaki, Antisense transcripts with rice full-length cDNAs, Genome Biology 5(1), R5, 2003
  220. Kayoko Yamada, Jun Lim, Joseph M. Dale, Huaming Chen, Paul Shinn, Curtis J. Palm, Audrey M. Southwick, , Hank C. Wu, Christopher Kim, Michelle Nguyen, Paul Pham, , Rosa Cheuk, George Karlin-Newmann, Shirley X. Liu, Bao Lam, Hitomi Sakano, Troy Wu, Guixia Yu, Molly Miranda, Hong L. Quach, Matthew Tripp, Charlie H. Chang, Jeong M. Lee, Mitsue Toriumi, Marie M. H. Chan, Carolyn C. Tang, Courtney S. Onodera, Justine M. Deng, Kenji Akiyama, YasserAnsar i, Takahiro Arakawa, Jenny Banh, Fumika Banno, Leah Bowser, Shelise Brooks, Piero Carninci, Qimin Chao, Nathan Choy, Akiko Enju, Andrew D. Goldsmith, Mani Gurjal, Nancy F. Hansen, Yoshihide Hayashizaki, Chanda Johnson-Hopson, Vickie W. Hsuan, Kei Iida, Meagan Karnes, Shehnaz Khan, Eric Koesema, Junko Ishida, Paul X. Jiang, Ted Jones, Jun Kawai, Asako Kamiya, Cristina Meyers, Maiko Nakajima, Mari Narusaka, Motoaki Seki, Tetsuya Sakurai, Masakazu Satou, Racquel Tamse, Maria Vaysberg, Erika K. Wallender, Cecilia Wong, Yuki Yamamura, Shiaulou Yuan, Kazuo Shinozaki, Ronald W. Davis, Athanasios Theologis, Joseph R. Ecker, Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome, Science 302, 842-846, 2003
  221. Wenzheng Zhang, Yoshihide Hayashizaki, Bruce C. Kone, Structure and Regulation of the mDot1 Gene, a Murine Histone H3 Methyltransferase. Biochem. J., 377, 641?651 (2004)
  222. Chikara Kokubu, Bettina Wilm, Tomoko Kokubu, Matthias Wahl, Isabel Rodrigo, Norio Sakai, Fabio Santagati, Yoshihide Hayashizaki, Misao Suzuki, Ken-ichi Yamamura, Kuniya Abeand Kenji Imai, Undulated short-tail Deletion Mutation in the Mouse Ablates Pax1 and Leads to Ectopic Activation of Neighboring Nkx2-2 in Domains That Normally Express Pax1. Genetics 165, 299?307 (2003)
  223. Martin Madera, Christine Voge, Sarah K. Kummerfeld, Cyrus Chothia and@Julian GoughAThe SUPERFAMILY database in 2004: additions and@improvements Nucleic Acids Research, 32, 235-239 (2004)
  224. Vogel, C., Berzuini, C., Bashton, M., Gough, J., Teichmann, A. Supra-domains: Evolutionary units larger than single protein domains. J. Mol. Biol. 336, 809-823 (2004)
  225. Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki and Hideo Matsuda, MaXML: mouse annotation XML, In Silico Biol. 4, (2003)
  226. Rimantas Kodzius, Yonehiro Matsumurab, Takeya Kasukawa, Kazuro Shimokawa, Shiro Fukuda Toshiyuki Shiraki Mari Nakamura Takahiro Arakawa Daisuke Sasaki Jun Kawaia, Matthias Harbers, Piero Carnincia;, Yoshihide Hayashizakia, Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Letters 559i1-3j, 22-26, (2004)
  227. Hidenori Kiyosawa, Tsugumi Kawashima, Diego Silva, Nikolai Petrovsky, Yuki Hasegawa, Katsunaga Sakai, and Yoshihide Hayashizaki, A Systematic Genome-Wide Approach to Positional Candidate Cloning for Identification of Novel Human Disease Genes. Internal Medicine Journal, 34, 79-90 (2004)
  228. Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group and GSL Members, Akihiko Konagaya and Christian Schonbach. FREP: a database of functional repeats in mouse cDNAs, Nucl. Acid Res 32, 471-475 (2004)
  229. Hisako Ooka, Kouji Satoh, Koji Doi, Toshifumi Nagata, Yasuhiro Otomo, Kazuo Murakami, Kenichi Matsubara, Naoki Osato, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Koji Suzuki, Keiichi Kojima, Yoshinori Takahara, Koji Yamamoto, and Shoshi Kikuchi, Comprehensive Analysis of NAC Family Genes in Oryza sativa and Arabidopsis thaliana. DNA Research 10, 239?247 (2003)
  230. Kirk W. Beisel, Toshiyuki Shiraki, Ken A. Morris, Celine Pompeia, Bechara Kachar, Takahiro Arakawa, Hidemasa Bono, Jun Kawai, Yoshihide Hayashizaki, Piero Carninci, Identification of Unique Transcripts from a Mouse Full-Length, Subtracted Inner Ear cDNA Library. Genomics, 83, 1012-1023 (2004)
  231. Junshi Yazaki, Naoki Kishimoto, Yuko Nagata, Masahiro Ishikawa, Fumiko Fujii, Akiko Hashimoto, Kanako Shimbo, Zenpei Shimatani, Keiichi Kojima, Kouji Suzuki, Makoto Yamamoto, Sachiko Honda, Ayano Endo, Yumiko Yoshida, Yuki Sato, Keiko Takeuchi, Kazuko Toyoshima, Chikako Miyamoto, Jianzhong Wu, Takuji Sasaki, Katsumi Sakata,@Kimiko Yamamoto, Koh Iba, Takahiro Oda, Yasuhiro Otomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice. DNA Research 10, 249-261 (2003).
  232. Daisuke Shimizu, Takashi Ishikawa, Yasushi Ichikawa, Shinji Togo, Yoshihide Hayashizaki, Yasushi Okazaki, Hiroshi Shimada, Current Progress in the Prediction of Chemosensitivity for Breast Cancer.. Breast Cancer, 11, 42-48 (2004)
  233. Julian Gough,. Convergent evolution of domain architectures. Currents@in computational biology 2004. Ed.s Gramada, A. and Bourne, P.E. RECOMB(2004)
  234. Mammalian gene collection (MGC) program team, Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. PNAS, 99(26), 16899-16903, 2002
  235. Tanaka T, Tanimoto K, Otani K, Satoh K, Ohtaki M, Yoshida K, Toge T, Yahata H, Tanaka S, Chayama K, Okazaki Y, Hayashizaki Y, Hiyama K, Nishiyama M., Concise prediction models of anticancer efficacy of 8 drugs using expression data from 12 selected genes. Int. J .Cancer, 111, 617-626 (2004)
  236. Stefano Gustincich, Massimo Contini, Manuela Gariboldi, Michelino Puopolo, Koji Kadota, Hidemasa Bono, Julianna LeMieux, Pamela Walsh, Piero Carninci, Yoshihide Hayashizaki, Yasushi Okazaki, and Elio Raviola, Gene discovery in genetically labeled single dopaminergic neurons of the retina. PNAS, 101, 5069-5074 (2004)
  237. Tomonari Sasazuki Tatsuma Okazaki, Kurisu Tada, Sachiko Sakon-Komazawa, Mitsuo Katano, Masao Tanaka, Hideo Yagita, Ko Okumur, Naoko Tominaga, Yoshihide Hayashizaki, Yasush Okazaki, Hiroyasu Nakano, Genome wide analysis of TNF-inducible genes reveals that antioxidant enzymes are induced by TNF and responsible for elimination of ROS. Mol Immunol. 41, 547-551 (2004)
  238. Takuma Kasai, Makoto Inoue, Seizo Koshiba, Takashi Yabuki, Masaaki Aoki, Emi Nunokawa, Eiko Seki, Takayoshi Matsuda, Natsuko Matsuda, Yasuko Tomo, Mikako Shirouzu, Takaho Terada, Naomi Obayashi, Hiroaki Hamana, Naoko Shinya, Ayako Tatsuguchi, Satoko Yasuda, Mayumi Yoshida, Hiroshi Hirota, Yo Matsuo, Kazutoshi Tani, Harukazu Suzuki, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Takanori Kigawa, and Shigeyuki Yokoyama. Solution structure of a BolA-like protein from Mus musculus. Protein Sci. 13, 545-548 (2004)
  239. M. Stefania Lagonigro, Loris de Cecco, Piero Carninci, Dealia di Stasi, Tiziana Ranzani, Moniza Roudolfo, Manuela Gariboldi, CTAB?Urea Method Purifies RNA from Melanin for cDNA Microarray Analysis. Pigment Cell Res. 17 312-315 (2004)
  240. Yasumasa Mitani, Takayuki Nakayama, Matthias Harbers, Yoshihide Hayashizaki, Aptamer-dependent full-length cDNA synthesis by overlap extension PCR, BioTechniques 37, 124-129 (2004)
  241. Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire OfDonovan, Satoshi Fukuchi, Kanako O. Koyanagi, Roberto A. Barrero, Takuro Tamura, Yumi Yamaguchi-Kabata, Motohiko Tanino Kei Yura, Satoru Miyazaki5 Kazuho Ikeo, Keiichi Homma, Arek Kasprzyk, Tetsuo Nishikawa, Mika Hirakawa, Jean Thierry-Mieg, Danielle, Thierry-Mieg, Jennifer Ashurst, Libin Jia, Mitsuteru Nakao, Michael A. Thomas, Nicola Mulder, Youla Karavidopoulou, Lihua Jin, Sangsoo Kim, Tomohiro Yasuda, Boris Lenhard, Eric Eveno, Yoshiyuki Suzuki, Chisato Yamasaki, Jun-ichi Takeda, Craig Gough, Phillip Hilton, Yasuyuki Fujii, Hiroaki Sakai, Susumu Tanaka, Clara Amid, Matthew Bellgard, Maria de Fatima Bonaldo, Hidemasa Bono, Susan K. Bromberg, Anthony Brooke, Elspeth Bruford, Piero Carninci, Claude Chelala, Christine Couillault, Sandro J de Souza, Marie-Anne Debily, Marie-Dominique Devignes, Inna Dubchak, Toshinori Endo, Anne Estreicher, Eduardo Eyras, Kaoru Fukami-Kobayashi, Gopal Gopinathrao, Esther Graudens, Yoonsoo Hahn, Michael Han, Ze-Guang Han, Kousuke Hanada, Hideki Hanaoka, Erimi Harada, Katsuyuki Hashimoto, Ursula Hinz, Momoki Hirai, Teruyoshi Hishiki, Ian Hopkinson, Sandrine Imbeaud, Hidetoshi Inoko, Alexander Kanapin, Yayoi Kaneko, Takeya Kasukawa, Janet Kelso, Paul Kersey, Reiko Kikuno, Kouichi Kimura, Bernhard Korn, Vladimir Kuryshev, Izabela Makalowska, Takashi Makino, Shuhei Mano, Regine Mariage-Samson, Jun Mashima, Hideo Matsuda, Hans-Werner Mewes, Shinsei Minoshima, Keiichi Nagai, Hideki Nagasaki, Naoki Nagata, Rajni Nigam, Osamu Ogasawara, Osamu Ohara, Masafumi Ohtsubo, Norihiro Okada, Toshihisa Okido, Satoshi Oota, Motonori Ota, Toshio Ota, Tetsuji Otsuki, Dominique Piatier-Tonneau, Annemarie Poustka, Shuang-Xi Ren, Naruya Saitou, Katsunaga Sakai, Shigetaka Sakamoto, Ryuichi Sakate, Ingo Schupp, Florence Servant, Stephen Sherry, Rie Shiba, Nobuyoshi Shimizu, Mary Shimoyama, Andrew J. Simpson, Bento Soares, Charles Steward, Makiko Suwa, Mami Suzuki, Aiko Takahashi, Gen Tamiya, Hiroshi Tanaka, Todd Taylor, Joseph D. Terwilliger, Per Unneberg, Vamsi Veeramachaneni, Shinya Watanabe, Laurens Wilming, Norikazu Yasuda, Hyang-Sook Yoo, Marvin Stodolsky, Wojciech Makalowski, Mitiko Go, Kenta Nakai, Toshihisa Takagi, Minoru Kanehisa, Yoshiyuki Sakaki, John Quackenbush, Yasushi Okazaki, Yoshihide Hayashizaki, Winston Hide, Ranajit Chakraborty, Ken Nishikawa, Hideaki Sugawara, Yoshio Tateno, Zhu Chen, Michio Oishi, Peter Tonellato, Rolf Apweiler, Kousaku Okubo5, Lukas Wagner, Stefan Wiemann, Robert L. Strausberg, Takao Isogai, Charles Auffray, Nobuo Nomura, Takashi Gojobori, , Sumio Sugano, Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology, 2(6), e162 (2004)
  242. Taku Tanaka, Yasuhiro Tomaru, Yuki Nomura, Hisashi Miura, Masanori Suzuki, Yoshihide Hayashizaki, Comprehensive search for HNF-1b-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi, Nucl. Acid Res , 32, 2740-2750 (2004)
  243. Takeshi Maeda, Makoto Inoue, Seizo Koshiba, Takashi Yabuki, Masaaki Aoki, Emi Nunokawa, Eiko Seki, Takayoshi Matsuda, Yoko Motoda, Atsuo Kobayashi, Fumiko Hiroyasu, Mikako Shirouzu, Takaho Terada, Nobuhiro Hayami, Yoshiko Ishizuka, Naoko Shinya, Ayako Tatsuguchi, Mayumi Yoshida, Hiroshi Hirota, Yo Matsuo, Kazutoshi Tani, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Takanori Kigawa, and Shigeyuki YokoyamaSolution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA 125 (MUC16). J. Biol. Chem., 279(13), 13174-13182
  244. Gough, J. and Chothia, C. The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure 12, 1-20, (2004).
  245. Gherardi, E., Youles, M.E., Miguel, R.N., Blundell, T.L., Iamele, L., Gough, J., Bandyopadhyay, A., Hartmann, G. and Butler, P.J. Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc. Natl. Acad. Sci. U.S.A. 100(21): 12039 (2003)
  246. Shinji Togo, Hirochika Makino, Takatoshi Kobayashi, Tomoyuki Morita, Tetsuya Shimizu, Tori Kubota, Yasushi Ichikawa, Takashi Ishikawa, Yasushi Okazaki, Yoshihide Hayashizaki, Hiroshi Shimada. Mechanism of liver regeneration after partial hepatectomy using mouse cDNA microarray. J. Hepatology 40, 464-471 (2004)
  247. Hideaki Fujita, Yusuke Umezuki, Kanako Imamura, Daisuke Ishikawa, Seiko Uchimura, Atsuki Nara,@Tamotsu Yoshimori, Yoshihide Hayashizaki, Jun Kawai, Kazumi Ishidoh, Yoshitaka Tanaka, Masaru Himeno, Mammalian class E Vps proteins, SBP1 and@mVps2/CHMP2A, interact with and regulate@function of an AAA-ATPase SKD1/Vps4B. J. Cell Science, 117, 2997-3009.
  248. Harukazu Suzuki,, Rie Okunishi Wataru Hashizume, Shintaro Katayama, Noriko Ninomiya, Naoki Osato, Kenjiro Sato, Mari Nakamura, Juri Iida, Mutsumi Kanamori, Yoshihide Hayashizaki, Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR, FEBS Letters, 573, 214?218 (2004)
  249. Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai and Sumio Sugano. Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biology 4, 0036 (2004)
  250. Nagano. Y, Nagahari K., Yoshiro F., Hamaguchi Y., Ishikawa T., Ichikawa Y., Togo S., Okazaki Y., Hayashizaki Y., Shimada H., Gene expression profile analysis of regenerating liver after portal vein ligation in rats by a cDNA microarray system. Liver International 24, 253-258 (2004)
  251. David M. Lin, Yee Hwa Yang, Jonathan A. Scolnick, Lisa J. Brunet, Heather Marsh, Vivian Peng, Yasushi Okazaki, Yoshihide Hayashizaki, Terence P. Speed, and John Ngai, Spatial patterns of gene expression in the olfactory bulb. PNAS 101, 12718-12723
  252. Mutsumi Kanamori, Hideaki Konno, Naoki Osato, Jun Kawai,@Yoshihide Hayashizaki, Harukazu Suzuki, A genome-wide and nonredundant mouse transcription factor database., BBRC, 322, 787?793 (2004)
  253. Takeya Kasukawa Shintaro Katayama, Hideya Kawaji, Harukazu Suzuki, David A. Hume, Yoshihide Hayashizaki, Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis. Genomics, 84, 913-921 (2004)
  254. Yoshihide Hayashizaki, Reply to the Brief Communication Arising "Neutral evolution of non-coding cDNA", Nature 413, 757-758 (2004)
  255. Akira Watahiki, Kazunori Waki, Norihito Hayatsu, Toshiyuki Shiraki, Shinji Kondo, Mari Nakamura, Daisuke Sasaki, Takahiro Arakawa, Jun Kawai, Matthias Harbers, Yoshihide Hayashizaki, Piero Carninci, Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Nature Method 1, 233-239 (2004)
  256. Pang KC, Stephen S, Engstrom PG, Tajul-Arifin K, Chen W, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JS., Nucleic Acids Res. 33, D125-135 (2005)
  257. Harukazu Suzuki, Chihiro Ogawa, Kengo Usui, and Yoshihide Hayashizaki, In vitro pull-down assay without expression constructs. Bio techniques, 37, 918-920 (2004)
  258. Nobukazu Nameki, Misao Yoneyama, Seizo Koshiba, Naoya Tochio, Makoto Inoue, Eiko Seki, Takayoshi Matsuda, Yasuko Tomo, Takushi Harada, Kohei Saito, Naohiro Kobayashi, Takashi Yabuki, Masaaki Aoki, Emi Nunokawa, Natsuko Matsuda, Noriko Sakagami, Takaho Terada, Mikako Shirouzu, Mayumi Yoshida, Hiroshi Hirota, Takashi Osanai, Akiko Tanaka, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Kengo Kinoshita, Peter Guntert, Takanori Kigawa, Shigeyuki Yokoyama, Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci. 13, 2089 ? 2100 (2004)
  259. Ken A. Morris, Einat Snir, Celine Pompeia, Irina V Koroleva, Bechara Kachar,@Yoshihide Hayashizaki, Piero Carninci, M. Bento Soares, and Kirk W. Beisel, Differential Expression of Genes within the Cochlea as Defined by a Custom Mouse Inner Ear Microarray, J Assoc Res Otolaryngol. 6, 75-89 (2005)
  260. Francpis Lutzoni, Frank Kauff, Cymon J. Cox, David Mclaughlin, Gail Celio, Bryn Dentinger, Mahajabeen Padamsee, David Hibbett, Thiothy James, Elisabeth Baloch, Martin Grube, Vale Rewreeb, Vale Rie Hofstetter, Conrad Schoch, Elizabeth Arnold, Jolanta Miadlikowska, Joseph Spatafora, Desiree Johnson, Sarah Hambleton, Michael Crokett, Robert Shoemaker, Gi-Ho Sung, Robertlu Cking, Thorsten Kunbsch, Kerry Ofdonnell, Manfred Binderm Paul Diederich, Damien Ertz, Cecile Gueidan, Karen Hansen, Richard C. Harris, Kentaro Hosaka, Younf-Woon Lim, Brandon Matheny, Hiromi Nishida, Don Pfister, Jack Roger, Amy Rossaman Imeke Schmitt, Harrie Sipman, Jeffrey Stone, Junta Sugiyama, Rebecca Yahr, Rytas Vigalys, Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany, 91(10), 1446?1480, (2004)
  261. Timothy Ravasi, Harakazu Suzuki, Ken C. Pang, Shintaro Katayama, Masaaki Furuno, Rie Okunishi, Shiro Fukuda, Kelin Ru, Martin Frith, M. Milena Gongora, Sean M. Grimmond, David A. Hume, Yoshihide Hayashazaki and John S. Mattick, Experimental validation of the regulated expression of large numbers of noncoding RNAs from the mouse genome, Genome Research, Caldwell RB, Kierzek AM, Arakawa H, Bezzubov Y, Zaim J, Fiedler P, Kutter S, Blagodatski A, Kostovska D, Koter M, Plachy J, Carninci P, Hayashizaki Y, Buerstedde JM., Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biol. in press
  262. Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, Yanagawa H, Higo K, Satoh K, Ohtomo Y, Sunako T, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M. Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics. in press
  263. Manabu Ichikawa, Yuko Okamura-Oho, Rie Okunishi, Mutsumi Kanamori, Harukazu Suzuki, Akishige Ritani, Hiroaki Nitta, Naomi Eguchi, Yoshihiro Urade, and Yoshihide Hayashizaki, Expression Analysis of Genes Responsible for Serotonin Signaling in the Brain, Neurobiology of Disease, 19, 378-385 (2005)
  264. Miriam Barrios-Rodiles, Kevin R. Brown, Barish Ozdamar, Zhong Liu, Robert S. Donovan, Fukiko Shinjo, Yongmei Liu, Rohit Bose, Joanna Dembowy, Ian W. Taylor, Valbona Luga, Natasa Przulj, Mark Robinson, Harukazu Suzuki, Yoshihide Hayashizaki, Igor Jurisica, Jeffrey L., Wrana,@High-throughput mapping of a dynamic signaling network in mammalian cells, Science, 307, 1621-1625 (2005)
  265. Hidenori Kiyosawa, Nathan Mise, Shigeru Iwase, Yoshihide Hayashizaki, Kuniya Abe, Disclosing hidden transcripts: Mouse natural sense?antisense transcripts tend to be poly(A) negative and nuclear localized, Genome Research 15, 463-474 (2005)
  266. Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell1, Anastasia N. Nikolskaya, Sandra Orchard, Marco Pagni, Chris P. Ponting, Emmanue Quevillon, Jeremy Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan and Cathy H. Wu, InterPro, progress and status in 2005, Nucleic Acid Reserch, 33, D201-D205 (2005)
  267. Hiromi Nishida, Takahiro Suzuki, Yasuhiro Tomaru, Yoshihide Hayashizaki, A novel replication-independent histone H2a gene in mouse. BMC Genetics, 6, 10 (2005)
  268. Yonehiro Matsumura, Kazuro Shimokawa, Yoshihide Hayashizaki, Kazuho Ikeo, Yoshio Tateno, Jun Kawai, Development of a spot reliability evaluation score for DNA microarrays, Gene, 350, 149-160 (2005)
  269. K.Fukuda, C.Sakakura, K.Miyagawa, Y.Kuriu, S.kin, Y.Nakase, A.Hagiwara, S.Mitsufuji, Y.Okazaki, Y.Hayashizaki, H.Yamagishi, Differential gene expression profiles of radioresistant oesophageal cancer cell lines established by continuous fractionated irradiation, British J. Cancer, 91, 1543-1550 (2004)
  270. Atsushi Nakabachi, Shuji Shigenobu, Naoko Sakazume, Toshiyuki Shiraki, Yoshihide Hayashizaki, Piero Carninci, Hajime Ishikawa, Toshiaki Kudo, Takema Fukatsu, Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera, PNAS, 102, 5477?5482 (2005)
  271. Tomotaka Tanaka, Kenji Tanimoto, Keiko Otani, Kenichi Satoh, Megu Ohtaki, Kazuhiro Yoshida, Tetsuya Toge, Hiroshi Yahata, Shinji Tanaka, Kazuaki Chayama, Yasushi Okazaki, Yoshihide Hayashizaki, Keiko Hiyama, Masahiko Nishiyama, Concise prediction models of anticancer efficacy of 8 drugs using expression data from 12selected genes, Int. J. Cancer, 111, 617-626 (2004)
  272. Yutaka Furutani, Ri-ichiroh Manabe, Ko Tsutsui, Tomiko Yamada, Nagisa Sugimoto, Shiro Fukuda, Jun Kawai, Nobuo Sugiura, Koji Kimata, Yoshihide Hayashizaki, Kiyotoshi Sekiguchi, Identification and Characterization of Photomedins, Novel Olfactomedin Domain-containing Proteins with Chondroitin Sulfate-E Binding Activity, Biochem. J. 389, 675-684 (2005).
  273. Nishida H, Tomaru Y, Oho Y, Hayashizaki Y., Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines, BMC Genet.14, 23, (2005)
  274. Shimomura K, Sakakura C, Takemura M, Takagi T, Fukuda K, Kin S, Nakase Y, Miyagawa K, Ohgaki M, Fujiyama J, Fujita Y, Nakanishi M, Hagiwara A, Shirane M, Okazaki Y, Hayashizaki Y, Yamagishi H, Combination of L-3-phosphoserine phosphatase and CEA using real-time RT-PCR improves accuracy in detection of peritoneal micrometastasis of gastric cancer Anticancer Res. 24, 1113-1120 (2004)
  275. Arai R, Ito K, Wakiyama M, Matsumoto E, Sakamoto A, Etou Y, Otsuki M, Inoue M, Hayashizaki Y, Miyagishi M, Taira K, Shirouzu M, Yokoyama S. Establishment of stable hFis1 knockdown cells with an siRNA expression vector. J Biochem, 136, 421-425 (2005)
  276. Nameki N, Tochio N, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Fujikura Y, Saito M, Ikari M, Watanabe M, Terada T, Shirouzu M, Yoshida M, Hirota H, Tanaka A, Hayashizaki Y, Guntert P, Kigawa T, Yokoyama S., Solution structure of the PWWP domain of the hepatoma-derived growth factor family., Protein Sci, 14, 756-764 (2005)
  277. Hiyama K, Otani K, Ohtaki M, Satoh K, Kumazaki T, Takahashi T, Mitsui Y, Okazaki Y, Hayashizaki Y, Omatsu H, Noguchi T, Tanimoto K, Nishiyama M. Differentially expressed genes throughout the cellular immortalization processes are quite different between normal human fibroblasts and endothelial cells., Int J Oncol. 27(1), 87-95 (2005)
  278. Hiromi Nishida, Takahiro Suzuki, Hiroki Ookawa, Yasuhiro Tomaru, Yoshihide Hayashizaki, Comparative analysis of expression of histone H2a genes in mouse, BMC Genomics, 6, 108 (2005)
  279. P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter1, K. W. Beisel, T. Bersano-Begey, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A.F. Kruger,@S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg A. Sandelin, C. Schneider, C. Schonbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegene, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. S. Mattick, D. A. Hume, C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki , J. Aoki1, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K Waki, A. Watahiki , Y. Okamura-Oho, H. Suzuki, J. Kawai, Y. Hayashizaki, The Transcriptional Landscape of the Mammalian Genome, Science, 309, 1559-1563 (2005).
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