PUBLICATIONS(2001 - )
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PUBLICATIONS (2001 - )

    2009

    1. Takashi Oishi, Ken-ichi Tanaka, Takuya Hashimoto, Yoko Shinbo, Kanokwan Jumtee, Takeshi Bamba, Eiichiro Fukusaki, Hideyuki Suzuki, Daisuke Shibata, Hiroki Takahashi, Hiroko Asahi, Ken Kurokawa, Yukiko Nakamura, Aki Hirai, Kensuke Nakamura, Altaf-Ul-Amin, and Shigehiko Kanaya, "An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites," Plant Biotechnol. vol.26, pp167-174, (2009)


    2008

    1. Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, HiroshiUehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi, “tRNADB-CE: tRNA gene database curated manually by expert,” Nucleic Acids Res. vol.37, ppD163-D168, 2008.10
    2. Atsushi Fukushima, Masayoshi Wada, Shigehiko Kanaya, Masanori Arita, “SVD-based Anatomy of Gene Expressions for Correlation Analysis in Arabidopsis thaliana,” DNA Res. vol.15, pp367-374, 2008.10
    3. Yoko Iijima, Yukiko Nakamura, Yoshiyuki Ogata, Ken'ichi Tanaka, Nozomu Sakurai, Kunihiro Suda, Tatsuya Suzuki, Hideyuki Suzuki, Koei Okazaki , Masahiko Kitayama, Shigehiko Kanaya, Koh Aoki, and Daisuke Shibata, “Metabolite annotations based on the integration of mass spectral information,” Plant J. vol.54, no.5, pp949-962, Jun. 2008
    4. Hiroki Takahashi, Kosuke Kai, Shimbo Yoko, Kenich Tanaka, Daisaku Ohta, Taku Oshima, MD・ALTAF-UL-AMIN, Ken Kurokawa, Naotake Ogasawara, and Shigehiko Kanaya, “Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry,” Analytical Bioanalytical Chemistry Jun. 2008
    5. Suzuki, H., Sakurai, R., Ogata, Y., Nakamura, Y., Sakurai, N., Kitajima, M., Takayama, H., Kanaya, S., Aoki, K., Shibata, D.,, and Saito, K.,, “Metabolic profiling of flavonoid in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry,” Phytochemistry vol.69, no.1, pp99-111, Jan. 2008
    6. Kaori Uchida, Asako Furukohri, Yutaka Shinozaki, Tetsuya Mori, Daichi Ogawara, Shigehiko Kanaya, Takehiko Nohmi, Hisaji Maki, and Masahiro Akiyama, “Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal,” Molecular Microbiology vol.70, no.3, pp608-622, 2008
    7. Nathan Mise, Takuya Fuchikami, Michihiko Sugimoto, Satoru Kobayakawa, Fumio Ike, Takehiko Ogawa, Takeshi Tada, Shigehiko Kanaya, Tosiaki Noce, and Kuniya Abe, “Differences and similarityies in the developmental status of embryo-derived stem cells and primordial germ cells revealed by global expression profiling,” Gene to Cells vol.13, pp863-877, 2008
    8. Morimoto T, Kadoya R, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Shigehiko Kanaya, Ara K, Ozaki K, and Naotake Ogasawara, “Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis.,” DNA Res. vol.15, no.2, pp73-81, 2008
    9. Izutsu, K., Kurokawa, K., Tashiro, K., Kuhara, S., Hayashi, T., Honda, T., and Iida, T. Comparative genomic analysis using microarray demonstrates strong correlation between presence of Vp-PAI and pathogenicity in Kanagawa phenomenon-positive Vibrio parahaemolyticus. Infect. Immun. in press(2008)
    10. Kim MJ, Hirono I, Kurokawa K, Maki T, Hawke J, Kondo H, Santos M, Aoki T. Complete DNA sequence and analysis of the transferable multiple drug resistance plasmids (R-plasmids) from Photobacterium damselae subsp. piscicida isolated in Japan and USA. Antimicrob. Agents Chemother. in press (2007)


    2007

    1. Ogura Y, Ooka T, Asadulghani , Terajima J, Nougayrede JP, Kurokawa K, Tashiro K, Tobe T, Nakayama K, Kuhara S, Oswald E, Watanabe H, Hayashi T. Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biol. 8(7):R138. (2007)
    2. Goto N, Kurokawa K, Yasunaga T. Analysis of invariant sequences in 266 complete genomes. Gene. 401(1-2):172-80. (2007)
    3. Kobayashi H, Akitomi J, Fujii N, Kobayashi K, Amin MA, Kurokawa K, Ogasawara N, Kanaya S. The entire organization of transcription units on the Bacillus subtilis genome. BMC Genomics. 8(1):197 (2007)
    4. Aoki, T., Hirono, I., Kurokawa, K., Fukuda, H., Nahary, R., Eldar, A., Davison, A. J., Waltzek, T. B., Bercovier, H., and Hdrick, R. P. Genome sequence of three koi herpesvirus isolates representing the expanding distribution of an emerging disease threatening koi and common carp worldwide. J. Virol. 81(10):5058-65 (2007)
    5. Dryselius, R., Kurokawa, K., and Iida, T. Vibrionaceae, versatile bacterial family with evolutionary conserved variability. Res Microbiol. 158:479-486 (2007)
    6. Ishikawa, S., Ogura, Y., Yoshimura, M., Okumura, H., Cho, E., Kawai, Y., Kurokawa, K., Oshima, T., and Ogasawara, N. Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method. DNA Res. 14: 155-168 (2007)
    7. Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V.K., Srivastava, T.P., Taylor, T.D., Noguchi, H., Mori, H., Ogura, Y., Ehrlich, D.S., Itoh, K., Takagi, T., Sakaki, Y., Hayashi, T., and Hattori, M. Comparative metagenomics revealed commonly enriched gene sets in Human gut microbiomes. DNA Res. 14: 169-181 (2007)


    2006

    1. Oikawa A, Nakamura Y, Ogura T, Kimura A, Suzuki H, Sakurai N, Shinbo Y, Shibata D, Kanaya S, Ohta D. Clarification of pathway-specific inhibition by Fourier transform ion cyclotron resonance/mass spectrometry-based metabolic phenotyping studies. Plant Physiol. 142(2):398-413 (2006)
    2. Inoue N, Izui-Sarumaru T, Murakami Y, Endo Y, Nishimura J, Kurokawa K, Kuwayama M, Shime H, Machii T, Kanakura Y, Meyers G, Wittwer C, Chen Z, Babcock W, Frei-Lahr D, Parker CJ, Kinoshita T. Molecular basis of clonal expansion of hematopoiesis in 2 patients with paroxysmal nocturnal hemoglobinuria (PNH). Blood. 108(13):4232-6 (2006)
    3. Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 31;13(4):141-53 (2006)
    4. Ogura Y, Kurokawa K, Ooka T, Tashiro K, Tobe T, Ohnishi M, Nakayama K, Morimoto T, Terajima J, Watanabe H, Kuhara S, Hayashi T. Complexity of the genomic diversity in enterohemorrhagic Escherichia coli O157 revealed by the combinational use of the O157 Sakai OligoDNA microarray and the Whole Genome PCR scanning. DNA Res. 28;13(1):3-14 (2006)
    5. Morita YS, Sena CB, Waller RF, Kurokawa K, Sernee MF, Nakatani F, Haites RE, Billman-Jacobe H, McConville MJ, Maeda Y, Kinoshita T. PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of phosphatidylinositol mannoside in mycobacteria. J Biol Chem. 1;281(35):25143-55 (2006)
    6. Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A, Toyoda T. A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods. 2(1):5 (2006)
    7. Abe T, Sugawara H, Kanaya S, Kinouchi M, Ikemura T. Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes. Gene. 365:27-34. (2006)
    8. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440(7084):637-43.(2006)
    9. Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics. 7(1):207 (2006)
    10. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16(5):686-91. (2006)
    11. Genka H, Baba T, Tsuda M, Kanaya S, Mori H, Yoshida T, Noguchi MT, Tsuchiya K, Sawada H. Comparative analysis of argK-tox clusters and their flanking regions in phaseolotoxin-producing Pseudomonas syringae pathovars. J Mol Evol. 63(3):401-14 (2006)
    12. H. Maeno, ALTAF-UL-AMIN M., Shinbo, K. Kurokawa, N. Ogasawara, S. Kanaya. Elucidating Conservation of Genes in Multiple Genomes Based on Graphs Configured by Bidirectional Best-Hit Relationships. IPSJ Transactions on Bioinformatics. Vol.2 644-654 (2006)
    13. H. Tuji, Altaf-Ul-Amin M., M. Arita, H. Nishio, Y. Shinbo, K. Kurokawa,S. Kanaya. Comparison of Protein Complexes Predicted from PPI Networks by DPClus and Newman Clustering Algorithms. IPSJ Transactions on Bioinformatics. Vol.2 674-684 (2006)
    14. Nishio H, Altaf-Ul-Amin M, Kurokawa K,Kanaya S. Sperical SOM and arrangement of neurons using herix on sphere. IPSJ Transactions on Mathematical Modeling and Its Applications. Vol.47 No.SIG1(TOM14):56-60 (2006)
    15. Shinbo Y, Sakaguchi S, Nakamura Y, Altaf-Ul-Amin M, Kurokawa K, Funatsu K, Kanaya S. Species-metabolite database (KNApSAcK): Elucidating diversity of flavonoids. J. Comput. Aided Chem. (2006)
    16. Ohyama A, Kurokawa K, Enai K, Saitoh H, Kanaya S, Altaf-Ul Amin M, Ogasawara N. Bioinformatics tool for genomic era: A step towards the In silico experiments - focused on molecular cloning. J. Comput. Aided Chem. (2006)
    17. Kinouchi M, Kurokawa K. tRNA finder: A software system to find all tRNA genes in the DNA sequence based on the cloverleaf secondary structure. J. Comput. Aided Chem. (2006)
    18. Yano M, Kanaya S, Altaf-Ul-Amin M, Kurokawa K, Yokota Hirai M, Saito K. Integrated data mining of transcriptome and metabolome based on BL-SOM. J. Comput. Aided Chem. (2006)
    19. Nishi T, Masuda Y, Ujiie Y, Morita N, Kitayama M, Ikemura T, Kanaya S. The GeneLook Server: a Web-based tool for prediction of prokaryotic protein-coding sequences. J. Comput. Aided Chem. (2006)
    20. Altaf-Ul Amin M, Tsuji H, Kurokawa K, Asahi H, Shinbo Y, Kanaya S. DPClus: A density-periphery based graph clustering software mainly focused on detection of protein complexes in interaction networks. J. Comput. Aided Chem. (2006)
    21. Shinbo Y, Nakamura Y, Altaf-Ul-Amin M, Asahi H, Kurokawa K, Arita M, Saito K, Ohta D, Shibata D, Kanaya S. KNApSAcK: A comprehensive species-metabolite relationship database. Biotechnology in Agriculture and Forestry. 57:165-181 (2006)
    22. T. Abe, H. Sugawara, S. Kanaya, T. Ikemura. Sequences from Almost All Prokaryotic, Eukaryotic, and Viral Genomes Available Could be Classified According to Genomes on a Large-Scale Self-Organizing Map Constructed with the Earth Simulator J. Earth Simulator Vol.6 17-23 (2006)
    23. Iida, T., and Kurokawa, K. Comparative genomics: genome configuration and the driving forces in the evolution of vibrios. The Biology of Vibrios 2006　ASM press


    2005

    1. Hirai MY, Klein M, Fujikawa Y, Yano M, Goodenowe DB, Yamazaki Y, Kanaya S, Nakamura Y, Kitayama M, Suzuki H, Sakurai N, Shibata D, Tokuhisa J, Reichelt M, Gershenzon J, Papenbrock J, Saito K. Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem. 280(27):25590-5. (2005)
    2. Nishi T, Ikemura T, Kanaya S. GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences. Gene. 346:115-25. (2005)
    3. Okada K, Kanaya S, Asai K. Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinformatics. 21(9):2043-8.(2005)
    4. Yamazoe M, Adachi S, Kanaya S, Ohsumi K, Hiraga S. Sequential binding of SeqA protein to nascent DNA segments at replication forks in synchronized cultures of Escherichia coli. Mol Microbiol. 55(1):289-98. (2005)
    5. Sakaguchi Y, Hayashi T, Kurokawa K, Nakayama K, Oshima K, Fujinaga Y, Ohnishi M, Ohtsubo E, Hattori M, Oguma K. The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. Proc Natl Acad Sci U S A. 102(48):17472-7. (2005)
    6. Kabir MS, Yamashita D, Koyama S, Oshima T, Kurokawa K, Maeda M, Tsunedomi R, Murata M, Wada C, Mori H, Yamada M. Cell lysis directed by sigmaE in early stationary phase and effect of induction of the rpoE gene on global gene expression in Escherichia coli. Microbiology. 151(Pt 8):2721-35. (2005)
    7. Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res. (2005)


    2004

    1. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito K. Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 101(27):10205-10. (2004)
    2. Takagi T, Makino Y, Tanaka Y, Okamoto K, Yamashita N, Matsumoto T, Yokota M, Kurokawa K, Yasunaga T. Application of revised version of neural independent component analysis to classification problems of confiscated methamphetamine. Chem Pharm Bull (Tokyo). 52(12):1427-32. (2004)
    3. Sugino H, Yanase H, Hamada S, Kurokawa K, Asakawa S, Shimizu N, Yagi T. Distinct genomic sequence of the CNR/Pcdhalpha genes in chicken. Biochem. Biophys. Res. Commun. (2004)


    2003

    1. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. Informatics for unvailing hidden genome signatures, Genome Res. 13, 693-702 (2003)
    2. Nakagawa I, Kurokawa K, Yamashita A, Nakata M, Tomiyasu Y, Okahashi N, Kawabata S, Yamazaki K, Shiba T, Yasunaga T, Hayashi H, Hattori M, Hamada S. Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res. 13(6A):1042-55. (2003)
    3. Makino K, Oshima K, Kurokawa K, Yokoyama K, Uda T, Tagomori K, Iijima Y, Najima M, Nakano M, Yamashita A, Kubota Y, Kimura S, Yasunaga T, Honda T, Shinagawa H, Hattori M, Iida T. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet. 361(9359):743-9. (2003)
    4. Ohnishi M, Terajima J, Kurokawa K, Nakayama K, Murata T, Tamura K, Ogura Y, Watanabe H, Hayashi T. Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc Natl Acad Sci U S A. 99(26):17043-8. (2002)
    5. Takagi T, Okamoto K, Yokogawa Y, Yokota M, Kurokawa K, Yasunaga T. A new multiple comparison method using resampling technique for medical, pharmaceutical, and chemical data. J. Comput. Aided Chem. (2003)


    2002

    1. Hamada K, Horiike T, Kanaya S, Nakamura H, Ota H, Yatogo T, Okada K, Nakamura H, Shinozawa T. Changes in body temperature pattern in vertebrates do not influence the codon usages of alpha-globin genes, Genes Genet. Syst. 77, 197-207 (2002)
    2. Yamagishi K, Oshima T, Masuda Y, Ara T, Kanaya S, Mori H. Conservation of translation initiation sites based on dinucleotide frequency and codon usage in Escherichia coli K-12 (W3110), DNA Res. 9, 19-24 (2002)
    3. Kawano M, Kanaya S, Oshima T, Masuda Y, Ara T, Mori H. Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome, DNA Res. 9, 1-10 (2002)
    4. Sawada H, Kanaya S, Tsuda M, Suzuki F, Azegami K, Saitou N. A phylogenomic study of the OCTase genes in Pseudomonas syringae pathovars, J. Mol. Evol. 54, 437-457 (2002)
    5. Oshima T, Aiba H, Masuda Y, Kanaya S, Sugiura M, Wanner BL, Mori H, Mizuno T. Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12, Mol. Micorbiol. 46, 281-291 (2002)
    6. Fukushima A, Ikemura T, Kinouchi M, Oshima T, Kudo Y, Mori H, Kanaya S. Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis, Gene 300:203-211 (2002)
    7. Kondo Y, Watanabe M, Nishigushi S, Shimda K, Yamanishi H, Kurokawa K, Yasunaga T, Koyama K. Study of transcripts from AC010088, a 199,485 bp fragment of the human Y chromosome located in the azoospermia factor region c. Rep. Biol (2002)
    8. Fukushima A, Ikemura T, Oshima T, Mori H, Kanaya S. Detection of periodicity in eukaryotic genomes on the basis of power spectrum analysis. Genome Inf. (2002)
    9. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency. Genome Inf. (2002)
    10. Takagi T, Kurokawa E, Miyata K, Okamoto K, Tanaka Y, Kurokawa K, Yasunaga T. The comparison of generalized additive method with artificial hierarchical neural network in the analysis of pharmaceutical data. J. Comput. Aided Chem. (2002)


    2001

    1. T. Horiike, K. Hamada, S. Kanaya, T. Shinozawa, Origin of eukaryotic cell nuclei by symbiosis of archaea in bacteria is revealed by homology-hit analysis, Nature Cell Biol. 3:210-214 (2001)
    2. S. Kanaya, M. Kinouchi, T. Abe, Y. Kudo, Y. Yamada, T. Nishi, H. Mori, T. Ikemura, Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome, Gene 276:89-99 (2001)
    3. S. Kanaya, Y. Yamada, M. Kinouchi, Y. Kudo, T. Ikemura, Codon usage and tRNA genes in Eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis, J. Mol. Evol. 53:290-298 (2001)
    4. Nakano M, Iida T, Ohnishi M, Kurokawa K, Takahashi A, Tsukamoto T, Yasunaga T, Hayashi T, Honda T. Association of the urease gene with enterohemorrhagic Escherichia coli strains irrespective of their serogroups. J Clin Microbiol. 39(12):4541-3. (2001)
    5. Yokoyama K, Makino K, Kubota Y, Watanabe M, Kimura S, Yutsudo CH, Kurokawa K, Ishii K, Hattori M, Tatsuno I, Abe H, Yoh M, Iida T, Ohnishi M, Hayashi T, Yasunaga T, Honda T, Sasakawa C, Shinagawa H. Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai outbreak. Gene. 258(1-2):127-39. (2000)
    6. Ohnishi M, Kurokawa K, Hayashi T. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9(10):481-5. (2001)
    7. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8(1):11-22.(2001)


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