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  1. Mori K, Shirasawa K, Nogata H, Hirata C, Kosuke T, Habu T, Sangwan K, Himeno Shuichi, Kuhara S, Ikegami H. (2017)
    Identification of RNA1 orthologue associated with sex determination through whole genome sequencing analysis in fig ( Ficus carica L.). Nature Scientific Reports.

  2. Inoue A, Obayashi K, Sonoda Y, Nakamura A, Ueno T, Kuhara S, Tashiro K. (2016)
    Regulation of matrix metalloproteinase-1 and alpha-smooth muscle actin expression by interleukin-1 alpha and tumour necrosis factor alpha in hepatic stellate cells. Cytotechnology.

  3. Shibata M, Mekuchi M, Mori K, Muta S, Chowdhury VS, Nakamura Y, Ojima N, Saitoh K, Kobayashi T, Wada T, Inouye K, Kuhara S, Tashiro K.(2016)
    Transcriptomic features associated with energy production in the muscles of Pacific bluefin tuna and Pacific cod. Biosci Biotechnol Biochem. 29:1-11.

  4. Eguchi R, Yoshigai E, Koga T, Kuhara S, Tashiro K.(2015)
    Spatiotemporal expression of Prdm genes during Xenopus development. Cytotechnology.

  5. Nagayoshi K, Ueki T, Tashiro K, Mizuuchi Y, Manabe T, Araki H, Oda Y, Kuhara S, Tanaka M.(2014)
    Galanin plays an important role in cancer invasiveness and is associated with poor prognosis in stage II colorectal cancer. Oncol Rep. ;33(2):539-46.

  6. Yokoyama K, Ishimura R, Kariyasu T, Imai M, Nitatori T, Kuhara S, Nitta S, Takeguchi T, Matsumoto N.(2014)
    Clinical application of an automatic slice-alignment method for cardiac MR imaging. Magn Reson Med Sci. ;13(4):293-8.

  7. Hashikawa K, Yasumoto S, Nakashima K, Arakawa F, Kiyasu J, Kimura Y, Saruta H, Nakama T, Yasuda K, Tashiro K, Kuhara S, Hashimoto T, Ohshima K.(2014)
    Microarray analysis of gene expression by microdissected epidermis and dermis in mycosis fungoides and adult T-cell leukemia/lymphoma. Int J Oncol. ;45(3):1200-8.

  8. Oba T, Kusumoto K, Kichise Y, Izumoto E, Nakayama S, Tashiro K, Kuhara S, Kitagaki H.(2014)
    Variations in mitochondrial membrane potential correlate with malic acid production by natural isolates of Saccharomyces cerevisiae sake strains. FEMS Yeast Res. ;14(5):789-96.

  9. Hirakawa H, Shirasawa K, Kosugi S, Tashiro K, Nakayama S, Yamada M, Kohara M, Watanabe A, Kishida Y, Fujishiro T, Tsuruoka H, Minami C, Sasamoto S, Kato M, Nanri K, Komaki A, Yanagi T, Guoxin Q, Maeda F, Ishikawa M, Kuhara S, Sato S, Tabata S, Isobe SN.(2014)
    Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res. ;21(2):169-81.

  10. Ohtani K, Hirakawa H, Paredes-Sabja D, Tashiro K, Kuhara S, Sarker MR, Shimizu T.(2013)
    Unique regulatory mechanism of sporulation and enterotoxin production in Clostridium perfringens. Journal of Bacteriology.

  11. Pang X, Tashiro K, Eguchi R, Komatsu N, Sasada T, Itoh K, Kuhara S.(2013)
    Haptoglobin Proved a Prognostic Biomarker in Peripheral Blood of Patients with Personalized Peptide Vaccinations for Advanced Castration-Resistant Prostate Cancer. Biosci Biotechnol Biochem.

  12. Yoji Nakamura, Naobumi Sasaki, Masahiro Kobayashi, Nobuhiko Ojima, Motoshige Yasuike, Yuya Shigenobu, Masataka Satomi, Yoshiya Fukuma, Koji Shiwaku, Atsumi Tsujimoto, Takanori Kobayashi, Ichiro Nakayama, Fuminari Ito, Kazuhiro Nakajima, Motohiko Sano, Tokio Wada, Satoru Kuhara, Kiyoshi Inouye, Takashi Gojobori, Kazuho Ikeo.(2013)
    The First Symbiont-Free Genome Sequence of Marine Red Alga, Susabi-nori (Pyropia yezoensis). PLOS ONE. Volume 8, Issue 3, e57122.

  13. Doi K, Mori K, Tashiro K, Fujino Y, Nagayoshi Y, Hayashi Y, Kuhara S, Ohshima T.(2013)
    Draft Genome Sequence of Pediococcus lolii NGRI 0510Q(T) Isolated from Ryegrass Silage. Genome Announc. 1(1). pii: e00156-12.

  14. Porciuncula Jde O, Furukawa T, Mori K, Shida Y, Hirakawa H, Tashiro K, Kuhara S, Nakagawa S, Morikawa Y, Ogasawara W.(2013)
    Single Nucleotide Polymorphism Analysis of a Trichoderma reesei Hyper-Cellulolytic Mutant Developed in Japan. Biosci Biotechnol Biochem.;77(3):534-43.

  15. Akira Takeno, Akira Okamoto, Keizo Tori, Kenshiro Oshima, Hideki Hirakawa, Hidehiro Toh, Norio Agata, Keiko Yamada, Naotake Ogasawara, Tetsuya Hayashi, Tohru Shimizu, Satoru Kuhara, Masahira Hattori, and Michio Ohta. (2012)
    Complete Genome Sequence of Bacillus cereus NC7401, Which Produces High Levels of the Emetic Toxin Cereulide. Journal of Bacteriology.: 194, 17, 4767-4768.

  16. Nitta M, Furukawa T, Shida Y, Mori K, Kuhara S, Morikawa Y, Ogasawara W. (2012)
    A new Zn(II)(2)Cys(6)-type transcription factor BglR regulates β-glucosidase expression in Trichoderma reesei. Fungal Genet Biol.;49(5):388-97.

  17. Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG. (2012)
    Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res.;40(6):2377-98.

  18. Matsuzawa T; Mori K., Kadowaki T ., Shimada, M., Tashiro K., Kuhara S., Inagawa H., Soma G., Takegawa K.(2012)
    Genome Sequence of Pantoea agglomerans Strain IG1. JOURNAL OF BACTERIOLOGY:194, 5: 1258-1259.

  19. Yoshida S, Arakawa F, Higuchi F, Ishibashi Y, Goto M, Sugita Y, Nomura Y, Niino D, Shimizu K, Aoki R, Hashikawa K, Kimura Y, Yasuda K, Tashiro K, Kuhara S, Nagata K, Ohshima K. (2012)
    Gene expression analysis of rheumatoid arthritis synovial lining regions by cDNA microarray combined with laser microdissection: up-regulation of inflammation-associated STAT1, IRF1, CXCL9, CXCL10, and CCL5. Scand J Rheumatol.;41(3):170-9.

  20. Matsuzawa T;Mori K.,Kadowaki T.,Shimada M.,Tashiro K.,Kuhara S.,Inagawa H.,Soma G.,Takegawa K. (2012)
    Genome Sequence of Pantoea agglomerans Strain IG1. JOURNAL OF BACTERIOLOGY. 194, 1258-1259,2012.03.

  21. Nobukazu Komatsu, Satoko Matsueda, Kousuke Tashiro, Tetsuya Ioji, Shigeki Shichijo, Masanori Noguchi, Akira Yamada, Atsushi Doi, Shigetaka Suekane, Fukuko MoriyaKei Matsuoka, Satoru Kuhara, Kyogo Itoh, and Tetsuro Sasada, (2011)
    Gene expression profiles in peripheral blood as a biomarker in cancer patients receiving peptide vaccination. Cancer. 15;118(12):3208-21.

  22. Futagami T, Mori K, Yamashita A, Wada S, Kajiwara Y, Takashita H, Omori T, Takegawa K, Tashiro K, Kuhara S, Goto M.,(2011)
    Genome Sequence of the White Koji Mold Aspergillus kawachii IFO 4308, Used for Brewing the Japanese Distilled Spirit Shochu. EUKARYOTIC CELL. 10, 1586-1587,2011.1.

  23. Hishigaki H, Kuhara S. (2011)
    hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. ;2011:bar017.

  24. Takahiro OBA, Hikaru SUENAGA, Shunichi NAKAYAMA, Shinji MITSUIKI, Hiroshi KITAGAKI, Kosuke TASHIRO and Satoru KUHARA (2011)
    Properties of a High Malic Acid-Producing Strains of Saccharomyces cerevisiae Isolated from Sake Mash. Bioscience, Biotechnology, and Biochemistry. 75(10), 2025-9.

  25. Akao T, Yashiro I, Hosoyama A, Kitagaki H, Horikawa H, Watanabe D, Akada R, Ando Y, Harashima S, Inoue T, Inoue Y, Kajiwara S, Kitamoto K, Kitamoto N, Kobayashi O, Kuhara S, Masubuchi T, Mizoguchi H, Nakao Y, Nakazato A, Namise M, Oba T, Ogata T, Ohta A, Sato M, Shibasaki S, Takatsume Y, Tanimoto S, Tsuboi H, Nishimura A, Yoda K, Ishikawa T, Iwashita K, Fujita N, Shimoi H. (2011)
    Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res.;18(6):423-34.

  26. Miyake M, Takemasa I, Matoba R, Tanino M, Niijima S, Ikeda M, Yamamoto H, Sekimoto M, Kuhara S, Okayama T, Monden M, Matsubara K, Mori M. (2011)
    Heterogeneity of colorectal cancers and extraction of discriminator gene signatures for personalized prediction of prognosis. INTERNATIONAL JOURNAL OF ONCOLOGY.: 39, 4,: 781-789.

  27. Michio Asada, Hideki Hirakawa, Satoru Kuhara. (2011)
    Classification of Bacteria Based on the Biases of Terminal Amino Acid Residues. Protein J. 30:290-297.

  28. Nakamura A, Ueno T, Yagi Y, Okuda K, Ogata T, Nakamura T, Torimura T, Iwamoto H, Ramadoss S, Sata M, Tsutsumi V, Yasuda K, Tomiyasu Y, Obayashi K, Tashiro K, Kuhara S. (2010)
    Human primary cultured hepatic stellate cells can be cryopreserved. Med Mol Morphol. 43(2):107-15.

  29. Hirasaki M, Nakamura F, Yamagishi K, Numamoto M, Shimada Y, Uehashi K, Muta S, Sugiyama M, Kaneko Y, Kuhara S, Harashima S. (2010)
    Deciphering cellular functions of protein phosphatases by comparison of gene expression profiles in Saccharomyces cerevisiae. Journal of Bioscience and Bioengineering. 109(5):433-41.

  30. Ohtani K, Hirakawa H, Tashiro K, Yoshizawa S, Kuhara S, Shimizu T. (2010)
    Identification of a two-component VirR/VirS regulon in Clostridium perfringens. Anaerobe. 16(3):258-64.

  31. Yasukochi Y, Maruyama O, Mahajan MC, Padden C, Euskirchen GM, Schulz V, Hirakawa H, Kuhara S, Pan XH, Newburger PE, Snyder M, Weissman SM.(2010)
    X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. Proc Natl Acad Sci U S A. 23; 107(8):3704-9.

  32. Hirofumi Suzaki and Satoru Kuhara, (2010)
    An Extension Approach for Neural Networks by Introducting a Nearest Neighbor Algorithm in Relative Coordinates. Journal of Advanced Computational Intelligence and Interigent Informatics. 14, 325-343

  33. Sasada, Tetsuro, Komatsu Nobukazu, Matsueda Satoko, Ioji Tetsuya, Shichijo Shigeki, Noguchi Masanori, Kuhara Satoru, Itoh Kyogo, (2010)
    Gene Expression Profiling Useful for Predicting Clinical Responses to Personalized Peptide Vaccination.JOURNAL OF IMMUNOTHERAPY. 33, 8, 909-909

  34. Kim Sangwan, Hideki Hirakawa, Shigeru Muta, Satoru Kuhara, (2010)
    Identification and a classification of two-component system based on the domain structures in bacteria and difference in domain structure between Gram-positive and Gram-negative bacteria. Biosci, Biotechnol, Biochem. 74, 4 716-720.

  35. Hiromitsu Araki, Yoshinori Tamada, Seiya Imoto, Ben Dunmore, Deborah Sanders, Sally Humphrey, Masao Nagasaki, Atsushi Doi, Yukiko Nakanishi, Kaori Yasuda, Yuki Tomiyasu, Kousuke Tashiro, Cristin Print, D. Stephen Charnock-Jones, Satoru Kuhara, Satoru Miyano. (2009)
    Analysis of PPARα-dependent and PPARα-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis. 12(3):221-9

  36. Tamada Y, Araki H, Imoto S, Nagasaki M, Doi A, Nakanishi Y, Tomiyasu Y, Yasuda K, Dunmore B, Sanders D, Humphreys S, Print C, Charnock-Jones DS, Tashiro K, Kuhara S, Miyano S. (2009)
    Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pacific Symposium on Biocomputing. Vol.14, 251-63.

  37. Hideki Hirakawa, Hidenori Akita, Tamaki Fujiwara, Motoyuki Sugai and Satoru Kuhara,(2009)
    Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan. Protein Engineering Design and Selection. 22(7):385-39119457979

  38. Kawakami Y, Yoshida K, Yang JH, Suzuki T, Azuma N, Sakai K, Hashikawa T, Watanabe M, Yasuda K, Kuhara S, Hirabayashi Y, Furuya S. (2009)
    Impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model. Neurosci Res. 63(3):184-93.

  39. Nakayama-Imaohji H, Hirakawa H, Ichimura M, Wakimoto S, Kuhara S, Hayashi T, Kuwahara T.(2009)
    Identification of the site-specific DNA invertase responsible for the phase variation of SusC/SusD family outer membrane proteins in Bacteroides fragilis.J Bacteriol. 191(19):6003-11.

  40. Azuma Y, Hosoyama A, Matsutani M, Furuya N, Horikawa H, Harada T, Hirakawa H, Kuhara S, Matsushita K, Fujita N, Shirai M.(2009)
    Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res. 37(17):5768-83.

  41. Emi Yoshigai, Shinobu Kawamura, Satoru Kuhara and Kosuke Tashiro (2009)
    Trim36/Haprin plays a critical role in the arrangement of somites during Xenopus embryogenesis. Biochemical and Biophysical Research Communications. 378, 428-432

  42. Noriko Nakanishi, Kosuke Tashiro, Satoru Kuhara, Tetsuya Hayashi, Nakaba Sugimoto, and Toru Tobe (2009)
    Regulation of virulence by butyrate sensing in enterohemorrhagic Escherichia coli. Microbiology. 155(Pt 2):521-30

  43. Yagi Y, Ito Y, Kuhara S, Tashiro K (2008)
    Cephalic Hedgehog expression is regulated directly by Sox17 in endoderm development of Xenopus laevis. Cytotechnology. 57(2):151-9.

  44. Osamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, Satoru Kuhara, (2008)*
    Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data by Gene Ontology Annotations. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine. 417-420,.
    (2008 IEEE International Conference on Bioinformatics and Biomedicine Philadelphia, PA, USA, Nov. 3]5, 2008)

  45. Takahiro Oba , Hikaru Suenaga, Shigeru Muta, Kosuke Tashiro and Satoru Kuhara (2008)
    Properties of a sucrose-tolerant Mutant of Saccharomyces cerevisiae. World Journal of Microbiology and Biotechnology24. 24:1233-1238.

  46. Shinobu Kawamura, Emi Yoshigai, Satoru Kuhara, Kosuke Tashiro (2008)
    smyd1 and smyd2 are expressed in muscle tissue in Xenopus laevis.
    Cytotechnology. 57:161-168.

  47. Takahiro OBA, Kosuke TASHIRO, Satoru KUHARA (2008)
    Trifluoroleucine-resistant mutant of Saccharomyces cerevisiae also exhibits pleiotropic drug resistance. Annals of Microbaiology. 58(2), 293-296.

  48. Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H, Nakayama K, Toh H, Yoshimura F, Kuhara S, Hattori M, Hayashi T, Nakayama K. (2008)
    Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis. DNA research. 15, 215-25.. 2

  49. Furuya S, Yoshida K, Kawakami Y, Yang JH, Sayano T, Azuma N, Tanaka H, Kuhara S, Hirabayashi Y. (2008)
    Inactivation of the 3-phosphoglycerate dehydrogenase gene in mice:changes in gene expression and associated regulatory networks resulting from serine deficiency. Funct Integr Genomics. 8(3):235-49.

  50. Goto T, Yamashita A, Hirakawa H, Matsutani M, Todo K, Ohshima K, Toh H, Miyamoto K, Kuhara S, Hattori M, Shimizu T, Akimoto S. (2008)
    Complete Genome Sequence of Finegoldia magna, an Anaerobic Opportunistic Pathogen. DNA Research. 15:39-47.

  51. Abe H, Miyahara A, Oshima T, Tashiro K, Ogura Y, Kuhara S, Ogasawara N, Hayashi T, Tobe T. (2008)
    Global Regulation by Horizontally Transferred Regulators Establishes the Pathogenicity of Escherichia coli. DNA Res. 15(1):25-38.

  52. Izutsu K, Kurokawa K, Tashiro K, Kuhara S, Hayashi T, Honda T, Iida T. (2008)
    Comparative genomic analysis using microarray demonstrates a strong correlation between the presence of the 80-kilobase pathogenicity island and pathogenicity in Kanagawa phenomenon-positive Vibrio parahaemolyticus strains. Infect Immun. 76(3):1016-23

  53. Koshiro Miura , Hidehiro Toh, Hideki Hirakawa, Manabu Sugii, Masayuki Murata, Kenta Nakai, Kosuke Tashiro, Satoru Kuhara, Yoshinao Azuma,* and Mutsunori Shirai.(2008)
    Genome-wide Analysis of Chlamydophila pneumoniae Gene Expression at the Late Stage of Infection
    DNA Res. 30;15(2):83-91.

  54. Furuya S, Yoshida K, Kawakami Y, Yang JH, Sayano T, Azuma N, Tanaka H, Kuhara S, Hirabayashi Y. (2008)
    Inactivation of the 3-phosphoglycerate dehydrogenase gene in mice: changes in gene expression and associated regulatory networks resulting from serine deficiency. Funct Integr Genomics. 8(3):235-49.

  55. Goto T, Yamashita A, Hirakawa H, Matsutani M, Todo K, Ohshima K, Toh H, Miyamoto K, Kuhara S, Hattori M, Shimizu T, Akimoto S. (2008)
    Complete Genome Sequence of Finegoldia magna, an Anaerobic Opportunistic Pathogen. DNA Res. 15, 39-47.

  56. Miura K, Toh H, Hirakawa H, Sugii M, Murata M, Nakai K, Tashiro K, Kuhara S, Azuma Y, Shirai M. (2008)
    Genome-wide Analysis of Chlamydophila pneumonia Gene Expression at the Late Stage of Infection. DNA Res. 15, 83-91.

  57. Abe H, Miyahara A, Oshima T, Tashiro K, Ogura Y, Kuhara S, Ogasawara N, Hayashi T, Tobe T. (2008)
    Global Regulation by Horizontally Transferred Regulators Establishes the Pathogenicity of Escherichia coli. DNA Res. 15, 25-38.

  58. Katekaew S, Torikata T, Hirakawa H, Kuhara S, Araki T. (2007)
    Enzymatic Properties of Newly Found Green Turtle Egg White Ribonuclease. Protein J. 26, 75-85.

  59. Qin T, Hirakawa H, Iida K, Oshima K, Hattori M, Tashiro K, Kuhara S, Yoshida S. (2007)
    Complete nucleotide sequence of pLD-TEX-KL, a 66-kb plasmid of Legionella dumoffii TEX-KL strain. Plasmid. 58, 261-8.

  60. Niijima S, and Kuhara S. (2006)
    Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE. BMC Bioinformatics. 7,543.

  61. Niijima S. and Kuhara S. (2006)
    Gene subset selection in kernel-induced feature space. Pattern Recognition Letters. 27, 16, 1884-1892.

  62. Oba T, Yamamoto Y, Nomiyama S, Suenaga H, Muta S, Tashiro K, Kuhara S. (2006)
    Properties of a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae. Biosci Biotechnol Biochem. 776-9.

  63. Hirakawa H, Kawahara Y, Ochi A, Muta S, Kawamura S, Torikata T, Kuhara S. (2006)
    Construction of Enzyme-Substrate Complexes between Hen Egg-White Lysozyme and N-Acetyl-D-Glucosamine Hexamer by Systematic Conformational Search and Molecular Dynamics Simulation. J Biochem. 140, 221-7.

  64. Azuma Y, Hirakawa H, Yamashita A, Cai Y, Rahman MA, Suzuki H, Mitaku S, Toh H, Goto S, Murakami T, Sugi K, Hayashi H, Fukushi H, Hattori M, Kuhara S, Shirai M. (2006)
    Genome sequence of the cat pathogen, Chlamydophila felis. DNA Res. 13, 15-23.

  65. Nakanishi N, Abe H, Ogura Y, Hayashi T, Tashiro K, Kuhara S, Sugimoto N, Tobe T. (2006)
    ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes. Mol Microbiol. 61, 194-205.

  66. Ogura Y, Kurokawa K, Ooka T, Tashiro K, Tobe T, Ohnishi M, Nakayama K, Morimoto T, Terajima J, Watanabe H, Kuhara S, Hayashi T. (2006)
    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. 13, 3-14.

  67. Kayano M., Konishi S., Hirakawa H., Kuhara S. (2006)
    Functional Principal Component Analysis via Regularized Basis Expansion and Its Application. J. Appl. Statist. 35, 1-16.

  68. Kuroda M, Yamashita A, Hirakawa H, Kumano M, Morikawa K, Higashide M,Maruyama A, Inose Y, Matoba K, Toh H, Kuhara S, Hattori M, Ohta T. (2005)
    Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc Natl Acad Sci U S A. 102(37), 13272-7.

  69. Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, Yamada O, Yamagata Y, Anazawa H, Hata Y, Koide Y, Komori T, Koyama Y, Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H.(2005)
    Genome sequencing and analysis of Aspergillus oryzae. Nature. 438(7071):1157-61.

  70. Tobe T, Ando H, Ishikawa H, Abe H, Tashiro K, Hayashi T, Kuhara S, Sugimoto N. (2005)
    Dual regulatory pathways integrating the RcsC-RcsD-RcsB signalling system control enterohaemorrhagic Escherichia coli pathogenicity. Mol Microbiol. 58(1):320-33.

  71. Niijima, S., and Kuhara, S., (2005)
    Multiclass molecular cancer classification by Kernel subspace methods with effective Kernel parameter selection. J.B.C.B. 3(5), 1071-1088.

  72. Kuwahara T, Yamashita A, Hirakawa H, Nakayama H, Toh H, Okada N, Kuhara S, Hattori M, Hayashi T, Ohnishi Y.(2004)
    Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc Natl Acad Sci U S A. 101(41):14919-14924.

  73. Maki Y, Takahashi Y, Arikawa Y, Watanabe S, Aoshima K, Eguchi Y, Ueda T, Aburatani S, Kuhara S, Okamoto M. (2004)
    An integrated comprehensive workbench for inferring genetic networks: voyagene. J Bioinform Comput Biol. 2(3):533-550.

  74. Imoto S, Kim S, Goto T, Miyano S, Aburatani S, Tashiro K, Kuhara S, H. Toh, N. Kamikawaji, T. Sasazuki and S. Kuhara (2004)
    Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J Bioinform Comput Biol. 1(2):231-52.

  75. Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S.,(2004)
    Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol. 2(1):77-98

  76. Sato N, Ohmori M, Ikeuchi M, Tashiro K, Wolk CP, Kaneko T, Okada K, Tsuzuki M, Ehira S, Katoh H, Okamoto S, Yoshimura H, Fujisawa T, Kamei A, Yoshihara S, Narikawa R, Hamano T, Tabata S, Kuhara S. (2004)
    Use of segment-based microarray in the analysis of global gene expression in response to various environmental stresses in the cyanobacterium Anabaena sp. PCC 7120. J Gen Appl Microbiol. 50(1):1-8.

  77. Tamada Y, Kim S, Bannai H, Imoto S, Tashiro K, Kuhara S, Miyano S.(2003)
    Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics. 2003 Suppl 2:II227-II236.

  78. S. Aburatani, S. Kuhara, H. Toh, K. Horimoto, (2003)
    Deduction of a gene regulatory relationship framework from gene expression data by the application of graphical Gaussian modeling. Signal Processing. 83, 777-788.

  79. Aburatani S, Tashiro K, Savoie CJ, Nishizawa M, Hayashi K, Ito Y, Muta S, Yamamoto K, Ogawa M, Enomoto A, Masaki M, Watanabe S, Maki Y, TakahashiY, Eguchi Y, Sakaki Y, Kuhara S. (2003)
    Discovery of novel transcription control relationships with gene regulatory networks generated from multiple-disruption full genome expression libraries. DNA Res. 10(1):1-8.

  80. Savoie CJ, Aburatani S, Watanabe S, Eguchi Y, Muta S, Imoto S, Miyano S, Kuhara S, Tashiro K.(2003)
    Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Res. 10(1):19-25.

  81. Aburatani S, Kuhara S, Toh H, Horimoto K, (2003)
    Deduction of a gene expression data by the application of graphical Gaussian modeling. Signal Processing. 83:777.

  82. Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S, Hayashi H. (2002)
    Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci U S A. 99(2):996-1001.

  83. Maruyama O. Syoudai T, Furuichi E, Kuhara S, Miyano S (2001)
    Conformation rules proceeding of the 4nd international conference of discovery science lecture notes in artificial intelligence. Springer-Verlag. 2226:243.

  84. 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.(2001)
    Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8(1):11-22.

  85. Kuroda M, (2001)
    Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet. 357:1225.

  86. Toh H, Kamikawaji N, Sasazuki T, Kuhara S, (2001)
    Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide. Protein Eng. 13(6):423-9.

  87. Ito Y, Tashiro K, Kuhara S, (2001)
    In synergy with noggin and follistatin,Xenopus nodal-rerated gene induces sonic hedgehog on notochord and floor plate. Biochem. Biophys. Res. Commun. 281(3):714-9.

  88. Arimura Gi, Tashiro K, Kuhara S, Nishioka T, Ozawa R, Takabayashi J.(2000)
    Gene Responses in Bean Leaves Induced by Herbivory and by Herbivore-Induced Volatiles. Biochem. Biophys. Res. Commun. 277(2):305-10.

  89. Toh H, Savoie CJ, Kamikawaji N, Tana T, Muta S, Sasazuki T, Kuhara S (2000)
    Changes at the floor of the peptide-binding groove induce a strong preference for proline at position 3 of the bound peptide: molecular dynamics simulations of HLA-A*0217. Biopolymers 54(5):318-27.

  90. Nagao Y, Kitada S, Kojima K, Toh H, Kuhara S, Ogishima T, Ito A. (2000)
    Glycine-rich region of mitochondrial processing peptidase a-subunit is essential for binding and cleavage of the precursor proteins. J. Bio. Chem. 275(44):34552-6.

  91. Akutsu T, Miyano S, Kuhara S (2000)
    Algorithms for inferring qualitative models of biological networks. Pac. Symp. Biocomput. 293-304.

  92. Toh H, Kamikawaji N, Tana T, Muta S, Sasazuki T, Kuhara S (2000)
    Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide. Protein Eng. 13(6):423-9.

  93. Shirai M, Hirakawa H, Tabuchi M, Kishi F, Ouchi K, Shiba T, Ishii K, Hattori M, Kuhara S, Nakazawa T (2000)
    Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from US. Nucleic Acids Res. 28(12):2311-4.

  94. Sakiyama T, Takami H, Ogasawara N, Kuhara S, Kozuki T, Doga K, Ohyama A, Horikoshi K (2000)
    An automated system for genome analysis to support microbial whole-genome shotgun sequencing. Biosci. Biotechnol. Biochem. 64(3):670-3.

  95. Shirai M, Hirakawa H, Ouchi K, Tabuchi M, Kishi F, Kimoto M, Takeuchi H, Nishida J, Shibata K, Fujinaga R, Yoneda H, Matsushima H, Tanaka C, Fukukawa S, Nakazawa A, Ishii K, Shibata T, Hattori M, Kuhara S, Nakazawa T (2000)
    Comparison of outer membrane protein genes omp and pmp in the whole genome sequences of Chlamydia pneumoniae isolates from Japan and the United States. J. Infect Dis. 181 Suppl 3:S524-7.

  96. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y (2000)
    Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA 97(3):1143-7.

  97. Ohnishi M, Tanaka C, Kuhara S, Ishii K, Hattori M, Kurokawa K, Yasunaga T,Makino K, Shinagawa H, Murata T, Nakayama K, Terawaki Y, Hayashi T (2000)
    Chromosome of the enterohemorrhagic Escherichia coli O157:H7; comparative analysis with K-12 MG1655 revealed the acquisition of a large amount of foreign DNAs. DNA Res. 6(6):361-8.

  98. Nagano T, Ito Y, Tashiro K, Kobayakawa Y, Sakai M (2000)
    Dorsal induction from dorsal vegetal cells in xenopus occurs after mid-blastula transition. Mech. Dev. 93(1-2):3-14.