Research Output

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

Ogura, Y., Kurokawa, K., Ooka, T., Tashiro, K., Tobe, T., Ohnishi, M., Nakayama, K., Morimoto, T., Terajima, J., Watanabe, H., Kuhara, S. & Hayashi, T., Jun 14 2006, In : DNA Research. 13, 1, p. 3-14 12 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles

Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C. G., Charnock-Jones, S. D., Sanders, D., Savoie, C. J., Tashiro, K., Kuhara, S. & Miyano, S., Dec 1 2006, Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. p. 559-571 13 p. (Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

26 Citations (Scopus)

Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences

Yamamoto, K., Narukawa, J., Kadono-Okuda, K., Nohata, J., Sasanuma, M., Suetsugu, Y., Banno, Y., Fujii, H., Goldsmith, M. R. & Mita, K., May 1 2006, In : Genetics. 173, 1, p. 151-161 11 p.

Research output: Contribution to journalArticle

70 Citations (Scopus)

Construction of enzyme-substrate complexes between hen egg-white lysozyme and N-acetyl-D-glucosamine hexamer by systematic conformational search and molecular dynamics simulation

Hirakawa, H., Kawahara, Y., Ochi, A., Muta, S., Kawamura, S., Torikata, T. & Kuhara, S., Aug 1 2006, In : Journal of biochemistry. 140, 2, p. 221-227 7 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Gene expression profiling in common cormorant liver with an oligo array: Assessing the potential toxic effects of environmental contaminants

Nakayama, K., Iwata, H., Kim, E. Y., Tashiro, K. & Tanabe, S., Feb 1 2006, In : Environmental Science and Technology. 40, 3, p. 1076-1083 8 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Genes encoding small heat shock proteins of the silkworm, Bombyx mori

Sakano, D., Li, B., Xia, Q., Yamamoto, K., Fujii, H. & Aso, Y., Nov 6 2006, In : Bioscience, Biotechnology and Biochemistry. 70, 10, p. 2443-2450 8 p.

Research output: Contribution to journalArticle

57 Citations (Scopus)

Genetic analysis of basic chymotrypsin inhibitors in the hemolymph of the silkworm, Bombyx mori

Ueno, Y., Takao, M., He, N., Yamamoto, K., Banno, Y. & Fujii, H., Jun 1 2006, In : Journal of Insect Biotechnology and Sericology. 75, 2, p. 65-69 5 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Genetic variations in the vitellogenin of Japanese populations of the wild silkworm Bombyx mandarina

Meng, Y., Liu, C., Shiomi, K., Nakagaki, M., Banno, Y. & Kajiura, Z., Oct 1 2006, In : Journal of Insect Biotechnology and Sericology. 75, 3, p. 127-134 8 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Identification of a sigma-class glutathione-S-transferase from the silkworm, Bombyx mori

Yamamoto, K., Zhang, P. B., Banno, Y. & Fujii, H., Dec 1 2006, In : Journal of Applied Entomology. 130, 9-10, p. 515-522 8 p.

Research output: Contribution to journalArticle

50 Citations (Scopus)

Identification of genes involved in the suppression of antibody production from human peripheral blood lymphocytes

Aiba, Y., Yamashita, M., Katakura, Y., Furukawa, Y., Matsumoto, S. E., Tomimatsu, K., Teruya, K. & Shirahata, S., May 5 2006, In : Bioscience, Biotechnology and Biochemistry. 70, 4, p. 966-970 5 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Identification of novel genes with prognostic value in childhood leukemia using cDNA microarray and quantitative RT-PCR

Hattori, H., Matsukaki, A., Suminoe, A., Koga, Y., Tashiro, K. & Hara, T., Mar 1 2006, In : Pediatric Hematology and Oncology. 23, 2, p. 115-127 13 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

In vitro immunization can elicit the expansion of diverse repertoire of B cells from peripheral blood mononuclear cells

Matsumoto, S. E., Yamashita, M., Katakura, Y., Noguchi, E., Aiba, Y., Ichikawa, A., Teruya, K. & Shirahata, S., Nov 1 2006, In : Cytotechnology. 52, 3, p. 227-233 7 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Lactococcin Q, a novel two-peptide bacteriocin produced by Lactococcus lactis QU 4

Zendo, T., Koga, S., Shigeri, Y., Nakayama, J. & Sonomoto, K., May 1 2006, In : Applied and environmental microbiology. 72, 5, p. 3383-3389 7 p.

Research output: Contribution to journalArticle

63 Citations (Scopus)

Lantibiotics: Insight and foresight for new paradigm

Nagao, J. I., Asaduzzaman, S. M., Aso, Y., Okuda, K. I., Nakayama, J. & Sonomoto, K., Sep 1 2006, In : Journal of Bioscience and Bioengineering. 102, 3, p. 139-149 11 p.

Research output: Contribution to journalArticle

65 Citations (Scopus)

Lysine-oriented charges trigger the membrane binding and activity of nukacin ISK-1

Asaduzzaman, S. M., Nagao, J. I., Aso, Y., Nakayama, J. & Sonomoto, K., Sep 1 2006, In : Applied and environmental microbiology. 72, 9, p. 6012-6017 6 p.

Research output: Contribution to journalArticle

27 Citations (Scopus)

Molecular basis for the cellular senescence program and its application to anticancer therapy

Katakura, Y., May 29 2006, In : Bioscience, Biotechnology and Biochemistry. 70, 5, p. 1076-1081 6 p.

Research output: Contribution to journalReview article

17 Citations (Scopus)

Novel technique for preprocessing high dimensional time-course data from DNA microarray: Mathematical model-based clustering

Hakamada, K., Okamoto, M. & Hanai, T., Apr 1 2006, In : Bioinformatics. 22, 7, p. 843-848 6 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)
95 Citations (Scopus)

Properties of a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae

Oba, T., Yamamoto, Y., Nomiyama, S., Suenaga, H., Muta, S., Tashiro, K. & Kuhara, S., Aug 1 2006, In : Bioscience, Biotechnology and Biochemistry. 70, 7, p. 1776-1779 4 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Proteome analysis of silk gland proteins from the silkworm, Bombyx mori

Zhang, P., Aso, Y., Yamamoto, K., Banno, Y., Wang, Y., Tsuchida, K., Kawaguchi, Y. & Fujii, H., Apr 1 2006, In : Proteomics. 6, 8, p. 2586-2599 14 p.

Research output: Contribution to journalArticle

67 Citations (Scopus)

Purification and amino acid sequence of a bacteriocins produced by Lactobacillus salivarius K7 isolated from chicken intestine

Pilasombut, K., Sakpuaram, T., Wajjwalku, W., Nitisinprasert, S., Swetwiwathana, A., Zendo, T., Fujita, K., Nakayama, J. & Sonomoto, K., Mar 1 2006, In : Songklanakarin Journal of Science and Technology. 28, SUPPL. 1, p. 121-131 11 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Revised model for Enterococcus faecalis fsr quorum-sensing system: The small open reading frame fsrD encodes the gelatinase biosynthesis-activating pheromone propeptide corresponding to staphylococcal AgrD

Nakayama, J., Chen, S., Oyama, N., Nishiguchi, K., Azab, E. A., Tanaka, E., Kariyama, R. & Sonomoto, K., Dec 1 2006, In : Journal of bacteriology. 188, 23, p. 8321-8326 6 p.

Research output: Contribution to journalArticle

66 Citations (Scopus)

Rice protein digestion by sake Koji enzymes: Comparison between steamed rice grains and isolated protein bodies from rice endosperm

Hashizume, K., Okuda, M., Sakurao, S., Numata, M., Koseki, T., Aramaki, I., Kumamaru, T. & Sato, H., Oct 1 2006, In : Journal of Bioscience and Bioengineering. 102, 4, p. 340-345 6 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Silkworm midgut proteins interacting with a hemolymph protease inhibitor, CI-8

Ueno, Y., He, N., Ujita, M., Yamamoto, K., Banno, Y., Fujii, H. & Aso, Y., Aug 1 2006, In : Bioscience, Biotechnology and Biochemistry. 70, 7, p. 1557-1563 7 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Specific gene-expression profiles of noncancerous liver tissue predict the risk for multicentric occurrence of hepatocellular carcinoma in hepatitis C virus-positive patients

Okamoto, M., Utsunomiya, T., Wakiyama, S., Hashimoto, M., Fukuzawa, K., Ezaki, T., Hanai, T., Inoue, H. & Mori, M., Jul 1 2006, In : Annals of Surgical Oncology. 13, 7, p. 947-954 8 p.

Research output: Contribution to journalArticle

65 Citations (Scopus)

Structural and functional conversion of molecular chaperone ClpB from the gram-positive halophilic lactic acid bacterium Tetragenococcus halophilus mediated by ATP and stress

Sugimoto, S., Yoshida, H., Mizunoe, Y., Tsuruno, K., Nakayama, J. & Sonomoto, K., Dec 1 2006, In : Journal of bacteriology. 188, 23, p. 8070-8078 9 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

The female-killing chromosome of the silkworm, Bombyx mori, was generated by translocation between the Z and W chromosomes

Fujii, T., Tanaka, N., Yokoyama, T., Ninaki, O., Oshiki, T., Ohnuma, A., Tazima, Y., Banno, Y., Ajimura, M., Mita, K., Seki, M., Ohbayashi, F., Shimada, T. & Abe, H., May 1 2006, In : Genetica. 127, 1-3, p. 253-265 13 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

The intrinsic ATPase activity of Mycobacterium tuberculosis DnaA promotes rapid oligomerization of DnaA on oriC

Madiraju, M. V. V. S., Moomey, M., Neuenschwander, P. F., Muniruzzaman, S., Yamamoto, K., Grimwade, J. E. & Rajagopalan, M., Mar 1 2006, In : Molecular Microbiology. 59, 6, p. 1876-1890 15 p.

Research output: Contribution to journalArticle

32 Citations (Scopus)

Visualization of the endocytic pathway in the filamentous fungus Aspergillus oryzae using an EGFP-fused plasma membrane protein

Higuchi, Y., Nakahama, T., Shoji, J. Y., Arioka, M. & Kitamoto, K., Feb 17 2006, In : Biochemical and Biophysical Research Communications. 340, 3, p. 784-791 8 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways

Sekiguchi, T. & Okamoto, M., Jun 1 2006, In : Journal of bioinformatics and computational biology. 4, 3, p. 621-638 18 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Xylooligosaccharide fermentation with Leuconostoc lactis

Ohara, H., Owaki, M. & Sonomoto, K., May 1 2006, In : Journal of Bioscience and Bioengineering. 101, 5, p. 415-420 6 p.

Research output: Contribution to journalArticle

35 Citations (Scopus)
2007

A bio-inspired adaptive routing based on enzymatic feedback control mechanism in metabolic networks

Nozoe, T., Kawauchi, T. & Okamoto, M., Dec 1 2007, IMECS 2007 - International MultiConference of Engineers and Computer Scientists 2007. p. 1361-1365 5 p. (Lecture Notes in Engineering and Computer Science; vol. 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

A gram-negative characteristic segment in Escherichia coli DnaK is essential for the ATP-dependent cooperative function with the co-chaperones DnaJ and GrpE

Sugimoto, S., Higashi, C., Saruwatari, K., Nakayama, J. & Sonomoto, K., Jun 26 2007, In : FEBS Letters. 581, 16, p. 2993-2999 7 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Anti-peptide antibody production elicited by in vitro immunization of human peripheral blood mononuclear cells

Tamura, T., Tomimatsu, K., Katakura, Y., Yamashita, M., Matsumoto, S. E., Aiba, Y., Jung, Y. S., Abe, Y., Fujiki, T., Teruya, K. & Shirahata, S., Dec 1 2007, In : Bioscience, Biotechnology and Biochemistry. 71, 12, p. 2871-2875 5 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

A simple and highly accurate numerical differentiation method for sensitivity analysis of large-scale metabolic reaction systems

Shiraishi, F., Furuta, S., Ishimatsu, T. & Akhter, J., Aug 1 2007, In : Mathematical Biosciences. 208, 2, p. 590-606 17 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)

A specific gene-expression signature quantifies the degree of hepatic fibrosis in patients with chronic liver disease

Utsunomiya, T., Okamoto, M., Wakiyama, S., Hashimoto, M., Fukuzawa, K., Ezaki, T., Aishima, S., Yoshikawa, Y., Hanai, T., Inoue, H., Barnard, G. F. & Mori, M., Jan 21 2007, In : World Journal of Gastroenterology. 13, 3, p. 383-390 8 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Availability of a novel criterion for peritoneal diffusive selectivity on peritoneal dialysis

Hamada, H., Mamun, A. A., Karino, T., Namoto, S., Yamashita, A. C., Ishizaki, M. & Okamoto, M., Jan 1 2007, In : IFMBE Proceedings. 14, 1, p. 3201-3204 4 p.

Research output: Contribution to journalConference article

1 Citation (Scopus)

Calculation of metabolic flow of xylose in Lactococcus lactis

Ohara, H., Owaki, M. & Sonomoto, K., Jan 1 2007, In : Journal of Bioscience and Bioengineering. 103, 1, p. 92-94 3 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Carotenoid silk coloration is controlled by a carotenoid-binding protein, a product of the Yellow blood gene

Sakudoh, T., Sezutsu, H., Nakashima, T., Kobayashi, I., Fujimoto, H., Uchino, K., Banno, Y., Iwano, H., Maekawa, H., Tamura, T., Kataoka, H. & Tsuchida, K., May 22 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 21, p. 8941-8946 6 p.

Research output: Contribution to journalArticle

88 Citations (Scopus)

Catalyser-21™, a mineral water derived from leaf soil, inhibits tumor cell invasion and angiogenesis

Ye, J., Li, Y., Hamasaki, T., Nakamichi, N., Kawahara, T., Osada, K., Teruya, K., Kato, Y., Toh, K., Abe, M., Katakura, Y., Noguchi, K. & Shirahata, S., Jan 1 2007, In : Cytotechnology. 55, 2-3, p. 61-70 10 p.

Research output: Contribution to journalArticle

Cell-specific expression of neutral glycosphingolipids in vertebrate brain: Immunochemical localization of 3-O-acetyl-sphingosine-series glycolipid(s) in myelin and oligodendrocytes

Dasgupta, S., Bhat, N. R., Spicer, S. S., Hogan, E. L., Furuya, S. & Hirabayashi, Y., Oct 1 2007, In : Journal of Neuroscience Research. 85, 13, p. 2856-2862 7 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Characterization, N-terminal sequencing and classification of cerein MRX1, a novel bacteriocin purified from a newly isolated bacterium: Bacillus cereus MRX1

Sebei, S., Zendo, T., Boudabous, A., Nakayama, J. & Sonomoto, K., Nov 1 2007, In : Journal of Applied Microbiology. 103, 5, p. 1621-1631 11 p.

Research output: Contribution to journalArticle

26 Citations (Scopus)

Characterization and structure analysis of a novel bacteriocin, lacticin Z, produced by Lactococcus lactis QU 14

Iwatani, S., Zendo, T., Yoneyama, F., Nakayama, J. & Sonomoto, K., Nov 21 2007, In : Bioscience, Biotechnology and Biochemistry. 71, 8, p. 1984-1992 9 p.

Research output: Contribution to journalArticle

42 Citations (Scopus)
1 Citation (Scopus)

Complete nucleotide sequence of pLD-TEX-KL, a 66-kb plasmid of Legionella dumoffii TEX-KL strain

Qin, T., Hirakawa, H., Iida, K. I., Oshima, K., Hattori, M., Tashiro, K., Kuhara, S. & Yoshida, S. I., Nov 1 2007, In : Plasmid. 58, 3, p. 261-268 8 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Design of bio-inspired fault-tolerant adaptive routing based on enzymatic feedback control in the cell: Towards averaging load balance in the network

Iwasaki, A., Nozoe, T., Kawauchi, T. & Okamoto, M., Dec 1 2007, Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007. p. 845-850 6 p. 4524217. (Proceedings of the Frontiers in the Convergence of Bioscience and Information Technologies, FBIT 2007).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Development of a computer-aided diagnosis system for continuous peritoneal dialysis: An availability of the simultaneous numerical optimization technique for kinetic parameters in the peritoneal dialysis model

Hamada, H., Namoto, S., Yamada, R., Al Mamun, A., Yamashita, A. C., Ishizaki, M. & Okamoto, M., Dec 1 2007, In : Computers in Biology and Medicine. 37, 12, p. 1700-1708 9 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Differences in developing intestinal microbiota between allergic and non-allergic infants: A pilot study in Japan

Songjinda, P., Nakayama, J., Tateyama, A., Tanaka, S., Tsubouchi, M., Kiyohara, C., Shirakawa, T. & Sonomoto, K., Nov 21 2007, In : Bioscience, Biotechnology and Biochemistry. 71, 9, p. 2338-2342 5 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

Direct l-lactic acid fermentation with sago starch by a novel amylolytic lactic acid bacterium, Enterococcus faecium

Shibata, K., Flores, D. M., Kobayashi, G. & Sonomoto, K., Jul 2 2007, In : Enzyme and Microbial Technology. 41, 1-2, p. 149-155 7 p.

Research output: Contribution to journalArticle

50 Citations (Scopus)