ELSI

研究・活動

研究者

黒川 顕

黒川 顕
氏 名
黒川 顕
役 職
フェロー
専門分野
ゲノム科学&バイオインフォマティクス
E-mail
ken_at_elsi.jp

主要業績/受賞歴

41. Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J, Sebaihia M, Coulthurst S, Gotoh N, Thomson NR, Ewbank JJ, Hayashi T. (2014) Genome evolution and plasticity of Serratia marcescens, an important multidrug resistant nosocomial pathogen. Genome Biol. Evol. evu160 PubMed

40. Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H, Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T, Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Shimojima M, Masuda S, Iwai M, Nobusawa T, Narise T, Kondo S, Saito H, Sato R, Murakawa M, Ihara Y, Oshima-Yamada Y, Ohtaka K, Satoh M, Sonobe K, Ishii M, Ohtani R, Kanamori-Sato M, Honoki R, Miyazaki D, Mochizuki H, Umetsu J, Higashi K, Shibata D, Kamiya Y, Sato N, Nakamura Y, Tabata S, Ida S, Kurokawa K, Ohta H. (2014) Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun. 5:3978 PubMed

39. Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura Y, Hayashi T, Kurokawa K, Ohnishi M, Sekine Y. (2014) A novel small regulatory RNA enhances cell motility in enterohemorrhagic Escherichia coli. J Gen Appl Microbiol. 60(1): 44-50 PubMed

38. Tajima N, Sato S, Maruyama F, Kurokawa K, Ohta H, Tabata S, Sekine K, Moriyama T, Sato N. (2014) Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum. J Plant Res. in press. PubMed

37. Suda K, Ueno Y, Yoshizaki M, Nakamura H, Kurokawa K, Nishiyama E, Yoshino K, Hongoh Y, Kawachi K, Omori S, Yamada K, Yoshida N, Maruyama S. (2014) Origin of methane in serpentinite-hosted hydrothermal systems: The CH4–H2–H2O hydrogen isotope systematics of the Hakuba Happo hot spring. Earth and Planetary Science Letters, 386: 112–125. Journal

36. Mori H,†, Maruyama F,†, Kato H,†, Toyoda A, Dozono A, Ohtsubo Y, Nagata Y, Fujiyama A, Tsuda M, and Kurokawa K. (2014) Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes. DNA Res., 21: 217-227. PubMed

35. Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR, Mino S, Nakagawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R, Thompson FL, Gomez-Gil B, Christen R, Maruyama F, Kurokawa K, Hayashi T. (2013) Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol. 4:414. PubMed.

34. Masuda S, Hori K, Maruyama F, Ren S, Sugimoto S, Yamamoto N, Mori H, Yamada T, Sato S, Tabata S, Ohta H, Kurokawa K (2013) Whole-genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum strain W4. Genome Announc., 1:e00577-13. PubMed

33. Minegishi K, Aikawa C, Furukawa A, Watanabe T, Nakano T, Ogura Y, Ohtsubo Y, Kurokawa K, Hayashi T, Maruyama F, Nakagawa I, Eishi Y (2013) Complete Genome Sequence of a Propionibacterium acnes Isolate from a Sarcoidosis Patient. Genome Announc., 1:e00016-12. PubMed

32. Suzuki S, Ishida T, Kurokawa K, Akiyama Y (2012) GHOSTM: A GPU-accelerated homology search tool for metagenomics. PLoS one, 7:e36060.PubMed

31. Nonaka L, Maruyama F, Miyamoto M, Miyakoshi M, Kurokawa K, Masuda M. (2012) Novel Conjugative Transferable Multiple Drug Resistance Plasmid pAQU1 from Photobacterium damselae subsp. damselae Isolated from Marine Aquaculture Environment. Microbes Environ., Mar 23 Epub. PubMed

30. Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki NV, Kurokawa K, Ohta H, Kanesaki Y, Yoshikawa H, Tabata S, Ikeuchi M, Sato N (2011) Genomic Structure of the Cyanobacterium Synechocystis sp. PCC 6803 Strain GT-S. DNA Res., 18:393-399. 4.754 PubMed

29. Kuwahara T, Ogura Y, Oshima K, Kurokawa K, Ooka T, Hirakawa H, Itoh T, Nakayama-Imaohji H, Ichimura M, Itoh K, Ishifune C, Maekawa Y, Yasutomo K, Hattori M, Hayashi T (2011) The Lifestyle of the Segmented Filamentous Bacterium: A Non-Culturable Gut-Associated Immunostimulating Microbe Inferred by Whole-Genome Sequencing. DNA Res., 18:291-303. 4.754 PubMed

28. Watanabe T, Maruyama F, Nozawa T, Aoki A, Okano S, Shibata Y, Oshima K, Kurokawa K, Hattori M, Nakagawa I, and Abiko Y (2011) Complete genome sequence of the periodontogenic bacterium Porphyromonas gingivalis TDC60. J Bacteriol., 193:4259-60. 3.726 PubMed

27. Nozawa T, Furukawa N, Aikawa C, Watanabe T, Haobam B, Kurokawa K, Maruyama F, and Nakagawa I (2011) CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS one, 6:e19543. 4.411 PubMed

26. Kusuya Y, Kurokawa K, Ishikawa S, Ogasawara N, and Oshima T (2011) Transcription factor GreA contributes to resolve promoter proximal pausing of RNA polymerase in B. subtilis cells. J. Bacteriol., 193:3090-3099. 3.726 PubMed

25. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P.,Enterotypes of the human gut microbiome,Nature,473,7346,174-180,2011 PubMed

24. Ishikawa S, Oshima T, Kurokawa K, Kusuya Y, Ogasawara N (2010) RNA polymerase trafficking in Bacillus subtilis cells. J Bacteriol. 192:5778-5787. PubMed

23. Nakayama, K., Kurokawa, K., Fukuhara, M., Urakami, H., Yamamoto, S., Yamazaki, K., Ogura, Y., Ooka, T., and Hayashi, T. Genome comparison and phylogenetic analysis of Orientia tsutsugamushi strains., DNA Res., 17:281-291., 2010. PubMed

22. Mori H., Maruyama F. and Kurokawa K., VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics 2010, 11:332. PubMed

21. Toh, H., Oshima, K., Toyoda, A., Ogura, Y., Ooka, T., Sasamoto, H., Park, S.H., Iyoda, S., Kurokawa, K., Morita, H., Itoh, K., Taylor, T.D., Hayashi, T., and Hattori, M. Complete genome sequence of the wild-type commensal Escherichia coli strain SE15 belonging to phylogenetic group B2., J. Bacteriol., 192:1165-1166, 2009. PubMed

20. Masahira, H., Oshima, K., Kim, S., Kurokawa, K., Toh, H., and Taylor, T. Metagenomics and genomics decoding human gut microbiome, Genes Genet. Syst., 84:479-479, 2009.

19. Ogura, Y., Ooka, T., Iguchi, A., Toh, H., Asadulghani, M., Oshima, K., Kodama, T., Abe, H., Nakayama, K., Kurokawa, K., Tobe, T., Hattori, M., and Hayashi, T. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli., Proc. Natl. Acad. Sci. USA, 106:17939-17944, 2009. PubMed

18. Bermejo R, Capra T, Gonzalez-Huici V, Fachinetti D, Cocito A, Natoli G, Katou Y, Mori H, Kurokawa K, Shirahige K, and Foiani M. Genome-organizing factors Top2 and Hmo1 prevent chromosome fragility at sites of S phase transcription., Cell, 138:870-884, 2009. PubMed

17. Maruyama F, Kobata M, Kurokawa K, Nishida K, Sakurai A, Nakano K, Nomura R, Kawabata S, Ooshima T, Nakai K, Hattori M, Hamada S, and Nakagawa I. Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content., BMC Genomics, 10:358, 2009. PubMed

16. Ooka, T, Terajima, J, Kusumoto, M, Iguchi, A, Kurokawa, K, Ogura, Y, Asadulghani M, Nakayama K, Murase K, Ohnishi M, Iyoda S, Watanabe H, and Hayashi T. Development of a multiplex PCR-based rapid typing method for enterohemorrhagic Escherichia coli O157 strains., J. Clin. Microbiol., 47:2888-94, 2009. PubMed

15. Oishi, T., Tanaka, K., Hashimoto, T., Shinbo, Y., Jumtee, K., Bamba, T., Fukusaki, E., Suzuki, H., Shibata, D., Takahashi, H., Asahi, H., Kurokawa, K., Nakamura, Y., Hirai, A., Nakamura, K., Altaf-Ul-Amin, Kanaya, S. An approach to peak detection in GC-MS chromatograms and application of KNApSAcK database in prediction of candidate metabolites. Plant Biotechnol., 26:167-174, 2009. J-STAGE

14. Uyar, E., Kurokawa, K., Yoshimura, M., Ishikawa, S., Ogasawara, N., and Oshima, T. Differential binding profiles of StpA in wild-type and hns mutant cells: a comparative analysis of cooperative partners by ChIP-chip analysis. J. Bacteriol., Jan. 16 Epub, 2009. PubMed

13. Iguchi, A., Thomson, NR., Ogura, Y., Saunders, D., Ooka, T., Henderson, IR., Harris, D., Asadulghani, M., Kurokawa, K., Dean, P., Kenny, B., Quail, MA., Thurston, S., Dougan, G., Hayashi, T., Parkhill, J., and Frankel, G. Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. Bacteriol., 191:347-354, 2009. PubMed

12. Ogura, Y., Abe, H., Katsura, K., Kurokawa, K., Asadulghani, M., Iguchi, A., Ooka, T., Nakayama, K., Yamashita, A., Hattori, M., Tobe, T., and Hayashi, T. Systematic identification and sequence analysis of the genomic islands of the enteropathogenic Escherichia coli strain B171-8 by the combined use of whole-genome PCR scanning and fosmid mapping. J. Bacteriol., 190:6948-6940, 2008. PubMed

11. Takahashi, H., Kai, K., Shinbo, Y., Tanaka, K., Ohta, D., Oshima, T., Altaf-Ul-Amin, M., Kurokawa, K., Ogasawara, N., and Kanaya, S. Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron reasonance mass spectrometry. Anal. Bioanal. Chem., 391:2769-2782, 2008. PubMed

10. Izutsu, K., Kurokawa, K., Tashiro, K., Kuhara, S., Hayashi, T., Honda, T., and Iida, T. Pathogenicity island is the determinant of Kanagawa-phenomenon-positive V. parahaemolyticus: Comparative genomic analysis of V. parahaemolyticus strains. Infect. Immun., 76:1016-23, 2008. PubMed

9. 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. 52:606-611, 2008. PubMed

8. Nakayama, K., Yamashita, A., Kurokawa, K., Morimoto, T., Ogawa, M., Fukuhara, M., Urakami, H., Ohnishi, M., Uchiyama, I., Ogura, Y., Ooka, T., Oshima, K., Tamura, A., Hattori, M., and Hayashi, T. The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res., 15:616-620, 2007. PubMed

7. 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., 2007, 14: 155-168. PubMed

6. 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., Ehrich, 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., 2007, 14:169-181. PubMed

5. Goto, N., Kurokawa, K., and Yasunaga, T. Analysis of invariant sequences in 266 complete genomes. Gene, 2007, 401:172-180. PubMed

4. Ogura, Y., Ooka, T., Asadulghami, Terajima, J., Nougayrede, J. P., Kurokawa, K., Tashiro, K., Tobe, T., Nakayama, K., Kuhara, S., Oswald, E., Watanabe, H., and Hayashi, T. Extensive genomic diversity and selective conservation of virulence-determinants in Enterohaemorrhagic Escherichia coli strains of O157 and non-O157 serotypes. Genome Biolol., 2007, 8:R138. PubMed

3. Kobayashi, H., Akitomi, J., Fujii, N., Kobayashi, K., Amin, M. A., Kurokawa, K., Ogasawara, N., and Kanaya, S. The entire organization of transcription unites on the Bacillus subtilis genome. BMC Genomics. 2007, 8:197-201. PubMed

2. Dryselius, R., Kurokawa, K., and Iida, T. Vibrionaceae; versatile bacterial family with evolutionary conserved variability. Res. Microbiol., 2007, 158:479-486. PubMed

1. Aoki T, Hirono I, Kurokawa K, Fukuda H, Nahary R, Eldar A, Davison AJ, Waltzek TB, Bercovier H, Hedrick RP., Genome sequences of three koi herpesvirus isolates representing the expanding distribution of an emerging disease threatening koi and common carp worldwide. J Virol., 81:5058-5065, 2007. PubMed