Publications

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2016

  • Suzuki M, Segawa T, Mori H, Akiyoshi A, Ootsuki R, Kurihara A, Sakayama H, Kitayama T, Abe T, Kogame K, Kawai H, Nozaki H. (2016) Next-Generation Sequencing of an 88-Year-Old Specimen of the Poorly Known Species Liagora japonica (Nemaliales, Rhodophyta) Supports the Recognition of Otohimella gen. nov. PLoS One 11: e0158944. PubMed
  • Okai S, Usui F, Yokota S, Hori-i Y, Hasegawa M, Nakamura T, Kurosawa M, Okada S, Yamamoto K, Nishiyama E, Mori H, Yamada T, Kurokawa K, Matsumoto S, Nanno M, Naito T, Watanabe Y, Kato T, Miyauchi E, Ohno H, Shinkura R. (2016) High-affinity monoclonal IgA regulates gut microbiota and prevents colitis in mice. Nature Microbio. 1:16103. Japanese Press release
  • Matsuki T†, Yahagi K†, Mori H†, Matsumoto H†, Hara T, Tajima S, Ogawa E, Kodama H, Yamamoto K, Yamada T, Matsumoto S, Kurokawa K. (2016) A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nature Commun. 7:11939. PubMed Japanese Press release
  • Nishimoto Y, Mizutani S, Nakajima T, Hosoda F, Watanabe H, Saito Y, Shibata T, Yachida S, Yamada T. (2016) High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut. in press. PubMed Japanese Press release
  • Tajima N, Saitoh K, Sato S, Maruyama F, Ichinomiya M, Yoshikawa S, Kurokawa K, Ohta H, Tabata S, Kuwata A, Sato N. (2016) Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms). Curr Genet. in press. PubMed
  • Nakamura Y, Yamamoto N, Kino Y, Yamamoto N, Kamei S, Mori H, Kurokawa K, Nakashima N. (2016) Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl Microbiol Biotechnol. in press. PubMed
  • Moriya, Y., Yamada, T., Okuda, S., Nakagawa, Z., Kotera, M., Tokimatsu, T., Kanehisa, M. & Goto, S. (2016). Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate–Product Pairs. Journal of Chemical Information and Modeling. PubMed
  • Higashi K, Tobe T, Kanai A, Uyar E, Ishikawa S, Suzuki Y, Ogasawara N, Kurokawa K, Oshima T. (2016) H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PLoS Genet 12(1): e1005796. PubMed

2015

  • Tsukuda M, Nakashima N, Miyazaki K. (2015) Counterselection method based on conditional silencing of antitoxin genes in Escherichia coli. J Biosci Bioeng. 120:591-5. PubMed
  • Akita H, Watanabe M, Suzuki T, Nakashima N, Hoshino T. (2015) Molecular cloning and characterization of two YGL039w genes encoding broad specificity NADPH-dependent aldehyde reductases from Kluyveromyces marxianus strain DMB1. FEMS Microbiol Lett. 362(16). PubMed
  • Akita H, Watanabe M, Suzuki T, Nakashima N, Hoshino T. (2015) Characterization of the Kluyveromyces marxianus strain DMB1 YGL157w gene product as a broad specificity NADPH-dependent aldehyde reductase. AMB Express. 5:17. PubMed
  • Akita H, Nakashima N, Hoshino T. (2015) Bacterial production of isobutanol without expensive reagents. Appl Microbiol Biotechnol. 99:991-9. PubMed
  • Kato H†, Mori H†, Maruyama F, Toyoda A, Oshima K, Endo R, Fuchu G, Miyakoshi M, Dozono A, Ohtsubo Y, Nagata Y, Hattori M, Fujiyama A, Kurokawa K, Tsuda M. (2015) Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res. 22:413-424. PubMed
  • Yoshida K, Maekawa T, Zhu Y, Renard-Guillet C, Chatton B, Inoue K, Uchiyama T, Ishibashi KI, Yamada T, Ohno N, Shirahige K, Okada-Hatakeyama M, Ishii S. (2015) The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory. Nat Immunol. 2015 Oct;16(10):1034-43. PubMed
  • Kato H, Ogawa N, Ohtsubo Y, Oshima K, Toyoda A, Mori H, Nagata Y, Kurokawa K, Hattori M, Fujiyama A, Tsuda M. (2015) Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), Isolated from a Phenanthrene-Degrading Consortium. Genome Announc. 3:e00782-15 PubMed
  • Sato Y, Yamagishi J, Yamashita R, Shinozaki N, Ye B, Yamada T, Yamamoto M, Nagasaki M, Tsuboi A. (2015) Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLoS One 10:e0131607 PubMed
  • Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T. (2015) FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data. PLoS One 10:e0126967 PubMed
  • Kojima H, Ogura Y, Yamamoto N, Togashi T, Mori H, Watanabe T, Nemoto F, Kurokawa K, Hayashi T, Fukui M. (2015) Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence. ISME J. 9:1166–1176 PubMed
  • Wang T, Mori H, Zhang C, Kurokawa K, Xing X, Yamada T. (2015) DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. BMC Bioinformatics 16:96 PubMed
  • Yamaichi Y, Chao MC, Sasabe J, Clark L, Davis BM, Yamamoto N, Mori H, Kurokawa K, Waldor MK. (2015) High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4. Nucleic Acids Res. 43:348–360 PubMed
  • Matsumura Y, Al-saari H, Kuga K, Inohara Y, Mino S, Nakagawa S, Maruyama F, Ogura Y, Hayashi T, Kurokawa K, Sawabe T, Sawabe T (2015) Identification of a gene cluster responsible for hydrogen evolution in Vibrio tritonius strain AM2 with transcriptional analyses. Int. J. Hydrogen Energy, 40:9137-46. doi:10.1016/j.ijhydene.2015.05.137.

2014

  • Nakashima N, Akita H, Hoshino T. (2014) Establishment of a novel gene expression method, BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin. Metab Eng. 25:204-14 PubMed
  • Nakashima N, Miyazaki K. (2014) Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci. 15:2773-93 PubMed
  • Nakashima N, Ohno S, Yoshikawa K, Shimizu H, Tamura T. (2014) A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli. Appl Environ Microbiol. 80:564-73 PubMed
  • Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K. (2014) CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinformatics 15:406 PubMed
  • Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. (2014) Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol. Syst. Biol. 10:766 PubMed
  • 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
  • Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW,Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD. (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnol. 2014 Jul 06. PubMed
  • 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
  • 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
  • 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
  • Alison S Waller, Takuji Yamada, David M Kristensen, Jens Roat Kultima, Shinichi Sunagawa, Eugene V Koonin and Peer Bork. (2014) Classification and quantification of bacteriophage taxa in human gut metagenomes. The ISME Journal , (13 March 2014) | doi:10.1038/ismej.2014.30 [ PubMed ]
  • Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. (2014) BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J. Biomed. Semantics, 5:5. PubMed
  • 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
  • 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
  • Suda K, Ueno Y, Yoshiazaki M, Nakamura H,Kurokawa K, Nishiyama E, Yoshino K, Hongoh Y, Kawachi K, Omori S, Yamada K, Yoshida N, Maruyama S (2014) Reply to comment on “Origin of methane in serpentinite-hosted hydrothermal systems: The CH4–H2–H2O hydrogen isotope systematics of the Hakuba Happo hot spring” by Suda et al. [Earth Planet. Sci. Lett. 386 (2014) 112–125]. Earth Planetary Sci. Lett., 401: 376-377. doi: 10.1016/j.epsl.2014.06.005

2013

  • 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.
  • Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M’Rini C, Mérieux A, Yamada T. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature. 29;500(7464):541-6. PubMed
  • 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
  • Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV (2013) Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J. Bacteriol., 195:941-50. PubMed
  • 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

2012

  • Tuama EÓ, Deck J, Dröge G, Döring M, Field D, Kottmann R, Ma J, Mori H, Morrison N, Sterk P, Sugawara H, Wieczorek J, Wu L, Yilmaz P (2012) Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012). Stand Genomic Sci., 7:166-70. PubMed
  • Suzuki S, Ishida T, Kurokawa K, Akiyama Y (2012) GHOSTM: A GPU-accelerated homology search tool for metagenomics. PLoS one, 7:e36060.PubMed
  • Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P. (2012) Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours., Mol Syst Biol. 8:58 PubMed
  • 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
  • Aikawa C, Furukawa N, Watanabe T, Minegishi K, Furukawa A, Eishi Y, Oshima K, Kurokawa K, Hattori M, Nakano K, Maruyama F, Nakagawa I, Ooshima T (2012) Complete genome sequence of the serotype k Streptococcus mutans strain LJ23. J. Bacteriol. 194:2754-2755. DOI: 10.1128/JB.00350-12.

2011

  • 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
  • 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
  • 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
  • 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
  • Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P.,iPath2.0: interactive pathway explorer.,Nucleic Acids Res. 2011 Jul;39(Web Server issue):W412-5. PubMed
  • 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
  • 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

2010

  • Ishikawa S, Oshima T, Kurokawa K, Kusuya Y, Ogasawara N (2010) RNA polymerase trafficking in Bacillus subtilis cells. J Bacteriol. 192:5778-5787. PubMed
  • 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
  • Mori H., Maruyama F., Kurokawa K., VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics 2010, 11:332. PubMed
  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J.,A human gut microbial gene catalogue established by metagenomic sequencing.,Nature. 2010 Mar 4;464(7285):59-65. PubMed

2009

  • 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
  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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
  • Wiwegweaw A, Seki K, Mori H, Asami T. Asymmetric reproductive isolation during simultaneous reciprocal mating in pulmonates. (2009) Biol Lett., 5:240-243. PubMed
  • 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
  • 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

2008

  • 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
  • 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
  • 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
  • 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

2007

  • 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
  • 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
  • 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
  • Goto, N., Kurokawa, K., and Yasunaga, T. Analysis of invariant sequences in 266 complete genomes. Gene, 2007, 401:172-180. PubMed
  • 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
  • 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
  • Dryselius, R., Kurokawa, K., and Iida, T. Vibrionaceae; versatile bacterial family with evolutionary conserved variability. Res. Microbiol., 2007, 158:479-486. PubMed
  • 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

和文総説・著書

  • 森宙史, 東光一, 山田拓司, 黒川顕 (2015) 微生物統合データベースによる微生物と環境の研究への貢献, 難培養微生物研究の最新技術 III—微生物の生き様に迫り課題解決へ—, シーエムシー出版, pp10-19.
  • 森宙史, 黒川顕 (2014) MicrobeDB.jp, 今日から使えるデータベース・ウェブツール, 羊土社, pp76-77.
  • 山本希, 森宙史, 山田拓司, 黒川顕 (2014) メタゲノミクスの現状と未来, 生命のビッグデータ利用の最前線, シーエムシー出版, pp48-57.
  • 森宙史, 山田拓司, 黒川顕 (2013) ヒトメタゲノムの大規模コホート研究, 遺伝, pp279-282, 2013年5月号:67(3).
  • 森宙史, 山田拓司, 黒川顕(2012)メタゲノム解析の現状と将来, 情報管理, 55(3):167-175.
  • 黒川顕 (2011) 微生物統合データベース”MicrobeDB.JP”, 細胞工学, vol.30, No.12.
  • 森宙史, 丸山史人, 黒川顕 (2010) メタゲノムデータベース, メタゲノム解析技術の最前線, シーエムシー出版, pp42-53.
  • 森宙史, 丸山史人, 黒川顕 メタゲノムインフォマティクス, 難培養微生物研究の最新技術II, pp82-91, 2010, シーエムシー出版, 東京
  • 森宙史, 林哲也,黒川顕 メタゲノム研究の最前線,蛋白質核酸酵素,45:1264-1270, 2009.
  • 黒川顕, 服部正平 メタゲノムデータベース, 実験医学4月増刊号「バイオインフォマティクスツールの開発と生命研究への応用の最前線」, 37-42, 羊土社, 東京, 2008.
  • 黒川顕,服部正平 細菌叢のメタゲノム解析, 細胞工学別冊「比較ゲノム学から読み解く生命システム」, 2007.
  • 服部正平,林哲也,黒川顕,伊藤武彦,桑原知巳 ヒト腸内細菌叢のゲノムシークエンス, 腸内細菌学雑誌,2007. 21:187-197.
  • 黒川顕 メタゲノミクスのバイオインフォマティクス, 化学と生物, 2007. 45:495-501, 学会出版センター, 東京.
  • 黒川顕 GeneMarkおよびGlimmer, バイオデータベースとウェブツールの手とり足とり活用法(改訂第2版), 2007, 羊土社, 東京.
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