<2012>

1)      Okushita, K., Chikayama, E. and Kikuchi, J.*Solubilization mechanism and characterization of the structural change of bacterial cellulose in regenerated states through ionic liquid treatmentBiomacromolecules. 13, 1323-1330 (2012).

2)      Ogata, Y., Chikayama, E., Morioka, Y., Everroad, R.C., Shino, A., Matsushima, A., Haruna, H., Moriya, S., Toyoda, T., and Kikuchi, J.* “ECOMICS: A web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach” PLoS ONE. 7, e30263 (2012).

3)      Tominaga, T., Sano, K., Kikuchi, J., Mitomo, H., Ijiro, K. and Osada, H. “Hydrophilic double-network polymers that sustain mechanical modules under 80% humidity” ACS Macro Lett. 1, 432-436 (2012).

4)      Matsuda, F., Okazaki, Y., Oikawa, A., Kusano, M., Nakabayashi, R., Kikuchi, J., Yonemaru, J., Ebana, K., Yano, M. and Saito, K. “Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis” Plant J. 70, 624-636 (2012).

5)      Everroad, C. R., Yoshida, S., Tsuboi, Y., Date, Y., Kikuchi, J.* and Moriya, S. “Concentration of metabolites from low-density planktonic communities for environmental metabolomics using nuclear magnetic resonance spectroscopy”. J. Vis. Exp. e3163 (2012).

6)      Date, Y., Sakata, K. and Kikuchi, J.* “Physicochemical characterization of complex biochemical mixtures from diversed seaweeds” Polymer J. (in press).

7)      Watanabe, T., Shino, A., Akashi, K. and Kikuchi, J.* “Spectroscopic investigation of tissue-specific biomass profiling of Jatropha curcas. LPlant Biotechnol. (in press).

8)      Yamamura, M., Noda, S., Hattori, T., Shino, A., Kikuchi, J., Takabe, K., Suzuki, S., Shibata, D. and Umezawa, T.* “Characterization of lignocellulose of Erianthus ravennae in relation to enzymatic saccharification efficiency” Plant Biotechnol.  (in press).

9)      Okushita, K., Komatsu, T., Chikayama, E. and Kikuchi, J.* “Statistical approach for solid-state NMR spectra of a cellulose derived from a series of variable parameters” Polymer J. (in press).

10)  Sakurai, N., Ogata, Y., Ara, T., Sano, R., Akimoto, N., Suzuki, H., Kajikawa, M., Widyastuti, W., Suharsono, S., Yokota, A., Akashi, K., Kikuchi, J. and Shibata, T. "Development of KaPPA-View4 for omics studies on Jatropha and a database system KaPPA-Loader for construction of local omics databases" Plant Biotechnol (in press).

11)  Mori, T. Chikayama, E., Tsuboi, Y., Ishida, N., Shisa, N., Moriya, S., and Kikuchi, J.*Exploring conformational space of amorphous cellulose based on NMR chemical shiftsCarbohydr. Polymers. (in press).

12)  菊地淳 微生物のもつ基本的な代謝を理解する 微生物機能学 ―微生物リソースと遺伝子リソースの利用― 三共出版 (2012).

13)  菊地淳 “核磁気共鳴法による多糖類の構造解析と細胞壁プロファイリング” 植物細胞壁 −基礎と応用― 講談社 (2013).

14)  関山恭代、近山英輔、菊地淳 “NMR計測により物質資源・情報資源を抽出する“ぶんせき (2012).

15)  本間信孝、末安草、石田宣弘、毛利誠、菊地淳、坪井裕理、守屋繁春 “バイオマス原料からフェノールを製造する方法” 特願2012-155007 平成24710出願

 

2011

16)  Sekiyama, Y., Chikayama, E. and Kikuchi, J.* “Evaluation of a semipolar solvent system as a step toward heteronuclear multidimensional NMR-based metabolomics for 13C-labeled bacteria, plants, and animalsAnal. Chem. 83, 719-726 (2011).

17)  Fukuda, S., Toh, H., Hase, K., Nakanishi, Y., Oshima, K., Yoshimura, K., Tobe, T., Clarke, J. M., Topping, D. L., Suzuki, T., Taylor, T. D., Itoh, K., Kikuchi, J., Morita, H., Hattori, M.*and Ohno, H.* “Bifidobacteria protect from enteropathogenic infection through production of acetate.Nature 469, 543-547 (2011).

18)  Nakanishi, Y., Fukuda, S., Chikayama, E. Kimura, Y., Ohno, H. and Kikuchi, J.* “Dynamic omics approach identifies nutrition-mediated microbial interactionsJ. Proteome Res. 10, 824-831 (2011).

19)  Takase, T., Ishikawa, H., Murakami, H., Kikuchi, J., Sato-Nara, K.* and Suzuki, H. “Circadian clock modulate water dynamics and aquaporin expression in the Arabidopsis rootPlant Cell Physiol. 52, 373-383 (2011).

20)  Kikuchi, J., Ogata, Y. and Shinozaki, K. “ECOMICS: ECosytem trans-OMICS tools and methods for complex environmental samples and datasets” J. Ecosys. Ecogr. S2 001 (2011).

21)  Sasagawa T, Matsui M, Kobayashi Y, Otagiri M, Moriya S, Sakamoto Y, Ito Y, Lee CC, Kitamoto K, Arioka M "High-throughput recombinant gene expression systems in Pichia pastoris using newly developed plasmid vectors” Plasmid  65, 65-69  (2011).

22)  Todaka N, Nakamura R, Moriya S, Ohkuma M, Kudo T, Takahashi H, Ishida N. “Screening of optimal cellulases from symbiotic protists of termites through expression in the secretory pathway of Saccharomyces cerevisiaeBiosci Biotechnol Biochem. 75, 2260-2263 (2011).

23)菊地淳、葭田征二、坪井裕理、伊達康博 (2011) “環境変動の情報を生物の代謝プロファイリングから捉える試み“ ケミカルエンジニヤリング 56, 38-43.

24)篠阿弥宇、近山英輔菊地淳 (2011) “リグノセルロースNMR解析技術の現状と展望 ケミカルエンジニヤリング 56, 32-37.

25)特願2011-156812 森哲哉、志佐倫子、菊地淳守屋繁春、坪井裕理、石田亘広 “バイオマス糖化率予測方法” 2011715

 

<2010>

26)  Sekiyama, Y., Chikayama, E. and Kikuchi, J.* “Profiling polar and semi-polar plant metabolites throughout extraction processes using a combined solution-state and HR-MAS NMR approach” Anal. Chem. 82, 1643-1652 (2010).

27)  Chikayama, E., Sekiyama, E., Okamoto, M., Nakanishi, Y., Tsuboi, Y., Akiyama, K., Saito, K., Shinozaki, K. and Kikuchi, J.* “Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum” Anal. Chem. 82, 1653-1658 (2010).

28)  Date, Y., Nakanishi, Y., Fukuda, S., Kato, T., Tsuneda, S., and Ohno, H. and Kikuchi, J.* “New monitoring approach for metabolic dynamics in microbial ecosystems using stable-isotope-labeling technologies” J. Biosci. Bioeng. 110, 87-93 (2010).

29)  Serve, O., Kamiya, Y., Maeno, A., Nakano, M., Murakami, C., Sasakawa, H., Kamiya, Y., Yamaguchi, Y., Harada, T., Kurimoto, E., Iguchi, T., Inaba, K., Kikuchi, J., Asami, O., Kajino, T., Oka, T., Nakasako, M and Kato, K.* “Redox-dependent domain arrangement of protein disulfide bond isomerase coupled with exposure of its substrate-binding hydrophobic surface” J. Mol. Biol. 396, 361-374 (2010).

30)  Todaka N, Inoue T , Saita K , Ohkuma M, Nalepa CA, Lenz M, Kudo T, Moriya S* “Phylogenetic Analysis of Cellulolytic Enzyme Genes from Representative Lineages of Termites and a Related Cockroach” PLoS ONE 2010 5 e8636.

31)  Todaka N, Lopez CM, Inoue T, Saita K, Maruyama J, Arioka M, Kitamoto K, Kudo T, Moriya S.* “Heterologous Expression and Characterization of an Endoglucanase from a Symbiotic Protist of the Lower Termite, Reticulitermes speratusAppl Biochem Biotechnol. 2010 160(4):1168-78.

32)  Chikayama E, Kurotani A, Tanaka T, Yabuki T, Miyazaki S, Yokoyama S, Kuroda Y.* "Mathematical model for empirically optimizing large scale production of soluble protein domains” BMC Bioinformatics. 11 e113 (2010).

33)  菊地淳、尾形善之 バイオマス利用の設計図入手を目指した物質・情報資源の探索 未利用バイオマスの活用技術と環境負荷・事業性評価 サイエンス&テクノロジー 105-114 (2010).

34)菊地淳、関山恭代、伊達康博 代謝解析におけるNMR技術開発の現状と将来展望 Radioisotopes 59, 637-658 (2010).

35)  菊地淳守屋繁春、福田真嗣、大野博司 微生物群集の統合メタボローム解析 難培養微生物研究の最新技術II CMC出版 147-155 (2010).

36)  菊地淳 “NMR法による代謝表現型解析 −その現状と展望―“ 遺伝子医学 16, 81-85 (2010).

37)  近山英輔、赤木謙一、菊地淳 “NMRメタボロームのソフトウエア開発 遺伝子医学 16, 126-130 (2010).

 

2009

38)  Mochida, K.*, Furuta, T., Ebana, K., Shinozaki, K. and Kikuchi, J.* “Correlation exploration of metabolic and genomic diversities in rice” BMC Genomics. 10, 563 (2009).

39)  Okamoto, M., Tsuboi, Y., Chikayama, E., Kikuchi, J. and Hirayama, T.* “Metabolomic movement upon abscisic acid and salicylic acid combined treatments” Plant Biotechnol. 26, 551-560 (2009).

40)  Fukuda, S., Nakanishi, Y., Chikayama, E., Ohno, H., Hino, T. and Kikuchi, J.* “Evaluation and characterization of bacterial metabolic dynamics by a novel profiling technique, real-time metabolotyping” PLoS ONE 4, e4893 (2009).

41)  Ohyama, K., Suzuki, M., Kikuchi, J., Saito, K. and Muranaka, T.* “Dual biosynthetic pathways to phytosterol via cycloartenol and lanosterol in Arabidopsis Proc. Natl. Acad. Sci. USA 106, 725-730 (2009).

42)  吉田欣史、久原とみ子、菊地淳 メタボロミクスとメタボノミクス ぶんせき 7, 371-378 (2009).

 

2008

43)  Chikayama, E., Suto, M., Nishihara, T., Shinozaki, K. and Kikuchi, J.* “Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: Coarse grained views of metabolic pathways” PLoS ONE  3, e3805 (2008).

44)  Akiyama, K., Chikayama, E., Yuasa, H., Shimada, Y., Tohge, T., Shinozaki, K., Hirai-Yokota, M., Sakurai, T*., Kikuchi, J.* and Saito, K. “PRIMe: a web site that assembles tools for metabolomics and transcriptomics” In Silico Biology 8, e27 (2008).

45)  Morita, H., Toh, H., Fukuda, S., Horikawa, H., Ohshima, K., Suzuki, T., Murakami, M., Hisamatsu, S., Kato, Y., Takizawa, T., Fukuoka, H., Yoshimura, T., Ito, K., O’Sullivan, D. J., McKay, L. L., Ohno, H., Kikuchi, J., Masaoka, T. and Hattori, M*. ”Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production” DNA Res. 15, 151-161 (2008).

46)  Yuki M, Moriya S, Inoue T, Kudo T.* “Transcriptome analysis of the digestive organs of Hodotermopsis sjostedti, a lower termite that hosts mutualistic microorganisms in its hindgut” Zoolog Sci. 2008 25(4):401-6.

47)  Sasaguri S, Maruyama J, Moriya S, Kudo T, Kitamoto K, Arioka M.* “Codon optimization prevents premature polyadenylation of heterologously-expressed cellulases from termite-gut symbionts in Aspergillus oryzae” J. Gener. Appl. Microb. 2008 54, 343-351.

48)   菊地淳 統合バイオリファイナリーへのNMR技術開発 −石油資源が生物資源に代替される時代を見据えてー 植物の生長調節 43, 144-155 (2008).

49)   菊地淳中西裕美子 代謝動態の追跡 −安定同位体利用の新局面 バイオサイエンスとインダストリー66, 143-144 (2008).

50)   守屋繁春、加藤完、福田真嗣、大野博司、菊地淳 原核生物、特に、真性細菌のcDNAの簡易な調整方法特願2008-52503. 

 

  <2007

51)   Tian C.J. Chikayama, E., Tsuboi, Y., Kuromori, T., Shinozaki, K., Kikuchi, J.* and Hirayama, T.* “Top-down phenomics of Arabidopsis thaliana –One and two-dimensional NMR metabolic profiling and transcriptome analysis of albino mutants” J. Biol. Chem. 282, 18532-18541 (2007).

52)   Sekiyama, Y and Kikuchi, J.* “Towards dynamic metabolic network measurement by multi-dimensional NMR-based fluxomics” Phytochemistry 68, 2320-2329 (2007).

53)   Kikuchi, J.* and Hirayama, T. “Practical aspects of stable isotope labeling of higher plants for a hetero-nuclear multi-dimensional NMR-based metabolomics” Method Mol. Biol. 358, 273-286 (2007).

54)   Sasaki, R., Sasaki, H., Fukuzawa, S.*, Kikuchi, J., Hirota, H. & Tachibana, K. “Thermal analyses of phospholipid mixtures by differential scanning calorimetry and effect of doping with a bolaform amphiphile” Bull. Chem. Soc. Jpn. 80, 1208-1216 (2007).

55)  Moriya S, Noda S, Ohkuma M, Kudo T.* “In situ hybridization of termite microbes” Methods Mol Biol. 2007 353:105-12.

56)  Todaka N, Moriya S, Saita K, Hondo T, Kiuchi I, Takasu H, Ohkuma M, Piero C, Hayashizaki Y, Kudo T.* “Environmental cDNA analysis of the genes involved in lignocellulose digestion in the symbiotic protist community of Reticulitermes speratusFEMS Microbiol Ecol. 2007 59(3):592-9.

57)   菊地淳 メタボノミクスとNMR技術開発 メタボロミクスの解析と応用技術CMC出版、86-99 (2007)

58)   菊地淳 森哲哉、雪真弘、西原崇、佐藤一、甲野裕之 植物バイオマスへの13C代謝・分解過程の追跡 −高分解能マジック核回転(hr-MAS)法によるアプローチ ブレインテクノニュース124, 16-21 (2007)

59)   松田史生、草野都、及川彰、菊地淳 斉藤和季 メタボローム解析技術の現状と展望 第1回 試料調整と計測技術 化学と生物45, 754-760 (2007).

60)   松田史生、草野都、及川彰、菊地淳 斉藤和季 メタボローム解析技術の現状と展望 第2回 データ解析技術 化学と生物45, 834-842 (2007).

61)   菊地淳、雪真弘、守屋繁春、工藤俊章 蛋白質の探索方法 特願2007-232792.