• 2021

  1. Liu, H., Dai, C., Yu, H., Guo, Q., Li, J., Hao, A., Kikuchi, J. and Zhao, M.* “Dynamics induced by environmental stochasticity in a phytoplankton-zooplankton system with toxic phytoplankton” Math. Biosci. Eng. (in press).
  2. Kurotani, A., Kakiuchi, T. and Kikuchi, J.* “Solubility prediction from molecular properties and analytical data using an in-phases deep neural network (ip-DNN)” ACS Omega (in press).
  3. Ito, K., Xu, X. and Kikuchi, J.* “Improved Prediction of Carbonless NMR Spectra by the Machine Learning of Theoretical and Fragment Descriptors for Environmental Mixture Analysis” Anal. Chem. (in press).
  4. Yamawaki, R., Tei, A., Ito, K. and Kikuchi, J.* “Decomposition Factor Analysis Based on Virtual Experiments Throughout Bayesian Optimization for Compost-Degradable Polymers” Appl. Sci. 11, 2820 (2021). DOI
  5. Watanabe, T.*, Nagai, S., Kawakami, Y., Asakura, T., Kikuchi, J., Inaba, N., Taniuchi, Y., Kurogi, H., Chow, S., Tomoda, T., Ambe, D. and Hasegawa, D. “18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific” Sci. Rep. 11, 5488 (2021). DOI
  6. Date, Y., Wei, F., Tsuboi, T., Ito, K., Sakata, K. and Kikuchi, J.* “Relaxometric learning: a pattern recognition method for T2 relaxation curves based on machine learning supported by an analytical framework” BMC Chemistry 15, 13 (2021). DOI
  7. Wei, F., Ito, K., Sakata, K., Asakura, T., Date, Y. and Kikuchi, J.* “Fish ecotyping based on machine learning and inferred network analysis of chemical and physical properties” Sci. Rep. 11, 3766 (2021). DOI
  8. Yamada, S., Chikayama, E. and Kikuchi, J.* “Signal Deconvolution and Generative Topographic Mapping Regression for Solid-state NMR of Multi-component Materials” Int. J. Mol. Sci. 22, 1086 (2021). DOI
  9. Kato, T., Kagawa, W.*, Suda, W., Tsuboi, Y., Suzuki, S., Kikuchi, J., Hattori, M., Ohta, T. and Ohno, H.* “Integrated multi-omics analysis reveals differential effects of fructo-oligosaccharides (FOS) supplementation on the human gut ecosystem” Sci. Rep. (under review).
  10. Akiyoshi, N., Ihara, A., Matsumoto, T., Takebayashi, A., Hiroyama, R., Kikuchi, J., Demura, T. and Ohtani, M.* “Functional Analysis of Poplar SOMBRERO-type NAC Transcription Factors Proposed Novel Strategy to Modify Woody Cell Wall Property” Plant Cell Physiol. (under review).
  11. Takamura, A., Tsukamoto, K., Sakata, K. and Kikuchi, J.* “Exploring important chemical measurement descriptors for physical properties of biopolymers (hairs)” Talanta Open (under review).
  12. Liu, H., Dai, C., Yu, H., Guo, Q., Li, J., Hao, A., Kikuchi, J. and Zhao, M.* “Dynamics of a stochastic phytoplankton-toxic phytoplankton-zooplankton system under regime switching” Math. Method. Appl. Sci. (under review).
  13. Kikuchi, J.* and Yamada, S. “The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science” RSC Adv. (submitted).
  14. 菊地淳 “NMRの分子構造情報” 化学便覧 基礎編第6版 (in press).
  15. 菊地淳 “量子化学理論と機械学習およびケモインフォマティクスによるNMR記述子予測” NMRによる有機材料分析とデータ解釈事例集(invited).



    1. Ito, K., Tsuboi, Y. and Kikuchi, J.* “Spatial molecular-dynamically ordered NMR spectroscopy of intact bodies and heterogeneous systems” Commun. Chem. 3, 1-8 (2020). DOI
    2. Ichihashi, Y.*, Date, Y., Shino, A., Shimizu, T., Shibata, A., Kumaishi, K., Funahashi, F., Wakayama, K., Yamazaki, K., Umezawa, A., Sato, T., Kobayashi, M., Kamimura, M., Kusano, M., Che, F.-S., O’Brien, M., Tanoi, K., Hayashi, M., Nakamura, R., Shirasu, K., Kikuchi, J. and Nihei, N.* “Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield” Proc. Natl. Acad. Sci. USA 117, 14552-14560 (2020). DOI
    3. Yamada, S., Kurotani, A., Chikayama, E. and Kikuchi, J.* “Signal Deconvolution and Noise Factor Analysis Based on Combination of Time–Frequency Analysis and Probabilistic Sparse Matrix Factorization” Int. J. Mol. Sci. 21, 2978 (2020). DOI
    4. Wei, F.*, Fukuchi, M., Ito, K., Sakata, K., Asakura, T., Date, Y. and Kikuchi, J.* “Large-Scale Evaluation of Major Soluble Macromolecular Components of Fish Muscle from Conventional 1H NMR Spectral Database” Molecules 25, 1966 (2020). DOI
    5. Zhang, J., Terayama, K., Sumita, M., Yoshizoe, K., Ito, K., Kikuchi, J. and Tsuda, K.* “NMR-TS: de novo molecule identification from NMR spectra” Sci. Technol. Adv. Mater. 21, 552-561 (2020). DOI
    6. Hori, C., Yu, X., Mortimer, J. C., Sano, R, Matsumoto, T., Kikuchi, J. and Demura, T. and Ohtani, M.* “Impact of abiotic stress on the regulation of cell wall biosynthesis in Populus trichocarpaPlant Biotechnol. 37, 273-283 (2020). DOI
    7. Kitami, T.*, Fukuda, S., Kato, T., Yamaguti, K., Nakatomi, T., Yamano, E., Kataoka, Y., Mizuno, K., Tsuboi, Y., Kogo, Y., Suzuki, H., Ito, M., Morioka, M., Kawaji, H., Koseki, H., Kikuchi, J., Hayashizaki, Y., Ohno, J., Kuratsune, H. and Watanabe, Y.* “Deep phenotyping of myalgic encephalomyelitis/chronic fatigue syndrome in Japanese population” Sci. Rep. 10, 1-12 (2020). DOI
    8. Kikuchi, J.* & Yamada, S. “Gut microbe transformation of natural products –plant polysaccharides are metabolized by animal symbionts” Comprehensive Natural Products III 519-528  (2020). DOI
    9. 菊地淳 “ブルーエコノミーを支える技術 -水産・環境試料分析とデータサイエンス技術―“ 東アジア海洋問題研究 169-181 (2020).
    10. 坂田研二、黒谷篤之、菊地淳、伊藤研悟、坪井裕理、松本朋子、鄭章代 “ポリマー物性推定装置および学習方法” 特願2020-217774 2020年12月25日 .
    11. 伊藤研悟、菊地淳、松本朋子、朝倉大河、黒谷篤之 “環境因子予測装置、方法、プログラム、学習済モデルおよび記憶媒体” PCT/JP2020/16472(特願2019-077300) 2020年4月14日. WIPO



    12. Mega, R., Abe, F., Kim, J.-S., Tsuboi, Y., Tanaka, K., Kobayashi, H., Sakata, Y., Hanada, K., Tsujimoto, H., Kikuchi, J., Cutler, S. R. and Okamoto, M.* “Tuning water use efficiency and drought tolerance in wheat using abscisic acid  receptors” Nature Plants 5, 153-159 (2019). DOI
    13. Yamada, S., Ito, K., Kurotani, A., Yamada, Y., Chikayama, E. and Kikuchi, J.* “InterSpin: Integrated supportive webtools for low and high-field NMR analysis toward molecular complexity” ACS Omega.4, 3361-3369 (2019). DOI
    14. Chow, S.*, Inaba, N., Nagai, S., Kurogi, H., Nakamura, Y., Yanagimoto, T., Tanaka, H., Hasegawa, D., Asakura, T., Kikuchi, J., Tomoda, T. and Kodama, T. “Molecular diet analysis of Anguilliformes leptocephalus larvae collected in the western North Pacific” PLoS One 14, e0225610 (2019). DOI
    15. Matsuda, C., Kato, T., Inoue-Suzuki, S., Kikuchi, J., Ohta, T., Kagawa, M., Hattori, M., Kobayashi, H., Shiba, D., Shirakawa, M., Mizuno, H.*, Furukawa, S., Mukai, C.* and Ohno, H.* “Dietary intervention of mice using an improved Multiple Artificial-gravity Research System (MARS) under artificial 1 gnpj Microgravity 5, 16 (2019). DOI
    16. Kato, T., Yamazaki, K., Nakajima, M., Date, Y., Kikuchi, J., Hase, K. and Ohno, H. and Yamazaki, K.* “Oral administration of Porphyromonas gingivalis alters the gut microbiome and serum metabolome” mSphere 3, e00460-18 (2019). DOI
    17. Kikuchi, J.* “Practical aspects of the analysis of low- and high-field NMR data from environmental complexity” Methods in Molecular Biology (Raftery, Gowda Ed.) 2037, 315-331 (2019). DOI
    18. Mekuchi, M., Asakura, T. and Kikuchi, J.* “New aquaculture technology based on host-symbiotic co-metabolism” Marine Metagenomics (Gojobori, Wada, Kobayashi, Mineta Ed.) 189-218 (2019). DOI
    19. 菊地淳 “魚類・水環境の恒常性評価と予測科学” 日本農学アカデミー会報 第31号 (2019).
    20. 和田時夫、渡部終五、伊藤文成、菊地淳、良永知義、伊藤暁、黒萩真悟 “持続可能な水産養殖業を目指して -研究開発・事業・政策の現状と展開方向-” 生物の科学 遺伝 73, 314-323 (2019).



    21. Ito, K., Obuchi, Y., Chikayama, E., Date, Y. and Kikuchi, J.* “Exploratory machine-learned theoretical chemical shifts can closely predict metabolic mixture signals” Chem. Sci. 9, 8213-8220 (2018). DOI
    22. Stranne, M., Ren, Y., Fimognari, L., Birdseye, D., Yan, J., Bardor, M., Mollet, J.-C., Komatsu, T., Kikuchi, J., Scheller, H. V. and Sakuragi, Y.* “TBL10 is required for O-acetylation of pectic rhamonogalacturonan-I in Arabidopsis thaliana” Plant J. 96, 772-785 (2018). DOI
    23. Mekuchi, M., Sakata, K., Asakura, T., Yamaguchi, T., Teruya, K. and Kikuchi, J.* “Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus)” PLoS On13, e0197256 (2018). DOI
    24. Saito, Y., Tsuchida, H., Matsumoto, T., Makita, Y., Kikuchi, J. and Matsui, M.* “Screening of fungi for decomposition of lignin-derived products from Japanese cedar” J. Biosci. Bioeng. 126, 573-579 (2018). DOI
    25. Oita, A., Tsuboi, Y., Date, Y., Oshima, T., Sakata, K., Yokoyama, A., Moriya, S. and Kikuchi, J.*  “Profiling physicochemical and planktonic features from discretely/continuously sampled surface water” Sci.Total Environ 636, 12-19 (2018). DOI
    26. Asakura, T., Sakata, K., Date, Y. and Kikuchi, J*. “Regional feature extraction of various fishes based on chemical and microbial variable selection using machine learning” Anal. Methods 10, 2160-2168 (2018). DOI
    27. Asakura, T., Date, Y. and Kikuchi, J*. “Application of ensemble deep neural network to metabolomics studies” Anal. Chim  Acta. 90, 1805-1810 (2018). DOI
    28. Vergara, F.*, Shino, M., Rymen, B. and Kikuchi, J. “The effect of ploidy on the concentration of soluble sugars in wheat seeds – Exploring the metabolome of Afghan wheat landraces” Current Metabolomics 6, 140-146 (2018). DOI
    29. Wei, F., Sakata, K., Asakura, T., Date, Y. and Kikuchi, J.* “Systemic Homeostasis in Metabolome, Ionome and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem” Sci. Rep. 8. 3478 (2018). DOI
    30. Shiokawa, Y., Date, Y. and Kikuchi, J.* “Application of kernel principal component analysis and computational machine learning to exploration of metabolites strongly associated with diet” Sci. Rep. 8, 3426 (2018). DOI
    31. Date, Y.* and Kikuchi, J.* “Application of a deep neural network to metabolomics studies and its performance in determining important variables” Anal. Chem. 90, 1805-1810 (2018). DOI
    32. Itouga, M., Hayatsu, M., Sato, M., Tsuboi, Y., Kato-Komatsu, Y., Toyooka, K., Suzuki, S., Ono, Y., Nakatsuka, S., Kawakami, S., Kikuchi, J. and Sakakibara, H.* “Protonema of the moss Funaria hygrometrica can function as a lead (Pb) adsorbent” PLoS One. 12, e0189726 (2018). DOI
    33. Kikuchi, J.*, Ito, K. and Date, Y. “Environmental metabolomics with data science as investigation of ecosystem homeostasis” Progress in NMR Spectroscopy 104, 56-88 (2018). DOI
    34. Hsu Y, Koizumi H, Otagiri M, Moriya S, Arioka M. “Trp residue at subsite - 5 plays a critical role in the substrate binding of two protistan GH26 β-mannanases from a termite hindgut” App. Microbiol. Biotechnol. 102, 1737-1747 (2018). DOI
    35. 菊地淳*、武部孝行 “エコインフォマティクスによる難養殖魚種の持続的生産管理構想” アグリバイオ 2, 28-31 (2018)



    36. Oska, T.*, Moriyama, E., Arai, S., Date, Y., Yagi, J., Kikuchi, J. and Tsuneda, S.* “Meta-analysis of fecal microbiota and metabolites in experimental colitic mice during the inflammatory and healing phases” Nutrients 9, e1329 (2017). DOI
    37. Shima, H., Masuda, S., Date, Y., Shino, A., Tsuboi, Y., Kajikawa, M., Inoue, Y., Kanamoto, T. and Kikuchi, J.* “Exploring the impact of food on gut ecosystem based on the combination of machine learning and network visualization” Nutrients 9, e1307 (2017). DOI
    38. Uchimiya, M.*, Tsuboi, Y., Ito, K., Date, Y. and Kikuchi, J.* “Bacterial substrate transformation tracked by stable-isotope-guided NMR metabolomics: Application in a natural aquatic microbial community” Metabolites 7, e52 (2017). DOI
    39. Qin, X.-Y., Hara, M., Arner, E., Kawaguchi, Y., Inoue, I., Tatsukawa, H., Furutani, Y., Nagatsuma, K., Matsuura, T., Wei, F., Kikuchi, J., Sone, H., Daub, C., Kawaji, H., Lassmann, T., Ito, M., Suzuki, H., Carninci, P., Hayashizaki, Y., FANTOM consortium, Kokudo, N., Forrest, A. and Kojima, S.* “Transcriptome analysis uncovers a growth-promoting activity of orosomucoid-1 on hepatocytes” EBioMedicine 24, 257-266 (2017). DOI
    40. Tomita, S.*, Saito, K., Nakamura, T., Sekiyama, Y. and Kikuchi, J. “Rapid discrimination of strain-dependent fermentation characteristics among Lactobacillus strains by NMR-based metabolomics of fermented vegetable juice” PLoS One 12, e0182229 (2017). DOI
    41. Mekuchi, M., Sakata, K., Yamaguchi, T., Koiso, M. and Kikuchi, J.* “Trans-omics approaches represented used to characterize fish nutritional biorhythms in Leopard coral groupers (Plectropomus leopardus)” Sci. Rep7, 9372 (2017). DOI
    42. Tsutsui, S., Date, Y. and Kikuchi, J.* “Visualizing individual and region-specific microbial-metabolite relations by important variable selection using machine learning approach” J. Computer Aided Chem. 18, 31-41 (2017). DOI
    43. Teramura, H., Sasaki, K., Kawaguchi, H., Matsuda, F., Kikuchi, J., Shirai, T., Sazuka, T., Yamasaki, M., Takumi, S. Ogino, C. and Kondo, A.* “Differences in glucose yield of residues from among varieties of rice, wheat, and sorghum after dilute acid pretreatment” Biosci. Biotechnol. Biochem 81, 1650-1656 (2017). DOI
    44. Sekiyama, S.*, Okazaki, K., Kikuchi, J. and Ikeda, S. “NMR-based metabolic profiling of field-grown leaves from sugar beet plants harboring different levels of resistance to Cercospora leaf spot disease” Metabolites 7, 4-13 (2017). DOI
    45. Tomita, S., Ikeda, S., Tsuda, S., Someya, N., Asano, K., Kikuchi, J., Chikayama, E., Ono, H. and Sekiyama, Y.* “A survey of metabolic changes in potato leaves by non-targeted, NMR-based metabolic profiling in relation to resistance to late blight disease under field conditions “ Magn. Reson. Chem. 55, 120-127 (2017). DOI
    46. Kikuchi, J.* and Yamada, S. “NMR window of molecular complexity showing homeostasis in superorganisms” Analyst 142, 4161-4172 (2017). DOI
    47. Kikuchi, J.* “NMR analysis of molecular complexity” Experimental approaches of NMR spectroscopy –Methodology and application for life science and material science- 461-489 (2017). DOI
    48. Kikuchi, J.* and Komatsu, T. “Polysaccharides as major carbon sources in environmental biodiversity” NMR in Glycoscience and Glycotechnology 369-395 (2017). DOI
    49. Katahira, S., Muramoto, N., Moriya, S., Nagura, R., Tada, N, Yasutani, N., Ohkuma, M., Onishi, T. and Tokuhiro, K.* “Profiling physicochemical and planktonic features from discretely/continuously sampled surface water Screening and evolution of a novel protist xylose isomerase from the termite Reticulitermes speratus for efficient xylose fermentation in Saccharomyces cerevisiae Biotechnol. Biofuels 10, 203 (2017). DOI
    50. Otagiri, M., Khalid, A., Moriya, S., Osada, H. and Takahashi, S.* “Novel squalene-producing thraustochytrids found in mangrove water” Biosci. Bioeng. Biochem81, 2034-2037 (2017). DOI



    51. Chikayama, E.*, Yamashina, R., Komatsu, K., Tsuboi, Y., Sakata, K., Kikuchi, J. and Sekiyama, Y. “FoodPro: a web-based tool for evaluating covariance and correlation NMR spectra associated with food processes”  Metabolites 6, 36 (2016). DOI
    52. Okubo-Kurihara, E., Ohtani, M., Kurihara, Y., Kakegawa, K., Kobayashi, M., Nagata, N., Komatsu, T., Kikuchi, J., Cutler, S., Demura, T. and Matsui, M.* “Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium” Sci. Rep. 6, 34602 (2016). DOI
    53. Vergara, F.* Shino, A. and Kikuchi, J.* “Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae –A 2D NMR Metabolomics Study” Int. J. Mol. Sci. 17, 1470 (2016). DOI
    54. Sasaki, K., Okamoto, M., Shirai, T., Tsuge, Y., Fujino, A., Sasaki, D., Morita, M., Matsuda, F., Kikuchi, J. and Kondo, A.* “Toward the complete utilization of rice straw: Methane fermentation and lignin recovery by a combinational process involving mechanical milling, supporting material, and nanofiltration” Bioresource. Technol. 216, 830-837 (2016). DOI
    55. Misawa, T., Wei, F. and Kikuchi, J.* “Application of two-dimensional nuclear magnetic resonance for signal enhancement by spectral integration using a large dataset of metabolic mixtures” Anal. Chem88, 6130-6134 (2016). DOI
    56. Ogura, T., Date, Y., Masukujane, M., Coetzee, T., Akashi, K. and Kikuchi, J.* “Improvement of physical, chemical, and biological properties of aridisol from Botswana by incorporation of torrefied biomass” Sci. Rep6, 28011 (2016). DOI
    57. Vergara, F.* Kikuchi, J. Breuer, C. “Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0” Sci. Rep6, 26515 (2016). DOI
    58. Chikayama, E., Shimbo, Y., Komatsu, K. and Kikuchi, J.* “The effect of molecular conformation on the accuracy of theoretical 1H and 13C chemical shifts calculated by ab initio methods for metabolic mixture analysis” J. Phys. Chem. 120, 3479-3487 (2016). DOI
    59. Komatsu, T., Ohishi, R., Shino, A. and Kikuchi, J.* “Structure and metabolic flow analysis of molecular complexity in 13C-labeled tree by 2D and 3D-NMR” Angew. Chem. Int. Ed. 55, 6000-6003  (2016). DOI
    60. Shiokawa, Y., Misawa, T., Date, Y. and Kikuchi, J.* “Application of Maket Basket Analysis for Visualization of Transaction Data based on Human Lifestyle and Spectroscopic Measurements” Anal. Chem88, 2714-2719 (2016). DOI
    61. Ito, K., Tsutsumi, Y., Date, Y. and Kikuchi, J.* “Fragment Assembly Approach Based on Graph/Network Theory with Quantum Chemistry Verifications for Assigning Multidimensional NMR Signals in Metabolite Mixtures” ACS Chem. Biol. 11, 1030-1038 (2016). DOI
    62. Kikuchi, J.* Tsuboi, Y., Komatsu, K., Gomi, M., Chikayama, E. and Date, Y. “SpinCouple: Development of web-tool for analyzing metabolite mixtures via 2D-J resolved NMR spectra” Anal. Chem. 88, 659-666 (2016). DOI
    63. Misawa, T., Komatsu, T., Date, Y. and Kikuchi, J.* “SENSI: Signal ENhancement by Spectral Integration for Analysis of Metabolic Mixtures” Chem. Commun. 52, 2964-2967 (2016). DOI
    64. Ogura, T., Hoshino, R., Date, Y. and Kikuchi, J.* “Visualization of microfloral metabolism for marine waste recycling” Metabolites 6, 7 (2016). DOI
    65. Teramura, H., Sasaki, K., Oshima, T., Aikawa, S., Matsuda, F., Okamoto, M., Shirai, T., Kawaguchi, H., Ogino, C., Hirano, K., Sazuka, T., Kitano, H., Kikuchi, J. and Kondo, A.* “Organosolv pretreatment of sorghum bagasse using a low concentration of hydrophobic solvents such as 1-butanol or 1-pentanol” Biotech. Biofuels 9, 27 (2016). DOI
    66. 菊地淳 “食材とヒトの恒常性評価” フードケミカル 12, 53-57 (2016).
    67. 菊地淳 “メタボノミクスによる腸内微生物代謝と恒常性評価” FOOD STYLE21 20, 37-40 (2016).
    68. 菊地淳 “代謝混合物複雑系の非分離構造解析” 化学 71, 35-39 (2016).
    69. 菊地淳 “微生物群集およびヒト超有機体のメタボノミクス” ヒトマイクロバイオーム研究の最前線 エヌティーエス出版 69-79 (2016).



    70. Motegi, H., Tsuboi, Y., Saga, A., Kagami, T., Inoue, M., Toki, H., Minowa, O., Noda, T. and Kikuchi, J.* “Identification of reliable components in multivariate curve resolution-alternating least squares (MCR-ALS) for a data-driven approach across metabolic processes” Sci. Rep. 5, 15710 (2015). DOI
    71. Sugahara, H.*, Odamaki, T., Xiao J.Z., Abe, F., Kato, T., Kikuchi, J., Fukuda, S. and Ohno, H. “Bifidobacterium longum BB536 induces gut luminal metabolic changes through modulation of microbial community” Sci. Rep. 5, 13548 (2015). DOI
    72. Komatsu, T., Kobayashi, T., Hatanaka, M. and Kikuchi, J.* “Profiling planktonic biomass using element-specific, multicomponent nuclear magnetic resonance spectroscopy” Environ. Sci. Technol. 49, 7056-7062 (2015). DOI
    73. Radhika, V., Ueda, N., Tsuboi, Y., Kojima, M., Kikuchi, J., Kudo, T. and Sakakibara, H.* “Methylated cytokinins from phytopathogen Rhodococcus fascians mimic plant hormone activity” Plant Physiol169, 1118-1126 (2015). DOI
    74. Ogura, T., Date, Y., Tsuboi, Y. and Kikuchi, J.* “Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan” ACS Chem. Biol. 10, 1908-1915 (2015). DOI
    75. Sasaki, K., Okamoto, M., Shirai, T., Tsuge, Y., Teramura, H., Sasaki, D., Kawaguchi, H., Hasunuma, T., Ogino, C., Matsuda, F., Kikuchi, J. and Kondo, A.* “Precipitate obtained following membrane separation of hydrothermally pretreated rice straw liquid revealed by 2D NMR to have high lignin content” Biotech. Biofuels 8, 88 (2015). DOI
    76. Teramura, H., Sasaki, K., Oshima, T., Aikawa, S., Matsuda, F., Kawaguchi, H., Ogino, C., Yamazaki, M., Shirai, T., Okamoto, M., Kikuchi, J. and Kondo, A.* “Changes in lignin and polysaccharide components in 13 cultivars of rice straw following dilute acid pretreatment as studied by solution-state 2D 1H-13C NMR” PLoS ONE. 10, e0128417 (2015). DOI
    77. Mori, T., Tsuboi, Y., Ishida, N., Nishikubo, N., Demura, T. and Kikuchi, J.*  “Multidimensional high-resolution magic angle spinning and solution-state NMR characterization of 13C-labeled plant metabolites and lignocellulose” Sci. Rep. 5, 11848 (2015). DOI
    78. Tsuji, Y., Vanholme, R., Tobimatsu, Y., Ishikawa, Y., Foster, C. E., Kamimura, N., Hishiyama, S., Hashimoto, S., Shino, A., Hara, H., Sato-Izawa, K., Oyarce, P., Goeminne, G., Morreel, K., Kikuchi, J., Takano, T., Fukuda, M., Katayama, Y., Boerjan, W., Ralph, J., Masai, E. and Kajita, S.* “Introduction of chemically labile substructures in Arabidopsis lignin through the use of the Ca dehydrogenase from Sphingobium sp. Strain SYK-6” Plant Biotechnol. J. 13, 821-832 (2015). DOI
    79. Wei, F., Ito, K., Sakata, K., Date, Y. and Kikuchi, J.* “Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity” Anal. Chem. 87, 2819-2826 (2015). DOI
    80. Misawa, T., Date, Y. and Kikuchi, J.* “Human metabolic, mineral and microbiota fluctuations across daily nutritional intakes visualized by data-driven approach” J. Proteome Res. 14, 1526-1534 (2015). DOI
    81. Hsieh, C.-Y., Osaka, T., Moriyama, E., Date, Y., Kikuchi, J. and Tsuneda, S.* “Srengthening of the intestinal epithelial tight junction by Bifidobacterium bifidum” Physiol. Rep. 3, e12327 (2015). DOI
    82. Watanabe, M.*, Ohta, Y., Sun, L., Motoyama, N. and Kikuchi, J. “Profiling contents of water-soluble metabolites and mineral nutrients to evaluate the effects of pesticides and organic and chemical fertilizers on tomato fruit quality” Food. Chem. 169, 387-395 (2015). DOI
    83. Tomita, S., Nemoto, T., Matsuo, Y., Shoji, T., Tanaka, F., Ono, H., Kikuchi, J., Ohnishi-Kameyama, M. and Sekiyama, S.* “A NMR-based, non-targeted multistep metabolic profiling revealed L-rhamnitol as a metabolite that characterised apples from different geographic origins” Food Chem. 174, 163-172 (2015). DOI
    84. 菊地淳 “セルロース系材料の構造多型性解析” セルロースナノファイバーの調製、分散・複合化と製品応用 377-389 (2015).



    85. Ito, K., Sakata, K., Date, Y. and Kikuchi, J.* “Integrated analysis of seaweed components in seasonal fluctuation by data mining across heterogeneous chemical measurements with network visualization” Anal. Chem. 86, 1098-1105 (2014). DOI
    86. Date, Y., Nakanishi, Y., Fukuda, S. Nuijima, Y., Kato, T., Umehara, M., Ohno, H., and Kikuchi, J.* “In vitro evaluation method for screening of candidate prebiotic foods” Food Chem. 152, 251-260 (2014). DOI
    87. Yang, Z., Nakabayashi, R., Okazaki, Y., Mori, T., Takamatsu, S., Torizuka, K., Kitanaka, S., Kikuchi, J., Saito, K.* “Toward better annotation in plant metabolomics: Isolation and structure elucidation of 36 specialized metabolites from Oryza sativa by using MS/MS and NMR analyses” Metabolomics 10, 543-555 (2014). DOI
    88. Yamazawa, A., Iikura, T., Morioka, Y., Shino, A., Ogata, Y., Date, Y. and Kikuchi, J.* “Cellulose digestion and metabolisms induced biocatalytic transitions in anaerobic microbial ecosystems” Metabolites. 4, 36-52 (2014). DOI
    89. Asakura, T., Date, Y. and Kikuchi, J.* “Comparative analysis of chemical and microbial profiles in estuarine sediments sampled from Kanto and Tohoku regions in Japan” Anal. Chem. 86, 5425-5432 (2014). DOI
    90. Tokuda, T., Tsuboi, Y., Kihara, K. Saito, S. Moriya, S. Lo, N. and Kikuchi, J.* “Metabolomic profiling of 13C-cellulose digestion in a lower termite: insights into symbiont function” Proc. Royal Soc. B. 281, 20140990 (2014). DOI
    91. Kato, T., Fukuda, S., Fujiwara, A., Suda, W., Hattori, M., Kikuchi, J. and Ohno, H.* “Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation” DNA Res. 21, 469-480 (2014). DOI
    92. Watanabe, T., Shino, A., Akashi, K. and Kikuchi, J.* “Chemical profiling of Jatropha tissues under different torrefaction conditions: application to biomass waste recovery” PLoS ONE 9, e106893 (2014). DOI
    93. Asakura, T., Sakata, K., Yoshida, S., Date, Y. and Kikuchi, J.* “Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches” PeerJ. 2, e556 (2014). DOI
    94. Yoshida, S., Date, Y. and Kikuchi, J.* “Comparative metabolomic and ionomic approach for abundant fishes in estuarine environments of Japan” Sci. Rep. 4, 7005 (2014). DOI
    95. Ogawa, D., Moriya, S., Tsuboi, Y., Date, Y., Prieto, A., Bapista, G., Yamane, T. and Kikuchi, J.* “Biogeochemical typing of paddy field by a data-driven approach revelling sub-systems within a complex environment –A pipeline to filtrate, organize and frame massive dataset from multi- omics analyses” PLoS ONE 9, e110723 (2014). DOI
    96. Komatsu, T., Oishi, R., Shino, A. Akashi, K and Kikuchi, J.* “Multi-spectroscopic analysis of seed quality and 13C-stable-isotopologue monitoring in initial growth metabolism of Jatropha curcas L. using stable-isotope labeling” Metabolites 4, 1018-1033 (2014). DOI
    97. Tsukagoshi, H., Nakamura, A., Ishida, T., Touhara, K. K., Otagiri, M., Moriya, S., Samejima, M., Igarashi, K., Fushinobu, S., Kitamoro, K., and Arioka, M. “Structural and Biochemical Analyses of Glycoside Hydrolase Family 26 beta-Mannanase from a Symbiotic Protist of the Termite Reticulitermes speratus” J. Biol. Chem. 289, 10843-52 (2014). DOI
    98. Kudo T., Sakamoto K., Akinaga M., Kawauchi A., Nakahara T., Zhang X., Yamada A., Oshima K., Suda W., Kuwahara H., Nakamura N., Nogi Y., Kitamura K., Yuki M., Iida T., Moriya S., Inoue T., Hongoh Y., Hattori M., Ohkuma M. “Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047” Genome Annoucements 2, e00211-14 (2014). DOI
    99. Kudo T., Kidera A., Kida M., Kawauchi A., Shimizu R., Nakahara T., Zhang X., Yamada A., Amano M., Hamada Y., Taniyama S., Arakawa O., Yoshida A., Oshima K., Suda W., Kuwahara H., Nogi Y., Kitamura K., Yuki M., Iida T., Moriya S., Inoue T., Hongoh Y., Hattori M., Ohkuma M. “Draft genome sequences of Psychrobacter strains JCM 18900,JCM 18901, JCM 18902, and JCM 18903, isolated preferentially from frozen aquatic organisms” Genome Annoucements 2, e00280-14 (2014). DOI
    100. Tsukagoshi H, Nakamura A, Ishida T, Otagiri M, Moriya S, Samejima M, Igarashi K, Kitamoto K, Arioka M. “The GH26 β-mannanase RsMan26H from a symbiotic protist of the termite Reticulitermes speratus is an endo-processive mannobiohydrolase: heterologous expression and characterization” Biochem Biophys Res Commun. 452, 520-5 (2014). DOI
    101. 菊地淳 “安定同位体標識による生体分子混合物ならびに代謝経路解析” 生物工学会誌 92, 100-109 (2014).
    102. 菊地淳 “食と代謝のメタボノミクス” 実験医学 32, 699-705 (2014).
    103. 菊地淳 “食の来た道還る道” バイオインダストリー (in press).
    104. 小松功典、菊地淳 “複雑系高分子群に挑むバイオマスNMRの世界” 細胞工学 33, 843-849 (2014).
    105. 三澤拓真、伊藤研悟、菊地淳 “NMRで挑む複雑系の分子宇宙” 生物工学会誌  92, 504-510 (2014).
    106. 菊地淳 “分子複雑系” NMR 5, 75-82 (2014).
    107. 菊地淳 “NMRにおけるイノベーション” 生物工学会誌 92, 561 (2014).



    108. Furusawa, Y., Obata, Y., Fukuda, S.*, Endo, T., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., Takahashi, M., Fukuda, N., Murakami, S., Miyauchi, E., Hino, S., Atarashi, K., Onawa, S., Fujimura, Y., Lockett, T., Clarke, J. M., Topping, D. L., Tomita, M., Hori, S., Ohara, O., Morita, T., Koseki, H., Kikuchi, J., Honda, K., Hase, K.* and Ohno, H.* “Commensal microbe-derived butyrate induces colonic regulatory T cells” Nature 504, 446-450 (2013). DOI
    109. Komatsu, T. and Kikuchi, J.* “Comprehensive signal assignment of 13C-labeled lignocellulose using multidimensional solution NMR and 13C chemical shift comparison with solid-state NMR” Anal.Chem. 85, 8857-8865 (2013). DOI
    110. Yamazawa, A., Date, Y., Ito, K. and Kikuchi, J.* “Visualizing microbial dechlorination processes in underground ecosystem by statistical correlation and network analysis approach” J. Biosci. Bioeng. 117, 305-309 (2014). DOI
    111. Komatsu, T. and Kikuchi, J.* “Selective signal detection in solid-state NMR using rotor synchronized dipolar dephasing for the analysis of hemicellulose in lignocellulosic biomass” J. Phys. Chem.Lett. 4, 2279-2283 (2013). DOI
    112. Ogura, T., Date, Y. and Kikuchi, J.* “Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota” PLoS ONE 8, e66919 (2013). DOI
    113. Yamazawa, A., Iikura, T., Shino, A., Date, Y., and Kikuchi, J.* “Solid, solution and gas-state NMR monitoring of 13C-cellulose degradation in an anaerobic microbial ecosystem” Molecules. 18, 9021-9033 (2013). DOI
    114. Yamamura, M., Noda, S., Hattori, T., Shino, A., Kikuchi, J., Takabe, K., Tagane, S., Gau, M., Uwatoko, N., Mii, M., Suzuki, S., Shibata, D. and Umezawa, T.* “Characterization of lignocellulose of Erianthus arundinaceus in relation to enzymatic saccharification efficiency” Plant Biotechnol. 30, 25-35 (2013). DOI
    115. Guichard P., Hachet V., Majubu N., Neves A., Demurtas D., Olieric N., Fluckiger I., Yamada A., Kihara K., Nishida Y., Moriya S., Steinmentz M.O., Hongoh Y., Gönczy P.* “Native architecture of the centriole proximal region reveals novel features underlying their 9-fold radial symmetry” Curr. Biol. 23, 1620-1628 (2013). DOI
    116. Otagiri M, Lopez CM, Kitamoto K, Arioka M, Kudo T, Moriya S. “Heterologous expression and characterization of a glycoside hydrolase family 45 endo-β-1,4-glucanase from a symbiotic protist of the lower termite, Reticulitermes speratus” Appl Biochem Biotechnol. 169, 1910-1918 (2013). DOI
    117. 菊地淳 “糖質の分析 核磁気共鳴法” 植物細胞壁 -基礎と応用― 講談社 (2013).



    118. Date, Y., Iikura, T., Yamazawa, A., Moriya, S. and Kikuchi, J.* “Metabolic sequences of anaerobic fermentation on glucose-based feeding substrates based on correlation analyses of microbial and metabolite profiling” J. Proteome Res. 11, 5602-5610 (2012). DOI
    119. 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). DOI
    120. Okushita, K., Chikayama, E. and Kikuchi, J.* “Solubilization mechanism and characterization of the structural change of bacterial cellulose in regenerated states through ionic liquid treatment” Biomacromolecules. 13, 1323-1330 (2012). DOI
    121. 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 shifts” Carbohydr. Polymers. 90, 1197-1203 (2012). DOI
    122. Date, Y., Sakata, K. and Kikuchi, J.* “Chemical profiling of complex biochemical mixtures from various seaweeds” Polymer J. 44, 888-894 (2012). DOI
    123. 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. 44, 895-900 (2012). DOI
    124. Tominaga, T., Sano, K., Kikuchi, J., Mitomo, H., Ijiro, K. and Osada, H. “Hydrophilic Double-Network Polymers that Sustain High Mechanical Modulus under 80% Humidity” ACS Macro Lett. 1, 432-436 (2012). DOI
    125. 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). DOI
    126. 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). DOI
    127. Watanabe, T., Shino, A., Akashi, K. and Kikuchi, J.* “Spectroscopic investigation of tissue-specific biomass profiling of Jatropha curcas. L” Plant Biotechnol. 29, 163-170 (2012). DOI
    128. 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. 29, 131-135 (2012). DOI
    129. Vergara, F., Everroad, R. C., Andraca, G., Kikuchi, J. and Makihara, H. “Plant host differences between Cossus redtenbacheri and Cossus insularis: insights from mechanical tests and molecular phylogeny” Bull. Insect. 65, 217-222 (2012).
    130. 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).
    131. 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).
    132. 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24年7月10日.



    133. 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 animals” Anal. Chem. 83, 719-726 (2011). DOI
    134. 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 can protect from enteropathogenic infection through production of acetate” Nature. 469, 543-547 (2011). DOI
    135. Nakanishi, Y., Fukuda, S., Chikayama, E. Kimura, Y., Ohno, H. and Kikuchi, J.* “Dynamic omics approach identifies nutrition-mediated microbial interactions” J. Proteome Res. 10, 824-831 (2011). DOI
    136. Takase, T., Ishikawa, H., Murakami, H., Kikuchi, J., Sato-Nara, K.* and Suzuki, H. “The Circadian Clock Modulates Water Dynamics and Aquaporin Expression in Arabidopsis Roots” Plant Cell Physiol. 52, 373-383 (2011). DOI
    137. 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). DOI
    138. 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). DOI
    139. 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 cerevisiae” Biosci Biotechnol Biochem. 75, 2260-2263 (2011). DOI
    140. 菊地淳、葭田征二、坪井裕理、伊達康博 “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 (2011).
    141. 篠阿弥宇、近山英輔、菊地淳 “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 (2011).
    142. 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” 2011年7月15日.



    143. 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). DOI
    144. 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). DOI
    145. 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). DOI
    146. 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). DOI
    147. 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 5, e8636 (2010). DOI
    148. 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 speratus” Appl Biochem Biotechnol. 160,1168-78 (2010). DOI
    149. 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). DOI
    150. 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).
    151. 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).
    152. 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).
    153. 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).
    154. 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).



    155. 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). DOI
    156. 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). DOI
    157. 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). DOI
    158. 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). DOI
    159. 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).



    160. 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). DOI
    161. 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).
    162. 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). DOI
    163. 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. 25, 401-6 (2008). DOI
    164. 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. 54, 343-351 (2008). DOI
    165. 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).
    166. 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).
    167. 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.



    168. Sekiyama, Y and Kikuchi, J.* “Towards dynamic metabolic network measurement by multi-dimensional NMR-based fluxomics” Phytochemistry 68, 2320-2329 (2007). DOI
    169. 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). DOI
    170. 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). DOI
    171. 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). DOI
    172. Moriya S, Noda S, Ohkuma M, Kudo T.* “In situ hybridization of termite microbes” Methods Mol Biol. 2007 353,105-12 (2007). DOI
    173. 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 speratus” FEMS Microbiol Ecol. 59, 592-9 (2007). DOI
    174. 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)
    175. 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)
    176. 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).
    177. 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).
    178. 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.