実績

 研究実績

2024

  1. Ito, K., Miyamoto, H.*, Matsuura, M., Ishii, C., Nakanishi, Y., Suda, W., Satoh, T., Honda, F., Kurotani, A., Tsuji, N., Nakaguma, T., Shindo, C., Ito, T., Michibata, R., Yamada, R., Takahashi, Y., Kodama, H., Kikuchi, J.* and Ohno, H.* “A thermoprotective probiotic function by thermostable lactic acid bacteria and its causal structure” Journal of Functional Foods 113, 106001 (2024).
  2. Kurotani, A., Miyamoto, H. and Kikuchi, J. “Validation of causal inference data using DirectLiNGAM in an environmental small-scale model and calculation setting” MethodsX 12, 102508 (2024).
  3. Okada, M., Amamoto, Y., Kikuchi, J.* “Designing Sustainable Hydrophilic Interfaces via Feature Selection from Molecular Descriptors and Time-Domain Nuclear Magnetic Resonance Relaxation Curves” Polymers 16, 824 (2024).
  4. Yokoyama, D., Tsuboi, Y., Nagahata, R., Konno, H., Yoshida, M., Abe, T. and Kikuchi, J.* “Quantification of microbial community assembly processes during degradation on diverse plastispheres based on physicochemical characters and phylogenetic bin-based null model analysis” Sci. Total Environ. (in press).
  5. Miyamoto, H.*, Suda, W.*, Kodama, H., Takahashi, H., Nakanishi, Y., Moriya, S., Adachi, K., Kiriyama, N., Wada, M., Sudo, D., Ito, S., Shibata, M., Wada, S., Murano, T., Taguchi, H., Shindo, C., Tsuboi, A., Tsuji, N., Matsuura, M., Ishii, C., Nakaguma, T., Ito, T., Okada, T., Matsushidata, T., Sato, T., Kato, T., Inabu, T., Tashiro, T., Mori, K., Ido, A., Miura, T., Morita, H., Fukuda, S., Suzuki, K., Nishiuchi, T., Kurotani, A., Shima, H., Wada, S., Masuya, H., Kikuchi, J., Miyamoto, H., Hattori, M., Yamamoto, N. and Ohno, H. ” A cross-animal species protective biochemical symbiotic structure between gut inhabitant mesophiles and compost-derived thermophiles” Communications Biology (revised).
  6. Takeuchi, M., Fujiwara-Nagata, E., Kuroda, K., Sakata, K., Narihiro, T.* and Kikuchi, J.* “Fecal metagenomic and metabolomic analyses reveal biomarkers of Flavobacterium psychrophilum infection in ayu (Plecoglossus altivelis)” mSphere (revised).
  7. Taguchi, Y., Kurotani, A., Miyamoto, H.*, Kato, T., Tsuji, N., Matsuura, M., Etoh, T., Shiotsuka, Y., Fujino, R., Kikuchi, J., Ohno, H. and Takahashi, H.* “Statistical causal estimation of maternal-offspring gut commensal bacterial associations under livestock grazing management” Computational and Structural Biology Journal (revised) .
  8. Bashir, K., Rasheed, S., Matsui, A., Kim, J.-M., Tanaka, M., Kobayashi, M., Kusano, M., Saito, K., Tsuboi, Y., Kikuchi, J. and Seki, M.* “Exogenous acetic acid treatment reprograms transcriptome and metabolome and triggers gluconeogenesis in Arabidopsis thaliana” Plant Mol. Biol. (under review).
  9. Shima, H., Asakura, T., Sakata, K., Koiso, M and Kikuchi, J*. “Feed components and timing to improve feed conversion ratio for sustainable aquaculture using starch” Sci. Rep. (submitted).
  10. Iseri, N., Hao, A.*, Wang, Y., Mi, Q., Park, H.-D., Chen, J., Kikuchi, J., Zhao, M. and Kobayashi, S.* “Pulverization of cyanobacteria by impinging jet to increase edibility to zooplankton and facilitate trophic transfer in a eutrophic lake” Environ. Poll. (submitted).
  11. Bei, K., Wang, Y., Yang, D., Shao, Q., Xheng, X., Zhao, M., Chou, I.-M., Kikuchi, J. and Pan, Z. “Prediction of basic physical property parameters of CO2 geological storage based on machine learning” TBA.
  12. Miyamoto, H.*, Wada, S., Kurotani, A., Sato, T., Nishiuchi, T., Shindo, C., Tsuji, N., Ishii, C., Matsuura, M., Nakaguma, T., Shibata, M., Wada, S., Udagawa, M., Mori, K., Kikuchi, J., Kodama, H., Miyamoto, H., Hattori, M., Ohno, H.* and Yamamoto, N.* “Dual modulation of gut commensal bacterial structure and viral infectivity by compost-derived thermophile” TBA.
  13. Miyauchi, E., Yamazaki, K., Tsuboi, Y., Nakajima, T., Ono, S., Mizuno, K., Takahashi, N., Imamura, K., Morita, H., Miura, N., Okuda, S., Kikuchi, J., Sasaki, N., Ohno, H. and Yamazaki, K.* “Dysbiosis of gut microbiome is relevant to oral microbiome profiles in patients with periodontitis ” TBA.
  14. Kikuchi, J.* “NMR data science” Experimental approaches of NMR spectroscopy –Methodology and application for life science and material science-  2nd Edition (in press).
  15. 菊地淳　”環境データサイエンスによるDX・GX”　アグリバイオ　8, 7-8 (2024).

2023

  1. Yokoyama, D.* and Kikuchi, J. “Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water” Environmental Research 231, 116202 (2023).
  2. Kudo, H.*., Han, N., Yokoyama, D., Matsumoto, T., Chien, M.-F., Kikuchi, J. and Inoue, C. “Bayesian network highlights the contributing factors for efficient arsenic phytoextraction by Pteris vittata in a contaminated field” Sci. Total Environ. 899, 165654 (2023).
  3. Yamada, S., Tsuboi, Y., Yokoyama, D. and Kikuchi, J.* “Polymer composition optimization approach based on feature extraction of bound and free water using time-domain NMR” Journal of Magnetic Resonance 351, 107438 (2023).
  4. Miyamoto, H.*, Kawachi, N., Kurotani, A., Suda, W., Moriya, S., Suzuki, K., Matsuura, M., Tsuji, N., Nakaguma, T., Ishii, T., Tsuboi, A., Shindo, C., Kato, T., Udagawa, M., Wada, S., Masuya, H., Miyamoto, H., Ohno, H. and Kikuchi, J.* “Computational estimation of symbiotic sediment bacterial structures of seagrasses overgrowing downstream of onshore aquaculture” Environmental Research 219, 115130 (2023).
  5. Yokoyama, D., Takamura, A., Tsuboi, Y. and Kikuchi, J.* “Large-scale Omics Dataset of Polymer Degradation Provides Robust Interpretation for Microbial Niche and Succession on Different Plastisphere” ISME Communications 3, 67 (2023).
  6. Shima, H., Sakata, K. and Kikuchi, J.* “Prediction of influence transmission by water temperature of fish intramuscular metabolites and intestinal microbiota factor cascade using Bayesian networks” Applied Sciences 13, 3198 (2023). 
  7. Miyamoto, H.*, Shigeta, K., Suda, W., Ichihashi, Y., Nihei, N., Matsuura, M., Tsuboi, A., Tominaga, N., Aono, M., Sato, M., Taguchi, S., Shindo, C., Ito, T., Kato, T., Kurotani, A., Shima, H., Moriya, S., Wada, S., Horiuchi, S., Sato, T., Mori, K., Miyamoto, H., Kodama, H., Hattori, M., Ohno, H., Kikuchi, J.* and Hirai, M.* “An agroecological structure model of compost-soil-plant interactions for sustainable organic farming” ISME Communications 3, 28 (2023).
  8. Rungreungthanapol, T., Homma, C., Akagi, K., Tanaka, M., Kikuchi, J., Tomizawa, H., Sugizaki, Y., Isobayashi, A.,  Hayamizu, Y. and  Okochi, M.* “Volatile organic compound detection by graphene field-effect transistors functionalized with fly olfactory receptor mimetic peptides” Anal. Chem. 95, 4556-4563 (2023).
  9. Okada, S., Inabu, Y., Miyamoto, H.*, Suzuki, K., Kato, T., Kurotani, A., Fujino, R., Shiotsuka, Y., Eto, T., Tsuji, N., Matsuura, M., Tsuboi, A., Saito, A., Masuya, H., Kikuchi, J., Ohno, H.* and Takahashi, H.* “Estimation of silent phenotypes of calf antibiotic dysbiosis” Sci. Rep. (in press).
  10. Miyamoto, H. and Kikuchi, J.* “An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach” Computational and Structural Biotechnology Journal 21, 869-878 (2023).
  11. 菊地淳　”AIによるNMRデータ予測とプロセスインフォマティクスへの活用”　ケモインフォマティクスにおけるデータ解析の進め方と具体的応用法　9 (4) 641-649 (2023).
  12. 菊地淳、岡田真幸　”時間領域および固体NMRとプロセスインフォマティクス”　実験の自動化・自律化によるR&Dの効率化と運用方法　ーAI、ロボット技術、ChatGPT、MI、ベイズ最適化、秘密計算などー　6, 440-446 (2023).

2022

  1. Hara, K., Yamada, S., Kurotani, A., Chikayama, E. and Kikuchi, J.* “Materials informatics approach using domain modelling for exploring structure-property relationships of polymers” Sci. Rep. 12, 10558 (2022). DOI
  2. Shima, H., Murata, I., Wei, F., Sakata, K. and Kikuchi, J.* “Identification of salmoniformes aquaculture conditions to increase the creatine and anserine levels using multiomics dataset and nonnumerical information” Frontiers in Microbiology 13, 991819 (2022).
  3. Yokoyama, D., Suzuki, S., Asakura, T. and Kikuchi, J.*  “Chemometric analysis of NMR spectra and machine learning to investigate membrane fouling”  ACS Omega 7, 12654-12660 (2022). DOI
  4. Hara, K., Yamada, S., Chikayama, E. and Kikuchi, J.* “Parameter Visualization of Benchtop Nuclear Magnetic Resonance Spectra Toward Food Process Monitoring” Processes 10, 1264 (2022). DOI
  5. Miyamoto, H.*, Asano, F., Ishizawa, K., Suda, W., Miyamoto, H., Tsuji, N., Matsuura, M., Tsuboi, A., Ishii, C., Nakaguma, T., Shindo, C., Kato, T., Kurotani, A., Shima, H., Moriya, S., Hattori, M., Kodama, H., Ohno, H. and Kikuchi, J.* “A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae” Sci. Total Environ. 836, 155520 (2022). DOI
  6. Yokoyama, D., Suzuki, S., Asakura, T. and Kikuchi, J.*  “Microbiome and metabolome analyses in different closed-circulation aquarium systems and their network visualization”  ACS Omega  7, 30399-30404 (2022).
  7. Shono, N., Ito, M, Umezawa, A., Sakata, K., Li, A., Kikuchi, J., Ito, K. and Nakamura, R.* “Tracing and Regulating Redox Homeostasis of Model Benthic Ecosystems for Sustainable Aquaculture in Coastal Environments” Frontiers in Microbiology 13, 907733 (2022).
  8. Shima, H., Sato, Y., Sakata, K., Asakura, T., Kikuchi, J.* “Identifying correlation among qualitative non-numeric parameters in natural fish microbe dataset using machine learning” App. Sci. 12, 5927 (2022). DOI
  9. 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. Meth. Appl. Sci. 45, 9769-9786 (2022). DOI
  10. Matsui, A., Todaka, D., Tanaka, M., Mizunashi, K., Takahashi, S., Sunaoshi, Y., Tsuboi, Y., Ishida, J., Bashir, K., Kikuchi, J., Kusano, M., Kobayashi, M., Kawaura, K. and Seki, M. “Ethanol induces heat tolerance in plants by stimulating endoplasmic reticulum-mediated stress responses” Plant Mol. Biol. 110, 131-145 (2022). DOI
  11. Avellán-Llaguno, R. D., Zhang, X., Zhao, P., Kikuchi, J., Dong, S. and Huang, Q.* “Differential aggregation of polystyrene and titanium dioxide nanoparticles under various salinity conditions and against multiple proteins types” Environ. Sci. Pol. Res. 29, 74173-74184 (2022). DOI
  12. Ito, K., Miyamoto, H.*, Matsuura, M., Ishii, C., Tsuboi, A., Tsuji, N., Nakaguma, T., Nakanishi, Y., Kato, T., Suda, W., Honda, F., Ito, T., Moriya, S., Shima, H., Michibata, R., Yamada, R., Takahashi, Y., Koga, H., Kodama, H., Watanabe, Y., Kikuchi, J. and Ohno, H. “Noninvasive fecal metabolic profiling for the evaluation of probiotic characteristics of thermostable lactic acid bacteria, Weizmannia coagulans SANK70258, for broiler chickens” J. Biocsci. Bioeng. 134, 105-115 (2022).
  13. Nakano, Y., Endo, H., Hori, C., Ihara, A., Matsumoto, T., Kikuchi, J., Ohtani, M.* and Demura, M. “Enhancement of secondary cell wall formation in poplar xylem using a self-reinforced system of secondary cell wall-related transcription factors ” Front. Plant Sci. 13, 819360 (2022). DOI
  14. Liu, H., Dai, C., Yu, H., Guo, Q., Li, J., Hao, A., Kikuchi, J. and Zhao, M.* “Dynamics of a stochastic non-autonomous phytoplankton-zooplankton system involving toxin-producing phytoplankton and impulsive perturbations” Mathematics and Computers in Simulation 203, 368-386 (2022). DOI
  15. Sildever, S., Nishi, N., Inaba, N., Asakura, T., Kikuchi, J., Asano, Y., Kobayashi, T., Gojobori, T. and Nagai, S.* “Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding” Metabarcoding and Metagenomics 6, 261-280 (2022).
  16. Umeda-Hara, C., Iwakawa, H., Ohtani, M., Demura, T., Matsumoto, T., Kikuchi, J., Murata, K. and Umeda, M.* “Tetraploidization promotes radial stem growth in poplars” Plant Biotechnol. 39, 215-220 (2022).
  17. Bashir, K., Rasheed, S., Todaka, D., Matsui, A., Ahmad, Z., Sako, K., Utsumi, Y., Anh Thu, V., Tanaka, M., Takahashi, S., Ishida, J., Tsuboi, Y., Watanabe, S., Kanno, Y., Ando, E., Seito, M., Motegi, H., Sato, M., Li, R., Kikuchi, S., Fujita, M., Kusano, M., Habu, Y., Nagano, A., Kawaura, K., Kikuchi, J., Saito, K., Hirai, M., Seo, M., Shinozaki, K., Kinoshita, T., and Seki, M.* “Ethanol Enhances Drought Stress Tolerance in Plants” Plant Cell Physiol. 110, 269-285 (2022).
  18. Kato, T., Kagawa, W., Suda, W., Tsuboi, Y., Inoue-Suzuki, Y., 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” Int. J. Mol. Sci. 23, 11728 (2022).
  19. 相馬智史、横山佐一郎、菊地淳　”メタボローム解析を利用した飼料開発”　養殖ビジネス　5, 12-15 （2022).

 

2021

  1. 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. 93, 6901-6906 (2021). DOI
  2. 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
  3. Date, Y., Wei, F., Tsuboi, Y., 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
  4. 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
  5. 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
  6. Kurotani, A., Kakiuchi, T. and Kikuchi, J.* “Solubility prediction from molecular properties and analytical data using an in-phase deep neural network (ip-DNN)” ACS Omega 6, 14278-14287 (2021). DOI
  7. Takamura, A., Tsukamoto, K., Sakata, K. and Kikuchi, J.* “Integrative measurement analysis via machine learning descriptor selection for investigating physical properties of biopolymers in hairs” Sci.Rep. 11, 24359  (2021). DOI
  8. 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 Yields a Strategy to Modify Woody Cell Wall Properties” Plant Cell Physiol. pcab102 (2021). DOI
  9. 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. 18, 4101-4126 (2021). DOI
  10. 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
  11. Yamazaki, K., Kato, T., Tsuboi, Y., Miyauchi, E., Suda, W., Sato, K., Nakajima, M., Yokoji-Takeuchi, M., Yamada-Hara, M., Tsuzuno, T., Matsugishi, A., Takahashi, N., Tabeta, K., Miura, N., Okuda, S., Kikuchi, J., Ohno, H. and Yamazaki, K.* ” Oral Pathobiont-Induced Changes in Gut Microbiota Aggravate the Pathology of Nonalcoholic Fatty Liver Disease in Mice” Front. Immunol. 12, 766170 (2021). DOI
  12. 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. 11, 30426-30447 (2021). DOI
  13. 菊地淳　“NMRの分子構造情報”　化学便覧　基礎編第６版　15-3-2 (2021).
  14. 菊地淳　”NMRデータサイエンスによる食材評価　-物性・プロセス・摂食代謝の特徴抽出-” 　食品分野におけるメタボリック・プロファイリング活用最前線 (2021).
  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（2021）.
  16. 山口秀幸、関山恭代、菊地淳　“食品の研究開発におけるNMRの活用” NMRによる有機材料分析とデータ解釈事例集（2021）.

 

2020

  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 trichocarpa” Plant 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.* and 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

2019

  1. 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
  2. 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
  3. 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
  4. 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 g” npj Microgravity 5, 16 (2019). DOI
  5. 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
  6. 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
  7. 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
  8. 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).
  9. 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).

2018

  1. 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
  2. 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
  3. 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 One 13, e0197256 (2018). DOI
  4. 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
  5. 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
  6. 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
  7. Asakura, T., Date, Y. and Kikuchi, J.* “Application of ensemble deep neural network to metabolomics studies” Anal. Chim  Acta. 90, 1805-1810 (2018). DOI
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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)

2017

  1.  Osaka, 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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. Rep. 7, 9372 (2017). DOI
  7. 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
  8. 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
  9. 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
  10. 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
  11. Kikuchi, J.* and Yamada, S. “NMR window of molecular complexity showing homeostasis in superorganisms” Analyst 142, 4161-4172 (2017). DOI
  12. 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
  13. Kikuchi, J.* and Komatsu, T. “Polysaccharides as major carbon sources in environmental biodiversity” NMR in Glycoscience and Glycotechnology 369-395 (2017). DOI
  14. 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
  15. Otagiri, M., Khalid, A., Moriya, S., Osada, H. and Takahashi, S.* “Novel squalene-producing thraustochytrids found in mangrove water” Biosci. Bioeng. Biochem. 81, 2034-2037 (2017). DOI

2016

  1. 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
  2. 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. Chem. 88, 2714-2719 (2016). DOI
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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. Chem. 88, 6130-6134 (2016). DOI
  8. 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. Rep. 6, 28011 (2016). DOI
  9. Vergara, F.* Kikuchi, J. Breuer, C. “Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0” Sci. Rep. 6, 26515 (2016). DOI
  10. 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
  11. Ogura, T., Hoshino, R., Date, Y. and Kikuchi, J.* “Visualization of microfloral metabolism for marine waste recycling” Metabolites 6, 7 (2016). DOI
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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).
  17. 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).
  18. 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).
  19. 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).

2015

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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 Physiol. 169, 1118-1126 (2015). DOI
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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).

2014

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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).
  18. 菊地淳　“食と代謝のメタボノミクス”　実験医学　32, 699-705 (2014).
  19. 菊地淳　“食の来た道還る道”　バイオインダストリー　(in press).
  20. 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).
  21. 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).
  22. 菊地淳 “分子複雑系” NMR 5, 75-82 (2014).
  23. 菊地淳 “NMRにおけるイノベーション” 生物工学会誌 92, 561 (2014).

2013

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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).

2012

  1. 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
  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). DOI
  3. 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
  4. 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
  5. Date, Y., Sakata, K. and Kikuchi, J.* “Chemical profiling of complex biochemical mixtures from various seaweeds” Polymer J. 44, 888-894 (2012). DOI
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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).
  13. 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).
  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24年7月10日.

2011

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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).
  9. 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).
  10. 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.

2010

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

  1. 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
  2. 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).
  3. 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
  4. 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
  5. 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
  6. 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).
  7. 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).
  8. 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

  1. Sekiyama, Y and Kikuchi, J.* “Towards dynamic metabolic network measurement by multi-dimensional NMR-based fluxomics” Phytochemistry 68, 2320-2329 (2007). DOI
  2. 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
  3. 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
  4. 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
  5. Moriya S, Noda S, Ohkuma M, Kudo T.* “In situ hybridization of termite microbes” Methods Mol Biol. 2007 353,105-12 (2007). DOI
  6. 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
  7. 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)
  8. 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)
  9. 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).
  10. 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).
  11. 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.
  1. Miyamoto, H.*, Suda, W.*, Kodama, H., Takahashi, H., Nakanishi, Y., Moriya, S., Adachi, K., Kiriyama, N., Wada, M., Sudo, D., Ito, S., Shibata, M., Wada, S., Murano, T., Taguchi, H., Shindo, C., Tsuboi, A., Tsuji, N., Matsuura, M., Ishii, C., Nakaguma, T., Ito, T., Okada, T., Matsushidata, T., Sato, T., Kato, T., Inabu, T., Tashiro, T., Mori, K., Ido, A., Miura, T., Morita, H., Fukuda, S., Suzuki, K., Nishiuchi, T., Kurotani, A., Shima, H., Wada, S., Masuya, H., Kikuchi, J., Miyamoto, H., Hattori, M., Yamamoto, N. and Ohno, H. ” A cross-species protective biochemical symbiotic interaction between gut inhabitant mesophiles and external thermophiles” Nature Ecology Evolution. 
  2. 菊地淳　”AIによるNMRデータ予測とプロセスインフォマティクスへの活用”　ケモインフォマティクスにおけるデータ解析の進め方と具体的応用法　9 (4) 641-649 (2023).

2022

  1. Hara, K., Yamada, S., Kurotani, A., Chikayama, E. and Kikuchi, J.* “Materials informatics approach using domain modelling for exploring structure-property relationships of polymers” Sci. Rep. 12, 10558 (2022). DOI
  2. Shima, H., Murata, I., Wei, F., Sakata, K. and Kikuchi, J.* “Identification of salmoniformes aquaculture conditions to increase the creatine and anserine levels using multiomics dataset and nonnumerical information” Frontiers in Microbiology 13, 991819 (2022).
  3. Yokoyama, D., Suzuki, S., Asakura, T. and Kikuchi, J.*  “Chemometric analysis of NMR spectra and machine learning to investigate membrane fouling”  ACS Omega 7, 12654-12660 (2022). DOI
  4. Hara, K., Yamada, S., Chikayama, E. and Kikuchi, J.* “Parameter Visualization of Benchtop Nuclear Magnetic Resonance Spectra Toward Food Process Monitoring” Processes 10, 1264 (2022). DOI
  5. Miyamoto, H.*, Asano, F., Ishizawa, K., Suda, W., Miyamoto, H., Tsuji, N., Matsuura, M., Tsuboi, A., Ishii, C., Nakaguma, T., Shindo, C., Kato, T., Kurotani, A., Shima, H., Moriya, S., Hattori, M., Kodama, H., Ohno, H. and Kikuchi, J.* “A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae” Sci. Total Environ. 836, 155520 (2022). DOI
  6. Yokoyama, D., Suzuki, S., Asakura, T. and Kikuchi, J.*  “Microbiome and metabolome analyses in different closed-circulation aquarium systems and their network visualization”  ACS Omega  7, 30399-30404 (2022).
  7. Shono, N., Ito, M, Umezawa, A., Sakata, K., Li, A., Kikuchi, J., Ito, K. and Nakamura, R.* “Tracing and Regulating Redox Homeostasis of Model Benthic Ecosystems for Sustainable Aquaculture in Coastal Environments” Frontiers in Microbiology 13, 907733 (2022).
  8. Shima, H., Sato, Y., Sakata, K., Asakura, T., Kikuchi, J.* “Identifying correlation among qualitative non-numeric parameters in natural fish microbe dataset using machine learning” App. Sci. 12, 5927 (2022). DOI
  9. 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. Meth. Appl. Sci. 45, 9769-9786 (2022). DOI
  10. Matsui, A., Todaka, D., Tanaka, M., Mizunashi, K., Takahashi, S., Sunaoshi, Y., Tsuboi, Y., Ishida, J., Bashir, K., Kikuchi, J., Kusano, M., Kobayashi, M., Kawaura, K. and Seki, M. “Ethanol induces heat tolerance in plants by stimulating endoplasmic reticulum-mediated stress responses” Plant Mol. Biol. 110, 131-145 (2022). DOI
  11. Avellán-Llaguno, R. D., Zhang, X., Zhao, P., Kikuchi, J., Dong, S. and Huang, Q.* “Differential aggregation of polystyrene and titanium dioxide nanoparticles under various salinity conditions and against multiple proteins types” Environ. Sci. Pol. Res. 29, 74173-74184 (2022). DOI
  12. Ito, K., Miyamoto, H.*, Matsuura, M., Ishii, C., Tsuboi, A., Tsuji, N., Nakaguma, T., Nakanishi, Y., Kato, T., Suda, W., Honda, F., Ito, T., Moriya, S., Shima, H., Michibata, R., Yamada, R., Takahashi, Y., Koga, H., Kodama, H., Watanabe, Y., Kikuchi, J. and Ohno, H. “Noninvasive fecal metabolic profiling for the evaluation of probiotic characteristics of thermostable lactic acid bacteria, Weizmannia coagulans SANK70258, for broiler chickens” J. Biocsci. Bioeng. 134, 105-115 (2022).
  13. Nakano, Y., Endo, H., Hori, C., Ihara, A., Matsumoto, T., Kikuchi, J., Ohtani, M.* and Demura, M. “Enhancement of secondary cell wall formation in poplar xylem using a self-reinforced system of secondary cell wall-related transcription factors ” Front. Plant Sci. 13, 819360 (2022). DOI
  14. Liu, H., Dai, C., Yu, H., Guo, Q., Li, J., Hao, A., Kikuchi, J. and Zhao, M.* “Dynamics of a stochastic non-autonomous phytoplankton-zooplankton system involving toxin-producing phytoplankton and impulsive perturbations” Mathematics and Computers in Simulation 203, 368-386 (2022). DOI
  15. Sildever, S., Nishi, N., Inaba, N., Asakura, T., Kikuchi, J., Asano, Y., Kobayashi, T., Gojobori, T. and Nagai, S.* “Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding” Metabarcoding and Metagenomics 6, 261-280 (2022).
  16. Umeda-Hara, C., Iwakawa, H., Ohtani, M., Demura, T., Matsumoto, T., Kikuchi, J., Murata, K. and Umeda, M.* “Tetraploidization promotes radial stem growth in poplars” Plant Biotechnol. 39, 215-220 (2022).
  17. Bashir, K., Rasheed, S., Todaka, D., Matsui, A., Ahmad, Z., Sako, K., Utsumi, Y., Anh Thu, V., Tanaka, M., Takahashi, S., Ishida, J., Tsuboi, Y., Watanabe, S., Kanno, Y., Ando, E., Seito, M., Motegi, H., Sato, M., Li, R., Kikuchi, S., Fujita, M., Kusano, M., Habu, Y., Nagano, A., Kawaura, K., Kikuchi, J., Saito, K., Hirai, M., Seo, M., Shinozaki, K., Kinoshita, T., and Seki, M.* “Ethanol Enhances Drought Stress Tolerance in Plants” Plant Cell Physiol. 110, 269-285 (2022).
  18. Kato, T., Kagawa, W., Suda, W., Tsuboi, Y., Inoue-Suzuki, Y., 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” Int. J. Mol. Sci. 23, 11728 (2022).
  19. 相馬智史、横山佐一郎、菊地淳　”メタボローム解析を利用した飼料開発”　養殖ビジネス　5, 12-15 （2022).

 

2021

  1. 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. 93, 6901-6906 (2021). DOI
  2. 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
  3. Date, Y., Wei, F., Tsuboi, Y., 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
  4. 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
  5. 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
  6. Kurotani, A., Kakiuchi, T. and Kikuchi, J.* “Solubility prediction from molecular properties and analytical data using an in-phase deep neural network (ip-DNN)” ACS Omega 6, 14278-14287 (2021). DOI
  7. Takamura, A., Tsukamoto, K., Sakata, K. and Kikuchi, J.* “Integrative measurement analysis via machine learning descriptor selection for investigating physical properties of biopolymers in hairs” Sci.Rep. 11, 24359  (2021). DOI
  8. 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 Yields a Strategy to Modify Woody Cell Wall Properties” Plant Cell Physiol. pcab102 (2021). DOI
  9. 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. 18, 4101-4126 (2021). DOI
  10. 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
  11. Yamazaki, K., Kato, T., Tsuboi, Y., Miyauchi, E., Suda, W., Sato, K., Nakajima, M., Yokoji-Takeuchi, M., Yamada-Hara, M., Tsuzuno, T., Matsugishi, A., Takahashi, N., Tabeta, K., Miura, N., Okuda, S., Kikuchi, J., Ohno, H. and Yamazaki, K.* ” Oral Pathobiont-Induced Changes in Gut Microbiota Aggravate the Pathology of Nonalcoholic Fatty Liver Disease in Mice” Front. Immunol. 12, 766170 (2021). DOI
  12. 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. 11, 30426-30447 (2021). DOI
  13. 菊地淳　“NMRの分子構造情報”　化学便覧　基礎編第６版　15-3-2 (2021).
  14. 菊地淳　”NMRデータサイエンスによる食材評価　-物性・プロセス・摂食代謝の特徴抽出-” 　食品分野におけるメタボリック・プロファイリング活用最前線 (2021).
  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（2021）.
  16. 山口秀幸、関山恭代、菊地淳　“食品の研究開発におけるNMRの活用” NMRによる有機材料分析とデータ解釈事例集（2021）.

 

2020

  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 trichocarpa” Plant 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.* and 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

2019

  1. 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
  2. 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
  3. 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
  4. 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 g” npj Microgravity 5, 16 (2019). DOI
  5. 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
  6. 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
  7. 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
  8. 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).
  9. 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).

2018

  1. 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
  2. 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
  3. 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 One 13, e0197256 (2018). DOI
  4. 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
  5. 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
  6. 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
  7. Asakura, T., Date, Y. and Kikuchi, J.* “Application of ensemble deep neural network to metabolomics studies” Anal. Chim  Acta. 90, 1805-1810 (2018). DOI
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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)

2017

  1.  Osaka, 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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. Rep. 7, 9372 (2017). DOI
  7. 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
  8. 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
  9. 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
  10. 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
  11. Kikuchi, J.* and Yamada, S. “NMR window of molecular complexity showing homeostasis in superorganisms” Analyst 142, 4161-4172 (2017). DOI
  12. 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
  13. Kikuchi, J.* and Komatsu, T. “Polysaccharides as major carbon sources in environmental biodiversity” NMR in Glycoscience and Glycotechnology 369-395 (2017). DOI
  14. 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
  15. Otagiri, M., Khalid, A., Moriya, S., Osada, H. and Takahashi, S.* “Novel squalene-producing thraustochytrids found in mangrove water” Biosci. Bioeng. Biochem. 81, 2034-2037 (2017). DOI

2016

  1. 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
  2. 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. Chem. 88, 2714-2719 (2016). DOI
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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. Chem. 88, 6130-6134 (2016). DOI
  8. 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. Rep. 6, 28011 (2016). DOI
  9. Vergara, F.* Kikuchi, J. Breuer, C. “Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0” Sci. Rep. 6, 26515 (2016). DOI
  10. 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
  11. Ogura, T., Hoshino, R., Date, Y. and Kikuchi, J.* “Visualization of microfloral metabolism for marine waste recycling” Metabolites 6, 7 (2016). DOI
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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).
  17. 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).
  18. 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).
  19. 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).

2015

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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 Physiol. 169, 1118-1126 (2015). DOI
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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).

2014

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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).
  18. 菊地淳　“食と代謝のメタボノミクス”　実験医学　32, 699-705 (2014).
  19. 菊地淳　“食の来た道還る道”　バイオインダストリー　(in press).
  20. 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).
  21. 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).
  22. 菊地淳 “分子複雑系” NMR 5, 75-82 (2014).
  23. 菊地淳 “NMRにおけるイノベーション” 生物工学会誌 92, 561 (2014).

2013

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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).

2012

  1. 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
  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). DOI
  3. 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
  4. 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
  5. Date, Y., Sakata, K. and Kikuchi, J.* “Chemical profiling of complex biochemical mixtures from various seaweeds” Polymer J. 44, 888-894 (2012). DOI
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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).
  13. 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).
  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24年7月10日.

2011

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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).
  9. 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).
  10. 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.

2010

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

  1. 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
  2. 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).
  3. 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
  4. 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
  5. 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
  6. 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).
  7. 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).
  8. 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

  1. Sekiyama, Y and Kikuchi, J.* “Towards dynamic metabolic network measurement by multi-dimensional NMR-based fluxomics” Phytochemistry 68, 2320-2329 (2007). DOI
  2. 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
  3. 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
  4. 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
  5. Moriya S, Noda S, Ohkuma M, Kudo T.* “In situ hybridization of termite microbes” Methods Mol Biol. 2007 353,105-12 (2007). DOI
  6. 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
  7. 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)
  8. 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)
  9. 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).
  10. 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).
  11. 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.