Tomita, Masaru

Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology

Bacterial Genetics and BiotechnologyMicrobial Metabolic Engineering and Bioproduction

Cited by 7,858

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

Furusawa, Y., Obata, Y., Fukuda, S., Endo, T. A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., et al. (2013) · Nature

Gut microbiota and healthT-cell and B-cell Immunology

Cited by 5,549

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 3,060

E-CELL: software environment for whole-cell simulation

Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T. S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J. C., et al. (1999) · Bioinformatics

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 764

Large-scale identification of protein–protein interaction of Escherichia coli K-12

Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.-C., Hirai, A., et al. (2006) · Genome Research

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 403

bioinformatics tools for mass spectroscopy-based metabolomic data processing and analysis

Sugimoto, M., Kawakami, M., Robert, M., Soga, T., & Tomita, M. (2012) · Current Bioinformatics

Metabolomics and Mass Spectrometry StudiesBioinformatics and Genomic Networks

Cited by 307

Gene Knockout and Metabolome Analysis of Carnitine/Organic Cation Transporter OCTN1

Kato, Y., Kubo, Y., Iwata, D., Kato, S., Sudo, T., Sugiura, T., Kagaya, T., Wakayama, T., Hirayama, A., Sugimoto, M., et al. (2010) · Pharmaceutical Research

Drug Transport and Resistance MechanismsSulfur Compounds in Biology

Cited by 206

Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Kono, N., Nakamura, H., Mori, M., Yoshida, Y., Ohtoshi, R., Malay, A. D., Pedrazzoli Moran, D. A., Tomita, M., Numata, K., & Arakawa, K. (2021) · Proceedings of the National Academy of Sciences

Silk-based biomaterials and applicationsSpider Taxonomy and Behavior Studies

Cited by 99

Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Kono, N., Nakamura, H., Mori, M., Yoshida, Y., Ohtoshi, R., Malay, A. D., Pedrazzoli Moran, D. A., Tomita, M., Numata, K., & Arakawa, K. (2021) · Proceedings of the National Academy of Sciences

Silk-based biomaterials and applicationsSpider Taxonomy and Behavior Studies

Cited by 99

Non-targeted metabolite profiling in activated macrophage secretion

Sugimoto, M., Sakagami, H., Yokote, Y., Onuma, H., Kaneko, M., Mori, M., Sakaguchi, Y., Soga, T., & Tomita, M. (2012) · Metabolomics

Metabolomics and Mass Spectrometry StudiesOral microbiology and periodontitis research

Cited by 95

Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness

Bozek, K., Wei, Y., Yan, Z., Liu, X., Xiong, J., Sugimoto, M., Tomita, M., Pääbo, S., Pieszek, R., Sherwood, C. C., et al. (2014) · PLoS Biology

Metabolomics and Mass Spectrometry StudiesPrimate Behavior and Ecology

Cited by 93

Thymidine catabolism as a metabolic strategy for cancer survival

Tabata, S., Yamamoto, M., Goto, H., Hirayama, A., Ohishi, M., Kuramoto, T., Mitsuhashi, A., Ikeda, R., Haraguchi, M., Kawahara, K., et al. (2017) · Cell Reports

Cancer, Hypoxia, and MetabolismBiochemical and Molecular Research

Cited by 68

A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice

Yamamoto, Y., Nakanishi, Y., Murakami, S., Aw, W., Tsukimi, T., Nozu, R., Ueno, M., Hioki, K., Nakahigashi, K., Hirayama, A., et al. (2018) · Microorganisms

Gut microbiota and healthMetabolomics and Mass Spectrometry Studies

Cited by 30

Functional connectivity between the amygdala and subgenual cingulate gyrus predicts the antidepressant effects of ketamine in patients with treatment‐resistant depression

Nakamura, T., Tomita, M., Horikawa, N., Ishibashi, M., Uematsu, K., Hiraki, T., Abe, T., & Uchimura, N. (2021) · Neuropsychopharmacology Reports

Treatment of Major DepressionFunctional Brain Connectivity Studies

Cited by 28