Tomita, Masaru

写真a

Affiliation

University （Mita）

Position

Professor (Non-tenured)

External Links
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Other Affiliation 【 Display / hide 】

  • School of Medicine, 慶應義塾大学医学部兼担教授

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Career 【 Display / hide 】

  • 1987.07
    -
    1990.05

    カーネギーメロン大学 ,助教授

  • 1990.06
    -
    1997.03

    大学助教授(環境情報学部)

  • 1994.04
    -
    Present

    大学院政策・メディア研究科委員

  • 1997.04
    -
    Present

    大学教授(環境情報学部)

  • 1999.10
    -
    2001.09

    大学国際センター副所長

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Academic Background 【 Display / hide 】

  • 1976.04
    -
    1981.03

    Keio University, Faculty of Engineering, Department of Mathematics

    University, Graduated

  • 1981.09
    -
    1983.05

    Carnegie Mellon University, School of Computer Science

    United States, Graduate School, Completed, Master's course

  • 1983.05

    Other, コンピューター科学科

    United States, Graduate School, Completed, Master's course

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Academic Degrees 【 Display / hide 】

  • Ph.D in Computer Science, Carnegie Mellon University, Coursework, 1985.05

  • Ph.D in Electrical Engineering , Kyoto University, Dissertation, 1994.07

  • Ph.D in Molecular Biology, Keio University, Coursework, 1998.03

  • Ph.D in Media and Governance, Keio University, Dissertation, 2019.08

    The creation of Tsuruoka Science Park and regional development

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Research Areas 【 Display / hide 】

  • System Biology

  • Biological simulation

  • computer science

  • Genome Informatics

  • Bioinformatics

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Books 【 Display / hide 】

  • みんなで考えるAIとバイオテクノロジーの未来社会

    冨田 勝, かんき出版, 2022

  • Advances in Systems Immunology and Cancer

    Tomita, M., Selvarajoo, K. and Tsuchiya, M., Frontiers , 2014

  • E-Cell System : Basic Concepts and Applications

    Satya Nanda Vel ArjunanPawan K. DharMasaru Tomita, Springer, 2013

  • Metabolomics: A new omics technology for traditional herbal medicine analysis

    Iino K., Sugimoto M., Soga T., Tomita M., Chinese Medicine: Acupuncture, Herbal Medicine and Therapies, 2012.03

    　View Summary

    Identification of a small number of bioactive components in herbal medicines is often inadequate for elucidating biological effects and for quality control because of the complexity of the components. Qualitative and quantitative analyses of all the components in herbal medicines will therefore be of considerable value. Metabolomics is a new branch of "omics" science concerned with understanding the all the metabolites in living systems. Recent advances in the development of analytical technologies in metabolomics have made a considerable contribution to various studies of herbal medicines. In particular, mass spectrometry (MS) combined with separation systems have enabled us to simul-taneously obtain datasets for dozens or hundreds of molecules. MS-based non-targeted profiling techniques provide plentiful information about known bioactive components as well as all observable components. Here, we provide an overview of the metabolomic analysis of herbal medicines. Prospects for further research based on our primary results are also discussed. © 2012 Nova Science Publishers, Inc.

  • Metabolomics: A new paradigm for cancer biomarker discovery

    Sugimoto M., Soga T., Tomita M., Cancer Biomarkers, 2011.12

    　View Summary

    Currently, individual molecular biomarkersare often used to detect cancers. However, to identify cancer-specific signatures appropriate for clinical use, a paradigm shift is necessary in terms of using multiple molecular profiling techniques to identify new prognostic biomarkers and therapeutic targets, and to understand the aberrant biochemical pathways. Metabolomics, a new omics, provides a holistic view of the cellular dynamic behavior derived from various endogenetic and exogenetic perturbations as well as genomics, transcriptomics and proteomics. To simultaneously assess a broad range of metabolites, we have developed profiling techniques based on capillary electrophoresis-mass spectrometry (CE-MS) that can quantify charged molecules,principally those involved in the central metabolic pathways; i.e., glycolysis, pentose phosphate pathway, amino acid pathway, nucleotide pathway, tricarboxylic cycle, and urea cycle. Because tumors exhibit unique cellular metabolic profiles to survive or to enable excessive proliferation in an aberrant microenvironment, CE-MS can offera significant opportunity to fully understand cancer metabolism. Here, we provide an overview of CE-MS-based metabolomics and two applications; 1) pathway-level metabolic variation to provide novel insights into the microenvironmentof human tumor tissues, and 2) the potential use of salivary metabolites in cancer detection. © 2011 Nova Science Publishers, Inc. All rights reserved.

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Papers 【 Display / hide 】

  • iDMET: network-based approach for integrating differential analysis of cancer metabolomics

    Matsuta R., Yamamoto H., Tomita M., Saito R.

    BMC Bioinformatics （BMC Bioinformatics)  23 （ 1 ） 508 2022.12

    　View Summary

    Background: Comprehensive metabolomic analyses have been conducted in various institutes and a large amount of metabolomic data are now publicly available. To help fully exploit such data and facilitate their interpretation, metabolomic data obtained from different facilities and different samples should be integrated and compared. However, large-scale integration of such data for biological discovery is challenging given that they are obtained from various types of sample at different facilities and by different measurement techniques, and the target metabolites and sensitivities to detect them also differ from study to study. Results: We developed iDMET, a network-based approach to integrate metabolomic data from different studies based on the differential metabolomic profiles between two groups, instead of the metabolite profiles themselves. As an application, we collected cancer metabolomic data from 27 previously published studies and integrated them using iDMET. A pair of metabolomic changes observed in the same disease from two studies were successfully connected in the network, and a new association between two drugs that may have similar effects on the metabolic reactions was discovered. Conclusions: We believe that iDMET is an efficient tool for integrating heterogeneous metabolomic data and discovering novel relationships between biological phenomena.

  • Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli

    Morita T., Majdalani N., Miura M.C., Inose R., Oshima T., Tomita M., Kanai A., Gottesman S.

    mBio （mBio)  13 （ 6 ）  2022.12

    ISSN  21612129

    　View Summary

    The regulatory function of many bacterial small RNAs (sRNAs) requires the binding of the RNA chaperone Hfq to the 39 portion of the sRNA intrinsic terminator, and therefore sRNA signaling might be regulated by modulating its terminator. Here, using a multicopy screen developed with the terminator of sRNA SgrS, we identified an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof) that attenuate SgrS termination in Escherichia coli. Analyses of CyaR and YgjH, a putative tRNA binding protein, suggested that the CyaR activity was indirect and the effect of YgjH was moderate. Overproduction of the protein attenuators CspD and Rof resulted in more frequent readthrough at terminators of SgrS and two other sRNAs, and regulation by SgrS of target mRNAs was reduced. The effect of Rof, a known inhibitor of Rho, was mimicked by bicyclomycin or by a rho mutant, suggesting an unexpected role for Rho in sRNA termination. CspD, a member of the cold shock protein family, bound both terminated and readthrough transcripts, stabilizing them and attenuating termination. By RNA sequencing analysis of the CspD overexpression strain, we found global effects of CspD on gene expression across some termination sites. We further demonstrated effects of endogenous CspD under slow growth conditions where cspD is highly expressed. These findings provided evidence of changes in the efficiency of intrinsic termination, confirming this as an additional layer of the regulation of sRNA signaling. IMPORTANCE Growing evidence suggests that the modulation of intrinsic termination and readthrough of transcription is more widespread than previously appreciated. For small RNAs, proper termination plays a critical role in their regulatory function. Here, we present a multicopy screen approach to identify factors that attenuate small RNA termination and therefore abrogate signaling dependent on the small RNA. This study highlights a new aspect of regulation of small RNA signaling as well as the modulation of intrinsic termination.

  • Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades

    Yoshida Y., Satoh T., Ota C., Tanaka S., Horikawa D.D., Tomita M., Kato K., Arakawa K.

    BMC Genomics （BMC Genomics)  23 （ 1 ） 405 2022.12

    　View Summary

    Background: Tardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated state of suspended animation known as anhydrobiosis. While antioxidative stress proteins, antiapoptotic pathways and tardigrade-specific intrinsically disordered proteins have been implicated in the anhydrobiotic machinery, conservation of these mechanisms is not universal within the phylum Tardigrada, suggesting the existence of overlooked components. Results: Here, we show that a novel Mn-dependent peroxidase is an important factor in tardigrade anhydrobiosis. Through time-series transcriptome analysis of Ramazzottius varieornatus specimens exposed to ultraviolet light and comparison with anhydrobiosis entry, we first identified several novel gene families without similarity to existing sequences that are induced rapidly after stress exposure. Among these, a single gene family with multiple orthologs that is highly conserved within the phylum Tardigrada and enhances oxidative stress tolerance when expressed in human cells was identified. Crystallographic study of this protein suggested Zn or Mn binding at the active site, and we further confirmed that this protein has Mn-dependent peroxidase activity in vitro. Conclusions: Our results demonstrated novel mechanisms for coping with oxidative stress that may be a fundamental mechanism of anhydrobiosis in tardigrades. Furthermore, localization of these sets of proteins mainly in the Golgi apparatus suggests an indispensable role of the Golgi stress response in desiccation tolerance.

  • 1000 spider silkomes: Linking sequences to silk physical properties

    Arakawa K., Kono N., Malay A.D., Tateishi A., Ifuku N., Masunaga H., Sato R., Tsuchiya K., Ohtoshi R., Pedrazzoli D., Shinohara A., Ito Y., Nakamura H., Tanikawa A., Suzuki Y., Ichikawa T., Fujita S., Fujiwara M., Tomita M., Blamires S.J., Chuah J.A., Craig H., Foong C.P., Greco G., Guan J., Holland C., Kaplan D.L., Sudesh K., Mandal B.B., Norma-Rashid Y., Oktaviani N.A., Preda R.C., Pugno N.M., Rajkhowa R., Wang X., Yazawa K., Zheng Z., Numata K.

    Science Advances （Science Advances)  8 （ 41 ） eabo6043 2022.10

    　View Summary

    Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

  • Salivary metabolomics with machine learning for colorectal cancer detection

    Kuwabara H., Katsumata K., Iwabuchi A., Udo R., Tago T., Kasahara K., Mazaki J., Enomoto M., Ishizaki T., Soya R., Kaneko M., Ota S., Enomoto A., Soga T., Tomita M., Sunamura M., Tsuchida A., Sugimoto M., Nagakawa Y.

    Cancer Science （Cancer Science)  113 （ 9 ） 3234 - 3243 2022.09

    ISSN  13479032

    　View Summary

    As the worldwide prevalence of colorectal cancer (CRC) increases, it is vital to reduce its morbidity and mortality through early detection. Saliva-based tests are an ideal noninvasive tool for CRC detection. Here, we explored and validated salivary biomarkers to distinguish patients with CRC from those with adenoma (AD) and healthy controls (HC). Saliva samples were collected from patients with CRC, AD, and HC. Untargeted salivary hydrophilic metabolite profiling was conducted using capillary electrophoresis–mass spectrometry and liquid chromatography–mass spectrometry. An alternative decision tree (ADTree)-based machine learning (ML) method was used to assess the discrimination abilities of the quantified metabolites. A total of 2602 unstimulated saliva samples were collected from subjects with CRC (n = 235), AD (n = 50), and HC (n = 2317). Data were randomly divided into training (n = 1301) and validation datasets (n = 1301). The clustering analysis showed a clear consistency of aberrant metabolites between the two groups. The ADTree model was optimized through cross-validation (CV) using the training dataset, and the developed model was validated using the validation dataset. The model discriminating CRC + AD from HC showed area under the receiver-operating characteristic curves (AUC) of 0.860 (95% confidence interval [CI]: 0.828-0.891) for CV and 0.870 (95% CI: 0.837-0.903) for the validation dataset. The other model discriminating CRC from AD + HC showed an AUC of 0.879 (95% CI: 0.851-0.907) and 0.870 (95% CI: 0.838-0.902), respectively. Salivary metabolomics combined with ML demonstrated high accuracy and versatility in detecting CRC.

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Papers, etc., Registered in KOARA 【 Display / hide 】

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Reviews, Commentaries, etc. 【 Display / hide 】

  • Erratum: Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan (PLoS ONE (2021) 16:2 (e0246456) DOI: 10.1371/journal.pone.0246456)

    Shibutami E., Ishii R., Harada S., Kurihara A., Kuwabara K., Kato S., Iida M., Akiyama M., Sugiyama D., Hirayama A., Sato A., Amano K., Sugimoto M., Soga T., Tomita M., Takebayashi T.

    PLoS ONE (PLoS ONE)  16 ( 4 April ) e0250864 2021.04

    　View Summary

    In Table 2, the mean (10th-90th range)a of Rice for Male should be (250-680). Please see the correct Table 2 here. (Table Presented).

  • Publisher Correction: Base editors for simultaneous introduction of C-to-T and A-to-G mutations (Nature Biotechnology, (2020), 38, 7, (865-869), 10.1038/s41587-020-0509-0)

    Sakata R.C., Ishiguro S., Mori H., Tanaka M., Tatsuno K., Ueda H., Yamamoto S., Seki M., Masuyama N., Nishida K., Nishimasu H., Arakawa K., Kondo A., Nureki O., Tomita M., Aburatani H., Yachie N.

    Nature Biotechnology (Nature Biotechnology)  38 ( 7 ) 901 2020.07

    ISSN  10870156

    　View Summary

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  • Does the gut microbiota modulate host physiology through polymicrobial biofilms?

    Yang J., Yang Y., Ishii M., Nagata M., Aw W., Obana N., Tomita M., Nomura N., Fukuda S.

    Microbes and Environments (Microbes and Environments)  35 ( 3 ) 1 - 13 2020

    ISSN  13426311

    　View Summary

    Microbes inhabit various environments, such as soil, water environments, plants, and animals. Humans harbor a complex commensal microbial community in the gastrointestinal tract, which is known as the gut microbiota. The gut microbiota participates not only in various metabolic processes in the human body, it also plays a critical role in host immune responses. Gut microbes that inhabit the intestinal epithelial surface form polymicrobial biofilms. In the last decade, it has been widely reported that gut microbial biofilms and gut microbiota-derived products, such as metabolites and bacterial membrane vesicles, not only directly affect the host intestinal environment, but also indirectly influence the health of the host. In this review, we discuss the most recent findings from human and animal studies on the interactions between the gut microbiota and hosts, and their associations with various disorders, including inflammatory diseases, atopic dermatitis, metabolic disorders, and psychiatric and neurological diseases. The integrated approach of metabologenomics together with biofilm imaging may provide valuable insights into the gut microbiota and suggest remedies that may lead to a healthier society.

  • Detecting A-to-I RNA editing in RNA-Seq data

    Galipon Josephine(ガリポン・ジョセフィーヌ), 石黒宗, 富田勝, 程久美子

    NGS Professional シリーズRNA-Seqマスターブック (株式会社　羊土社)   2016.04

    Article, review, commentary, editorial, etc. (scientific journal), Joint Work

  • The application of omics technologies in the functional evaluation of inulin and inulin-containing prebiotics dietary supplementation

    Tsurumaki, M., Kotake, M., Iwasaki, M., Saito, M., Tanaka, K., Aw, W., and *Fukuda, S. and Tomita, M.

    Nutr Diabetes. 5   e185 2015

    Article, review, commentary, editorial, etc. (scientific journal), Joint Work

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Presentations 【 Display / hide 】

  • 越冬時における赤カブ‘温海かぶ’の胚軸の成分プロファイルの変化

    TOMITA MASARU

    第11回メタボロームシンポジウム (大阪府、吹田市) , 

    2017.11
    , 

    Poster presentation

  • 修復関連タンパクを用いたハイスループット変異検出手法の開発

    TOMITA MASARU

    生命情報科学 若手の会 第9回研究会 (愛知県蒲郡市) , 

    2017.10
    , 

    Poster presentation

  • Differential gene expression analysis of Euglena gracilis chloroplast deleted mutant

    TOMITA MASARU

    生命情報科学 若手の会 第9回研究会 (愛知県蒲郡市) , 

    2017.10
    , 

    Poster presentation

  • 配列類似性ネットワークに基づくHIV-1 Pol上のサブタイプ分化と対応する 領域の解析

    TOMITA MASARU

    生命情報科学 若手の会 第9回研究会 (愛知県蒲郡市) , 

    2017.10
    , 

    Poster presentation

  • Microbial communities of university campuses in Japan.

    TOMITA MASARU

    IIBMP2017 (北海道大学情報科学研究科) , 

    2017.09
    , 

    Poster presentation

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Research Projects of Competitive Funds, etc. 【 Display / hide 】

  • 「In vivoヒト代謝システム生物学拠点」

    2007
    -
    2009

    グローバルCOEプログラム, Other, No Setting

  • 「先端生命科学」

    2006
    -
    2010

    山形県研究教育補助金　第２期, Commissioned ｒesearch, No Setting

  • 「メタボローム解析のための計測技術開発とそれを用いた代謝経路推定」

    2006
    -
    2009

    科研費・特定領域研究「生命システム情報」公募研究A02, Commissioned ｒesearch, No Setting

  • 「システム生物学による生命機能の理解と制御」

    2005
    -
    2007

    ２１世紀ＣＯＥプログラム（生命科学分野）, Other, No Setting

  • 「システムバイオロジーのためのモデリング・シミュレーション環境の構築」

    2004
    -
    2009

    戦略的創造研究推進事業（CREST）「シミュレ-ション技術の革新と実用化基盤の構築」研究領域, Commissioned ｒesearch, No Setting

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Awards 【 Display / hide 】

  • 5th Bioindustry Awards GRAND PRIX

    2021.10, Bioindustry Association, Pioneering Research on Systems Biology and their Industrialization for Regional Promotion

    Type of Award： Award from Japanese society, conference, symposium, etc.

    　View Description

    一般財団法人バイオインダストリー協会が主催する第5回「バイオインダストリー大賞」を受賞。今回の受賞は、冨田勝所長の「システムバイオロジーの先駆的研究とその産業化による地域振興」の業績が評価されました。

  • 第68回河北文化賞

    2019, 公益財団法人河北文化事業団

    Type of Award： Award from publisher, newspaper, foundation, etc.

    　View Description

    東北の研究施設として最先端の研究成果を上げ、地域産業の活性化に寄与したことにより、この賞を受賞しました。

  • Yamagata Special Achievement Award

    2017.11, Yamagata Prefectural Government

    　View Description

    この賞は、幅広い分野において県勢全般の発展に大きな功績があった人物に贈られる賞であり、2001年の当研究所開設以来の、学術分野（生命科学）、産業振興、人材育成、教育振興、地域振興等における功績が認められて、今回の受賞となった。

  • Lifetime Honorary Fellow

    2017.06, International Metabolomics Society

    Type of Award： International academic award (Japan or overseas)

    　View Description

    CE-MSアプローチの最大の支持者の１人として、メタボローム学会の創設と発展に顕著な貢献をしたことを理由に授与された。歴代11人目、日本人及びアジア人としては初めての受賞。

  • WIRED Audi INNOVATION AWARD 2016

    2016.12

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Other 【 Display / hide 】

  • 2015年05月

    　View Details

    KAUST Computational Bioscience Research Center Scientific Advisory Board Meeting (Jeddah, Saudi Arabia)
    にて座長を務める

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Courses Taught 【 Display / hide 】

  • EVOLUTION OF LIFE AND INTELLIGENCE

    2023

  • SYSTEMS OF LIFE

    2022

  • SPECIAL RESEARCH PROJECT B

    2022

  • SEMINAR B

    2022

  • MASTER SEMINAR

    2022

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Courses Previously Taught 【 Display / hide 】

  • 生命と知能の進化

    Keio University

    2015.04
    -
    2016.03
    , 

    Autumn Semester, Within own ｆaculty

  • 生命システム

    Keio University

    2015.04
    -
    2016.03
    , 

    Spring Semester, Lecture, Within own ｆaculty, 512people

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Social Activities 【 Display / hide 】

  • 経産省・産業構造審議会商務流通情報分科会バイオ小委員会

    2016.03
    -
    Present

  • 山形ブランド特命大使

    2016.03
    -
    Present

  • 特定非営利活動法人全脳アーキテクチャ・イニシアティブ顧問

    2015.09
    -
    2017.06

  • 横浜市立横浜サイエンスフロンティア高等学校科学技術顧問

    2013.04
    -
    Present

  • 鶴岡ふるさと観光大使

    2010.04
    -
    Present

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Memberships in Academic Societies 【 Display / hide 】

  • 情報計算化学生物学会（CBI学会）, 

    2007.05
    -
    Present

  • International Society for Computational Biology(ISCB), 

    2001
    -
    Present

  • 日本バイオインフォマティクス学会, 

    2000
    -
    Present

  • 言語処理学会

    　

  • 日本分子生物学会

    　

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Committee Experiences 【 Display / hide 】

  • 2015
    -
    2018.03

    技術顧問, ㈱ヒューマン・メタボローム・テクノロジーズ

  • 2012.11
    -
    Present

    評議員, 全塾 評議員会

  • 2012.04
    -
    Present

    客員教授, 京都大学化学研究所

  • 2011.04
    -
    Present

    委員, 信濃町 慶應医学賞

  • 2011
    -
    Present

    所長, 先端生命科学研究所

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