Tomita, Masaru

写真a

Affiliation

University （Mita）

Position

Professor (Non-tenured) （慶應義塾大学 名誉教授）

Related Websites

External Links
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Profile 【 Display / hide 】


  • 1957年東京生まれ。慶應大学工学部卒業後、米カーネギーメロン大学に留学し、コンピュータ科学部で修士課程（1983）と博士課程（1985）修了。その後、カーネギーメロン大学助手、助教授、准教授、同大学自動翻訳研究所副所長 歴任。

    1990年より慶應義塾大学環境情報学部助教授、教授、学部長、先端生命科学研究所所長を歴任。

    米国National Science Foundation大統領奨励賞（1988）、日本 IBM 科学賞（2002）、科学技術政策担当大臣賞（2004）、文部科学大臣表彰科学技術賞（2007）、 International　Society of Metabolomics功労賞（2009）、福澤賞（2009）、大学発ベンチャー表彰特別賞（2014）、Audi Innovation Award（2016）、鶴岡市市政功労者（2016）、国際メタボローム学会終身名誉フェロー（2017）、山形県特別功労賞（2017）、第68回河北文化賞（2019）、第5回バイオインダストリー大賞（2021）、第27回安藤百福賞大賞（2023）、鶴岡市名誉市民（2023）などを受賞。

    慶應鶴岡発ベンチャー企業「ヒューマン・メタボローム・テクノロジーズ（株）」を創業し、2013年東証マザーズ上場。人工タンパク質素材の「スパイバー（株）」社外取締役。唾液でがん検査の「サリバテック社」、便検査で腸内環境評価の「メタジェン」など、計9
    社の慶應鶴岡発ベンチャーを創業または創業支援。

    取得学位：Ph.D（人工知能）、医学博士（分子生物学）、工学博士（電気工学）、政策メディア博士（地方政策）。

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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 】

  • 脱優等生のススメ

    冨田 勝 , 早川書房, 2023

  • 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.

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Papers 【 Display / hide 】

  • Metabolomics profiles alterations in cigarette smokers and heated tobacco product users.

    Harada S, Ohmomo H, Matsumoto M, Sata M, Iida M, Hirata A, Miyagawa N, Kuwabara K, Kato S, Toki R, Edagawa S, Sugiyama D, Sato A, Hirayama A, Sugimoto M, Soga T, Tomita M, Shimizu A, Okamura T, Takebayashi T

    Journal of epidemiology  2023.11

    ISSN  0917-5040

  • Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei

    Saito M., Inose R., Sato A., Tomita M., Suzuki H., Kanai A.

    Journal of Molecular Evolution （Journal of Molecular Evolution)  91 （ 5 ） 669 - 686 2023.10

    ISSN  00222844

    　View Summary

    The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5′ end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species to classify the diverse Clp1 family proteins. The average number of Clp1 family proteins in eukaryotes was 2.3 ± 1.0, and most representative species had both Clp1 and Nol9/Grc3 proteins, suggesting that the Clp1 and Nol9/Grc3 groups were already formed in the eukaryotic ancestor by gene duplication. We also detected an average of 4.1 ± 0.4 Clp1 family proteins in members of the protist phylum Euglenozoa. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. As in this example, N-terminal and C-terminal domain replacement also contributed to the diversification of the Clp1 family proteins in other eukaryotic species. Our analysis also revealed that the Clp1 family proteins in humans and plants diversified through isoforms created by alternative splicing.

  • Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis

    Abhinand C.S., Galipon J., Mori M., Ramesh P., Prasad T.S.K., Raju R., Sudhakaran P.R., Tomita M.

    Journal of Cell Communication and Signaling （Journal of Cell Communication and Signaling)  17 （ 3 ） 1067 - 1079 2023.09

    ISSN  18739601

    　View Summary

    Vascular endothelial growth factor-A (VEGF-A) is one of the primary factors promoting angiogenesis in endothelial cells. Although defects in VEGF-A signaling are linked to diverse pathophysiological conditions, the early phosphorylation-dependent signaling events pertinent to VEGF-A signaling remain poorly defined. Hence, a temporal quantitative phosphoproteomic analysis was performed in human umbilical vein endothelial cells (HUVECs) treated with VEGF-A-165 for 1, 5 and 10 min. This led to the identification and quantification of 1971 unique phosphopeptides corresponding to 961 phosphoproteins and 2771 phosphorylation sites in total. Specifically, 69, 153, and 133 phosphopeptides corresponding to 62, 125, and 110 phosphoproteins respectively, were temporally phosphorylated at 1, 5, and 10 min upon addition of VEGF-A. These phosphopeptides included 14 kinases, among others. This study also captured the phosphosignaling events directed through RAC, FAK, PI3K-AKT-MTOR, ERK, and P38 MAPK modules with reference to our previously assembled VEGF-A/VEGFR2 signaling pathway map in HUVECs. Apart from a significant enrichment of biological processes such as cytoskeleton organization and actin filament binding, our results also suggest a role of AAK1-AP2M1 in the regulation of VEGFR endocytosis. Taken together, the temporal quantitative phosphoproteomics analysis of VEGF signaling in HUVECs revealed early signaling events and we believe that this analysis will serve as a starting point for the analysis of differential signaling across VEGF members toward the full elucidation of their role in the angiogenesis processes. Graphical abstract: [Figure not available: see fulltext.]

  • Quality Control of Targeted Plasma Lipids in a Large-Scale Cohort Study Using Liquid Chromatography–Tandem Mass Spectrometry

    Hirayama A., Ishikawa T., Takahashi H., Yamanaka S., Ikeda S., Hirata A., Harada S., Sugimoto M., Soga T., Tomita M., Takebayashi T.

    Metabolites （Metabolites)  13 （ 4 ）  2023.04

    ISSN  2218-1989

    　View Summary

    High-throughput metabolomics has enabled the development of large-scale cohort studies. Long-term studies require multiple batch-based measurements, which require sophisticated quality control (QC) to eliminate unexpected bias to obtain biologically meaningful quantified metabolomic profiles. Liquid chromatography–mass spectrometry was used to analyze 10,833 samples in 279 batch measurements. The quantified profile included 147 lipids including acylcarnitine, fatty acids, glucosylceramide, lactosylceramide, lysophosphatidic acid, and progesterone. Each batch included 40 samples, and 5 QC samples were measured for 10 samples of each. The quantified data from the QC samples were used to normalize the quantified profiles of the sample data. The intra- and inter-batch median coefficients of variation (CV) among the 147 lipids were 44.3% and 20.8%, respectively. After normalization, the CV values decreased by 42.0% and 14.7%, respectively. The effect of this normalization on the subsequent analyses was also evaluated. The demonstrated analyses will contribute to obtaining unbiased, quantified data for large-scale metabolomics.

  • 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.

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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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