Tomita, Masaru

写真a

Affiliation

Faculty of Environment and Information Studies (Shonan Fujisawa)

Position

Professor

External Links

Other Affiliation 【 Display / hide

  • School of Medicine, 慶應義塾大学医学部兼担教授

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

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

 

Research Areas 【 Display / hide

  • System Biology

  • Biological simulation

  • computer science

  • Genome Informatics

  • Bioinformatics

 

Books 【 Display / hide

  • 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.

  • Salivary metabolomics for oral cancer detection

    Sugimoto M., Wong D., Soga T., Tomita M., Oral Cancer: Causes, Diagnosis and Treatment, 2011.04

     View Summary

    Saliva is an informative biofluid that can be used to monitor a wide range of oral and systemic diseases. This medium has gained much attention as a diagnostic fluid because of its simple collection, non-invasiveness, and low cost. Many studies have been conducted to identify diagnostic markers in saliva for several diseases, including HIV, diabetes, viral hepatitis and, importantly, cancers. The recently developed comprehensive molecular profiling approaches, such as transcriptomics and proteomics, can accelerate these studies. Metabolomics, profiling of all intracellular metabolites, has become a powerful new omics tool that can provide insight into cellular functions and facilitate biomarker discovery. Although there are several approaches to profiling metabolites, capillary electrophoresis time-of-flight-mass spectrometry (CE-TOFMS) has a prominent advantage because it enables comprehensive, simultaneous and quantitative analysis of key metabolites in various pathways, such as glycolysis, pentose phosphate pathway, tricarboxylic acid cycle and urea cycle, as well as amino acid and nucleotide metabolism. Thus, this method is well-suited to biomarker discovery in cancer cells because there are diverse metabolic aberrations related to energy metabolism and cellular proliferation in cancer cells. We recently applied CE-TOFMS-based metabolomic analysis to evaluate the potential of using the salivary metabolomic signature to detect oral cancer (oral squamous cell carcinoma cancers). The metabolic fingerprints embedded in the salivary specimens showed a prominent difference between oral cancer and healthy controls. Here, we introduce the marriage of CE and TOFMS, which has the potential to provide a state-of-the art salivary-based detection method for oral cancer. © 2011 by Nova Science Publishers, Inc. All rights reserved.

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Papers 【 Display / hide

  • High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance.

    Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T

    NAR genomics and bioinformatics 4 ( 2 ) lqac029 2022.06

  • Polarity protein SCRIB interacts with SLC3A2 to regulate proliferation and tamoxifen resistance in ER+ breast cancer.

    Saito Y, Matsuda S, Ohnishi N, Endo K, Ashitani S, Ohishi M, Ueno A, Tomita M, Ueda K, Soga T, Muthuswamy SK

    Communications biology 5 ( 1 ) 403 2022.05

  • Cinnamon bark extract suppresses metastatic dissemination of cancer cells through inhibition of glycolytic metabolism.

    Nakayama J, Konno Y, Maruyama A, Tomita M, Makinoshima H

    Journal of natural medicines  2022.04

    ISSN  1340-3443

  • Initial parasitic behaviour of the temporary social parasitic ant Polyrhachis lamellidens can be induced by host-like cuticles in laboratory environment.

    Kurihara Y, Iwai H, Kono N, Tomita M, Arakawa K

    Biology open (Biology Open)  11 ( 3 )  2022.02

     View Summary

    Polyrhachis lamellidens is a temporary social parasitic species. When a newly mated queen encounters a host worker, it opens its jaws and then mounts and rubs the body of the host worker, called rubbing behaviour. This behaviour is different from aggressive behaviour and is considered to be a preparatory action before invasion of the host colony. However, it is unclear what cues trigger rubbing behaviour. Therefore, in this study, we used glass beads that imitated the insect body surfaces and searched for triggers. Although P. lamellidens did not respond to the cuticular compounds only, cuticular compounds and chitin coatings on glass beads elicited responses that were similar to those towards live samples. The rubbing behaviour of P. lamellidens was elicited in response to a cuticle-like surface that mimicked a procuticle by combining the compounds with chitin. These results suggest that host recognition and nest-mate recognition are supported by different mechanisms.

  • Hao1 Is Not a Pathogenic Factor for Ectopic Ossifications but Functions to Regulate the TCA Cycle In Vivo.

    Kimura A, Hirayama A, Matsumoto T, Sato Y, Kobayashi T, Ikeda S, Maruyama M, Kaneko M, Shigeta M, Ito E, Soma T, Miyamoto K, Soga T, Tomita M, Oya A, Matsumoto M, Nakamura M, Kanaji A, Miyamoto T

    Metabolites (Metabolites)  12 ( 1 )  2022.01

     View Summary

    Ossification of the posterior longitudinal ligament (OPLL), a disease characterized by the ectopic ossification of a spinal ligament, promotes neurological disorders associated with spinal canal stenosis. While blocking ectopic ossification is mandatory to prevent OPLL development and progression, the mechanisms underlying the condition remain unknown. Here we show that expression of hydroxyacid oxidase 1 (Hao1), a gene identified in a previous genome-wide association study (GWAS) as an OPLL-associated candidate gene, specifically and significantly decreased in fibroblasts during osteoblast differentiation. We then newly established Hao1-deficient mice by generating Hao1-flox mice and crossing them with CAG-Cre mice to yield global Hao1-knockout (CAG-Cre/Hao1flox/flox; Hao1 KO) animals. Hao1 KO mice were born normally and exhibited no obvious phenotypes, including growth retardation. Moreover, Hao1 KO mice did not exhibit ectopic ossification or calcification. However, urinary levels of some metabolites of the tricarboxylic acid (TCA) cycle were significantly lower in Hao1 KO compared to control mice based on comprehensive metabolomic analysis. Our data indicate that Hao1 loss does not promote ectopic ossification, but rather that Hao1 functions to regulate the TCA cycle in vivo.

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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

 

Courses Taught 【 Display / hide

  • SYSTEMS OF LIFE

    2022

  • SPECIAL RESEARCH PROJECT B

    2022

  • SEMINAR B

    2022

  • MASTER SEMINAR

    2022

  • INDEPENDENT RESEARCH

    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

 

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
  • 日本分子生物学会

     
  • 日本オミックス医療学会

     

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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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