Updated on 2022/03/15

写真a

 
OTA Motonori
 
Organization
Graduate School of Informatics Department of Complex Systems Science 2 Professor
Graduate School
Graduate School of Information Science
Graduate School of Informatics
Undergraduate School
School of Informatics Department of Natural Science Informatics
School of Informatics and Sciences
Title
Professor
Contact information
メールアドレス

Degree 1

  1. 博士(理学) ( 1996.10   早稲田大学 ) 

Research Areas 2

  1. Life Science / Biophysics  / Theoretical biology, Bioinformatics

  2. Informatics / Life, health and medical informatics  / Bioinformatics

Research History 5

  1. 東京工業大学 学術国際情報センター 助教授

    2002.4 - 2008.3

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    Country:Japan

  2. 国立遺伝学研究所 DDBJ・生命情報研究センター 助手

    1996.8 - 2002.3

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    Country:Japan

  3. 日本学術振興会 特別研究員(DC2)

    1996.4 - 1996.7

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    Country:Japan

  4. 蛋白工学研究所 研究員

    1994.4 - 1995.3

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    Country:Japan

  5. 東燃(株)総合研究所 研究員

    1990.4 - 1994.3

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    Country:Japan

Education 1

  1. Waseda University

    1994.4 - 1996.10

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    Country: Japan

 

Papers 55

  1. Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2 Reviewed

    FEBS OPEN BIO   Vol. 12 ( 1 ) page: 285 - 294   2021.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/2211-5463.13337

    Web of Science

    Scopus

    PubMed

  2. Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins Invited Reviewed

    Hijikata Atsushi, Shionyu Clara, Nakae Setsu, Shionyu Masafumi, Ota Motonori, Kanaya Shigehiko, Shirai Tsuyoshi

    Biophys. Physicobiol.   Vol. 18 ( 0 ) page: 226 - 240   2021.10

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:一般社団法人 日本生物物理学会  

    <p>More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of <i>in silico</i> and <i>in vitro</i> screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity <i>in vitro</i>, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.</p>

    DOI: 10.2142/biophysico.bppb-v18.025

    Web of Science

  3. Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail Reviewed

    Takeda Shuichi, Koike Ryotaro, Fujiwara Ikuko, Narita Akihiro, Miyata Makoto, Ota Motonori, Maeda Yuichiro

    J. Mol. Biol.   Vol. 433 ( 9 ) page: 166891   2021.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of Molecular Biology  

    Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.

    DOI: 10.1016/j.jmb.2021.166891

    Web of Science

    Scopus

    PubMed

  4. Crystal structure of human V-1 in the apo form Reviewed

    S. Takeda, R. Koike, T. Nagae, I. Fujiwara, A. Narita, Y. Maéda, M. Ota

    Acta. Cryst. F   Vol. 77 ( Pt 1 ) page: 13 - 21   2021.1

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S2053230X20016829

    Web of Science

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  5. Knowledge-based Modeling of SARS-CoV-2 Proteins and Predicting its Potential Drugs Invited Reviewed

    HIJIKATA Atsushi, SHIONYU-MITSUYAMA Clara, NAKAE Setsu, SHIONYU Masafumi, OTA Motonori, KANAYA Shigehiko, SHIRAI Tsuyoshi

    Seibutsu Butsuri   Vol. 61 ( 2 ) page: 102 - 106   2021

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    Language:Japanese   Publishing type:Research paper (other academic)   Publisher:The Biophysical Society of Japan General Incorporated Association  

    <p>The novel coronavirus disease (COVID-19) pandemic has emerged in late 2019 and rapidly spread all over the world. In order to assist structure-based discovery efforts for repurposing drugs against the infectious disease, we constructed homology models of SARS-CoV-2 proteins. We identified several potential drugs by comparing the ligand molecules in the template structures with approved or experimental drugs and compounds of natural drugs, including carfilzomib, sinefungin, tecadenoson, and trabodenoson, that would be further investigated for their potential for treating COVID-19.</p>

    DOI: 10.2142/biophys.61.102

    CiNii Research

  6. Knowledge-based strutural models of SARS-CoV-2 proteins and their complexes with potential drugs Reviewed

    A. Hijikata, C. Shionyu-Mitsuyama, S. Nakae, M. Shionyu, M. Ota, S. Kanaya, T. Shirai

    FEBS Lett.   Vol. 594   page: 1960 - 1973   2020.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/1873-3468.13806

  7. All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins Reviewed

    R. Koike, M. Ota

    Biophys. Physicobiol.   ( 16 ) page: 280-286   2019.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.2142/biophysico.16.0_280

  8. Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins Reviewed

    R. Koike, M. Amano, K. Kaibuchi, M. Ota

    Protein Sci.   Vol. 29   page: 564-571   2019.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pro.3789

  9. MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers Reviewed

    S. Minami, K. Sawada, M. Ota, G. Chikenji

    Bioinformatics   Vol. 34   page: 3324-3331   2018.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/bioinformatics/bty369

  10. Using 1HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method Reviewed

    H. Okazaki, N. Matsuo, T. Tenno, N. Goda, Y. Shigemitsu, M. Ota, H. Hiroaki

    Protein Sci.   Vol. 27   page: 1821-1830   2018.8

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pro.3485

  11. Discovery of Cryoprotective Activity in Human Genome-Derived Intrinsically Disordered Proteins Reviewed

    N. Matsuo, N. Goda, K. Shimizu, S. Fukuchi, M. Ota, H. Hiroaki

    Int. J. Mol. Sci.   Vol. 19   page: 401   2018.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.3390/ijms19020401

  12. Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding Reviewed

    E. Uemura, T. Niwa, S. Minami, K. Takemoto, S. Fukuchi, K. Machida, H. Imataka, T. Ueda, M. Ota, H. Taguchi

    Sci. Rep.   Vol. 8   page: 678   2018.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41598-017-18977-5

  13. Structural changes of homodimers in the PDB Reviewed

    R. Koike, T. Amemiya, T. Horii, M. Ota

    J. Str. Biol.     page: in press   2018

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jsb.2017.12.004

  14. Rules for connectivity of secondary structure elements of proteins: Two-layer αβ sandwiches Reviewed

    S. Minami, G. Chikenji, M. Ota

    Prot. Sci.   Vol. 26   page: 2257-2267   2017.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/pro.3285

  15. Itinerary profiling to analyze a large number of protein-folding trajectories Reviewed

    M. Ota, M. Ikeguchi, A. Kidera

    Biophys. Physicobiol.   Vol. 13   page: 295-304   2016.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi.org/10.2142/biophysico.13.0_295

  16. Interface property responsible for effective interactions of protean segments: Intrinsically disordered regions that undergo disorder-to-order transitions upon binding Reviewed

    D. Shaji, T. Amemiya, R. Koike R, M. Ota

    BBRC   Vol. 478   page: 123-127   2016.9

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1016/j.bbrc.2016.07.082

  17. Profile comparison revealed deviation from structural constraint at the positively selected sites Reviewed

    H. Oda , M. Ota, H. Toh

    Biosystems   Vol. 147   page: 67-77   2016.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1016/j.biosystems.2016.07.007

  18. Multiple-localization and hub proteins Reviewed

    M. Ota, H. Gonja, R. Koike, S. Fukuchi

    PLoS ONE   Vol. 11   page: e0156455   2016.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1371/journal.pone.0156455

  19. Comprehensive analysis of motions in molecular dynamics trajectories of the actin capping protein and its inhibitor complexes Reviewed

    R. Koike, S. Takeda, Y. Maéda, M. Ota

    Proteins   Vol. 84   page: 948-956   2016.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1002/prot.25043

  20. Investigation of the fatty acid transporter-encoding genes SLC27A3 and SLC27A4 in autism Reviewed

    M. Maekawa, Y. Iwayama, T. Ohnishi, M. Toyoshima, C. Shimamoto, Y. Hisano, T. Toyota, S. Balan, H. Matsuzaki, Y. Iwata, S. Takagai, K. Yamada, M. Ota, S. Fukuchi, Y. Okada, W. Akamatsu, M. Tsujii, N. Kojima, Y. Owada, H. Okano, N. Mori, T. Yoshikawa

    Sci. Rep.   Vol. 5   page: 16239   2015.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi:10.1038/srep16239

  21. Domain-motion enhanced (DoME) model for efficient conformational sampling of multi-domain proteins Reviewed

    C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, Y. Sugita

    J. Phys. Chem. B   Vol. 119   page: 14584-14593   2015.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: doi: 10.1021/acs.jpcb.5b07668

  22. A method for systematic assessment of intrinsically disordered protein regions by NMR Reviewed

    N. Goda, K. Shimizu, Y. Kuwahara, T. Noguchi, T. Ikegami, M. Ota, H. Hiroaki

    Int. J. Mol. Sci.   Vol. 16   page: 15743-15760   2015.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.3390/ijms160715743

  23. Hierarchical domain-motion analysis of conformational changes in Sarcoplasmic Reticulum Ca2+-ATPase Reviewed

    C. Kobayashi, R. Koike, M. Ota, Y. Sugita

    Proteins   Vol. 83   page: 746-756   2015.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/prot.24763

  24. An optimized Npro-based method for the expression and purification of intrinsically disordered proteins for an NMR study Reviewed

    N. Goda, N. Matsuo, T. Tenno, S. Ishino, Y. Ishino, S. Fukuchi, M. Ota, H. Hiroaki

    IDP   Vol. 3   page: 1-6   2015.2

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1080/21690707.2015.1011004

  25. Hierarchical description and extensive classification of protein structural changes by Motion Tree Reviewed

    R. Koike, M. Ota, A. Kidera

    J. Mol. Biol.   Vol. 426   page: 752-762   2014.2

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jmb.2013.10.034

  26. IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners Reviewed

    S. Fukuchi, T. Amemiya, S. Sakamoto, Y. Nobe, K. Hosoda, Y. Kado, SD. Murakami, R. Koike, H. Hiroaki, M. Ota

    Nucleic Acids Res.   Vol. 42   page: D320-D325   2014.1

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  27. Exon resequencing of H3K9 methyltransferase complex genes, EHMT1, EHMT2 and WIZ, in Japanese autism subjects Reviewed

    S. Balan, Y. Iwayama, M. Maekawa, T. Toyota, T. Ohnishi, M. Toyoshima, C. Shimamoto, K. Esaki, K. Yamada, Y. Iwata, K. Suzuki, M. Ide, M. Ota, S. Fukuchi, M. Tsujii, N. Mori, Y. Shinkai, T. Yoshikawa

    Molecular Autism     page: in the press   2014

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  28. Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening Reviewed

    T. Tenno, N. Goda, Y. Umetsu, M. Ota, K. Kinoshita, H. Hiroaki

    Molecules   Vol. 18   page: 9567-9581   2013.8

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  29. Substrate-shielding and hydrolytic reaction in hydrolases Reviewed

    Y. Kanematsu, R. Koike, T. Amemiya, M. Ota

      Vol. 81   page: 926-932   2013.2

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  30. An assignment of intrinsically disordered regions of proteins based on NMR structures Reviewed

    M. Ota, R. Koike, T. Amemiya, T. Tenno, P. R. Romero, H. Hiroaki, A. K. Dunker, S. Fukuchi

    J. Str. Biol.   Vol. 181   page: 29-36   2013.1

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  31. Influence of structural symmetry on protein dynamics Reviewed

    Y. Matsunaga, R. Koike, M. Ota, J. Tame, A. Kidera

    PLos One   Vol. 7   page: e50011   2012.11

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  32. A nobel biclustering approach with iterative optimization to analyze gene expression data Reviewed

    S. Sutheworapong, M. Ota, H. Ohta, K. Kinoshita

    Adv. Appl. Bioinform. Chem.   Vol. 5   page: 23-59   2012.9

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  33. SCPC: A method to structurally compare protein complexes

    R. Koike, M. Ota

    Bioinformatics     page: in press   2012.2

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  34. IDEAL: intrinsically disordered proteins with extensive annotations and literature

    S. Fukuchi, S. Sakamoto, Y. Nobe, SD. Murakami, T. Amemiya, K. Hosoda, R. Koike, H. Hiroaki, M. Ota

    Nucleic Acids Res.     page: in press   2012

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  35. PSCDB: a database for protein structural change upon ligand binding

    T. Amemiya, R. Koike, A. Kidera, M. Ota

    Nucleic Acids Res.     page: in press   2012

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  36. SAHG, a comprehensive database of predicted structures of all human proteins Reviewed

    C. Motono, J. Nakata, R. Koike, K. Shimizu, M. Shirota, T. Amemiya, K. Tomii, N. Nagano, N. Sakaya, K. Misoo, M, Sato, A. Kidera, H. Hiroaki, T. Shirai, K. Kinoshita, T. Noguchi, M. Ota

    Nucleic Acids Res.   Vol. 39   page: D487   2011

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  37. Cover and spacer insertions: small non-hydrophobic accessories that assist protein oligomerization

    H. Nishi, R. Koike, M. Ota

    Proteins   Vol. 79   page: 2372-2379   2011

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  38. Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function Reviewed

    S. Takeda, R. Koike, Y. Nitanai, S. Minakata, Y. Maéda, M. Ota

    Phys. Biol.   Vol. 8   page: 035005   2011

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  39. Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design Reviewed

    Y. Matsuura, M. Ota, T. Tanaka, M. Takehira, K. Ogasahara, B. Bagautdinov, N. Kunishima, K. Yutani

    J. Biochem.   Vol. 148   page: 449-458   2010

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  40. Amino acid substitutions at protein-protein interfaces that modulate the oligomeric state Reviewed

    H. Nishi, M. Ota

    Proteins   Vol. 78   page: 1563-1574   2010

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  41. Two distinct mechanisms for actin capping proteinregulationTwo distinct mechanisms for actin capping proteinregulation- steric and allosteric inhibitionsteric and allosteric inhibition Reviewed

    S. Takeda, S. Minakata, R. Koike, I. Kawahata, A. Narita, M. Kitazawa, M. Ota, T.Yamakuni, Y. Maéda, Y. Nitanai

    PLos Biol.   Vol. 8   page: e1000416   2010

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  42. Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold Reviewed

    R. Koike, A. Kidera, M. Ota

    Protein Sci.   Vol. 18   page: 2060-2066   2009

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  43. An evaluation of minimal cellular functions to sustain a bacterial cell Reviewed

    Y. Azuma, M. Ota

    BMC Syst. Biol.   Vol. 3   page: 111   2009

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  44. Protein structural change upon ligand binding correlates with enzymatic reaction mechanism Reviewed

    R. Koike, T. Amemiya, M. Ota, A. Kidera

    J. Mol. Biol.   Vol. 379   page: 397-401   2008

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  45. An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories Reviewed

    H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang

    BMC Bioinformatics   Vol. 9   page: 344   2008

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  46. Enhanced partial order curve comparison over multiple protein folding trajectories Reviewed

    H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang

    Comput. Syst. Bioinformatics. Conf.   Vol. 6   page: 299-310   2007

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  47. Unfolding pathways of goat α-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories Reviewed

    T. Oroguchi, M. Ikeguchi, M. Ota, K. Kuwajima and A. Kidera

    J. Mol. Biol.   Vol. 371   page: 1354-64   2007

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  48. Stabilization of E. coli ribonuclease HI by the 'stability profile of mutant protein' (SPMP)-inspired random and non-random mutagenesis Reviewed

    M. Haruki, Y. Saito, M. Ota, K. Nishikawa, S. Kanaya

    J. Biotech.   Vol. 25   page: 512-522   2006

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  49. A hyperthermophilic protein acquires function at the cost of stability Reviewed

    A. Mukaiyama, M. Haruki, M. Ota, Y. Koga, K. Takano and S. Kanaya

    Biochemistry   Vol. 24   page: 12673-12679   2006

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  50. P-cats: Prediction of catalytic residues in proteins from the tertiary structures Reviewed

    K. Kinoshita and M. Ota

    Bioinformatics   Vol. 21   page: 3570-3571   2005

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  51. Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry Reviewed

    Y. Asada, M. Sawano, K. Ogasahara, J. Nakamura, M. Ota, C. Kuroishi, M. Sugahara, K. Yutani, N. Kunishima

    J Biochem (Tokyo)   Vol. 138   page: 343-353   2005

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  52. Design of λ Cro fold: solution structure of a monomeric variant of the de novo protein Reviewed

    Y. Isogai, Y. Ito, T. Ikeya, Y. Shiro, M. Ota

    J. Mol. Biol.   Vol. 354   page: 801-814   2005

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  53. Integrative annotation of 21,037 human genes validated by full-length cDNA clones Reviewed

    T. Imanishi et al.

    PLoS. Biol.   Vol. 2   page: E162   2004

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  54. The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus Reviewed

    Y. Hioki, K. Ogasahara K, S. Lee, J. Ma, M. Ishida, Y. Yamagata, Y. Matsuura, M. Ota, M. Ikeguchi, S. Kuramitsu, K. Yutani

    Eur. J. Biochem.   Vol. 271   page: 2624-2635   2004

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  55. Phylogeny of protein-folding trajectories reveals a unique pathway to native structure Reviewed

    M. Ota, M. Ikeguchi and A. Kidera

    Proc. Natl. Acad. Sci. USA   Vol. 101   page: 17658-17663   2004

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Books 1

  1. ドロプレット形成のデータベースと予測(相分離生物学の全貌 白木賢太郎編)

    太田元規,福地佐斗志( Role: Contributor)

    東京化学同人  2020.11 

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    Total pages:402   Responsible for pages:363-367   Language:Japanese Book type:Scholarly book

Industrial property rights 1

  1. タンパク質凍結保存用保護剤

    法人名大,産業技術総合研究所

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    Date applied:2015.1

    Announcement no:WO 2015/125501  Date announced:2015.8

    Country of applicant:Foreign country   Country of acquisition:Foreign country

 

Teaching Experience (On-campus) 25

  1. Large-scale Complex Systems Computation 2

    2021

  2. Physical and Life Science Informatics 3

    2021

  3. Introduction to Biophysics Ib

    2021

  4. First Year Seminar A

    2021

  5. Bioinformatics 1

    2021

  6. Complex Systems Exercise 4

    2021

  7. Physical and Life Science Informatics 10

    2021

  8. Simulation Science 2

    2021

  9. Informatics 4

    2021

  10. Nature as Information System 1:Life

    2021

  11. Bioinformatics 2

    2021

  12. Complex Systems Sciences 1

    2021

  13. First Year Seminar A

    2020

  14. Introduction to Biophysics Ib

    2020

  15. Simulation Science 2

    2020

  16. Informatics 4

    2020

  17. Nature as Information System 1:Life

    2020

  18. バイオインフォマティクス特論2

    2020

  19. バイオインフォマティクス特論1

    2020

  20. 複雑系科学特論1

    2020

  21. Complex Systems Exercise 4

    2020

  22. Physical and Life Science Informatics 10

    2020

  23. Physical and Life Science Informatics 3

    2020

  24. 計算科学フロンティア

    2020

  25. 大規模複雑系計算特論2

    2020

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