• Source: Scopus
  • Calculated based on no. of publications stored in Pure and citations from Scopus
19962021

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  • 2021

    Genome-wide role of hsf1 in transcriptional regulation of desiccation tolerance in the anhydrobiotic cell line, pv11

    Tokumoto, S., Miyata, Y., Deviatiiarov, R., Yamada, T. G., Hiki, Y., Kozlova, O., Yoshida, Y., Cornette, R., Funahashi, A., Shagimardanova, E., Gusev, O. & Kikawada, T., 2021 Jun 1, In: International journal of molecular sciences. 22, 11, 5798.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
  • 2020

    SBML Level 3: an extensible format for the exchange and reuse of biological models

    Keating, S. M., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., Hoops, S., Malik-Sheriff, R. S., Moodie, S. L., Moraru, I. I., Myers, C. J., Naldi, A., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P. & 121 others, Swat, M. J., Thieffry, D., Watanabe, L., Wilkinson, D. J., Blinov, M. L., Begley, K., Faeder, J. R., Gómez, H. F., Hamm, T. M., Inagaki, Y., Liebermeister, W., Lister, A. L., Lucio, D., Mjolsness, E., Proctor, C. J., Raman, K., Rodriguez, N., Shaffer, C. A., Shapiro, B. E., Stelling, J., Swainston, N., Tanimura, N., Wagner, J., Meier-Schellersheim, M., Sauro, H. M., Palsson, B., Bolouri, H., Kitano, H., Funahashi, A., Hermjakob, H., Doyle, J. C., Hucka, M., Adams, R. R., Allen, N. A., Angermann, B. R., Antoniotti, M., Bader, G. D., Červený, J., Courtot, M., Cox, C. D., Dalle Pezze, P., Demir, E., Denney, W. S., Dharuri, H., Dorier, J., Drasdo, D., Ebrahim, A., Eichner, J., Elf, J., Endler, L., Evelo, C. T., Flamm, C., Fleming, R. M. T., Fröhlich, M., Glont, M., Gonçalves, E., Golebiewski, M., Grabski, H., Gutteridge, A., Hachmeister, D., Harris, L. A., Heavner, B. D., Henkel, R., Hlavacek, W. S., Hu, B., Hyduke, D. R., de Jong, H., Juty, N., Karp, P. D., Karr, J. R., Kell, D. B., Keller, R., Kiselev, I., Klamt, S., Klipp, E., Knüpfer, C., Kolpakov, F., Krause, F., Kutmon, M., Laibe, C., Lawless, C., Li, L., Loew, L. M., Machne, R., Matsuoka, Y., Mendes, P., Mi, H., Mittag, F., Monteiro, P. T., Natarajan, K. N., Nielsen, P. M. F., Nguyen, T., Palmisano, A., Pettit, J. B., Pfau, T., Phair, R. D., Radivoyevitch, T., Rohwer, J. M., Ruebenacker, O. A., Saez-Rodriguez, J., Scharm, M., Schmidt, H., Schreiber, F., Schubert, M., Schulte, R., Sealfon, S. C., Smallbone, K., Soliman, S., Stefan, M. I., Sullivan, D. P., Takahashi, K., Teusink, B., Tolnay, D., Vazirabad, I., von Kamp, A., Wittig, U., Wrzodek, C., Wrzodek, F., Xenarios, I., Zhukova, A. & Zucker, J., 2020 Aug 1, In: Molecular systems biology. 16, 8, e9110.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    26 Citations (Scopus)
  • 2015

    The principles of whole-cell modeling

    Karr, J. R., Takahashi, K. & Funahashi, A., 2015 Oct 1, In: Current Opinion in Microbiology. 27, p. 18-24 7 p.

    Research output: Contribution to journalReview articlepeer-review

    37 Citations (Scopus)
  • 2010

    The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

    Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K. F., Yamamoto, Y., Yamaguchi, A., Kawashima, S., Chun, H. W., Aerts, J., Aranda, B., Barboza, L. H., Bonnal, R. J. P., Bruskiewich, R., Bryne, J. C., Fernández, J. M., Funahashi, A., Gordon, P. M. K., Goto, N., Groscurth, A. & 37 others, Gutteridge, A., Holland, R., Kano, Y., Kawas, E. A., Kerhornou, A., Kibukawa, E., Kinjo, A. R., Kuhn, M., Lapp, H., Lehvaslaiho, H., Nakamura, H., Nakamura, Y., Nishizawa, T., Nobata, C., Noguchi, T., Oinn, T. M., Okamoto, S., Owen, S., Pafilis, E., Pocock, M., Prins, P., Ranzinger, R., Reisinger, F., Salwinski, L., Schreiber, M., Senger, M., Shigemoto, Y., Standley, D. M., Sugawara, H., Tashiro, T., Trelles, O., Vos, R. A., Wilkinson, M. D., York, W., Zmasek, C. M., Asai, K. & Takagi, T., 2010 Aug 21, In: Journal of Biomedical Semantics. 1, 8.

    Research output: Contribution to journalReview articlepeer-review

    23 Citations (Scopus)
  • 2009

    The Systems Biology Graphical Notation

    Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M. & 19 others, Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H., 2009 Aug, In: Nature Biotechnology. 27, 8, p. 735-741 7 p.

    Research output: Contribution to journalReview articlepeer-review

    561 Citations (Scopus)
  • 2005

    Using process diagrams for the graphical representation of biological networks

    Kitano, H., Funahashi, A., Matsuoka, Y. & Oda, K., 2005 Aug, In: Nature Biotechnology. 23, 8, p. 961-966 6 p.

    Research output: Contribution to journalReview articlepeer-review

    332 Citations (Scopus)
  • 2004

    Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

    Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M., Shapiro, B. E., Matthews, J., Kovitz, B. L., Schilstra, M. J., Funahashi, A., Doyle, J. C. & Kitano, H., 2004 Jun, In: Systems biology. 1, 1, p. 41-53 13 p.

    Research output: Contribution to journalReview articlepeer-review

    161 Citations (Scopus)
  • 2003
    2 Citations (Scopus)