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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum. Hucka M, et al. Among authors: shimizu ts. Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015. Bioinformatics. 2003. PMID: 12611808
E-CELL: software environment for whole-cell simulation.
Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA 3rd. Tomita M, et al. Among authors: shimizu ts. Bioinformatics. 1999 Jan;15(1):72-84. doi: 10.1093/bioinformatics/15.1.72. Bioinformatics. 1999. PMID: 10068694
Non-genetic adaptation by collective migration.
Vo L, Avgidis F, Mattingly HH, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T. Vo L, et al. Among authors: shimizu ts. bioRxiv [Preprint]. 2024 Jan 3:2024.01.02.573956. doi: 10.1101/2024.01.02.573956. bioRxiv. 2024. PMID: 38260286 Free PMC article. Preprint.
Exploring the dynamics of vascular adaptation.
Shimizu TS, Kiers ET, Stone HA. Shimizu TS, et al. Elife. 2023 May 25;12:e88052. doi: 10.7554/eLife.88052. Elife. 2023. PMID: 37227267 Free PMC article.
Optimal inference of molecular interaction dynamics in FRET microscopy.
Kamino K, Kadakia N, Avgidis F, Liu ZX, Aoki K, Shimizu TS, Emonet T. Kamino K, et al. Among authors: shimizu ts. Proc Natl Acad Sci U S A. 2023 Apr 11;120(15):e2211807120. doi: 10.1073/pnas.2211807120. Epub 2023 Apr 4. Proc Natl Acad Sci U S A. 2023. PMID: 37014867 Free PMC article.
40 results