Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My NCBI Filters

Text availability

Article attribute

Article type

Publication date

Search Results

1,238 results

Filters applied: . Clear all
Results are displayed in a computed author sort order. The Results By Year timeline is not available.
Page 1
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Among authors: rodriguez n. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. Zhang F, et al. Among authors: rodriguez n. J Integr Bioinform. 2020 Jul 6;17(2-3):20200015. doi: 10.1515/jib-2020-0015. J Integr Bioinform. 2020. PMID: 32628633 Free PMC article.
Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N. Büchel F, et al. Among authors: rodriguez n. BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116. BMC Syst Biol. 2013. PMID: 24180668 Free PMC article.
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. Chaouiya C, et al. Among authors: rodriguez n. BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135. BMC Syst Biol. 2013. PMID: 24321545 Free PMC article.
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. Bergmann FT, et al. Among authors: rodriguez n. BMC Bioinformatics. 2014 Dec 14;15(1):369. doi: 10.1186/s12859-014-0369-z. BMC Bioinformatics. 2014. PMID: 25494900 Free PMC article.
JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A. Rodriguez N, et al. Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16. Bioinformatics. 2015. PMID: 26079347 Free PMC article.
The systems biology format converter.
Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. Rodriguez N, et al. BMC Bioinformatics. 2016 Apr 5;17:154. doi: 10.1186/s12859-016-1000-2. BMC Bioinformatics. 2016. PMID: 27044654 Free PMC article.
BioModels: expanding horizons to include more modelling approaches and formats.
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H. Glont M, et al. Among authors: rodriguez n. Nucleic Acids Res. 2018 Jan 4;46(D1):D1248-D1253. doi: 10.1093/nar/gkx1023. Nucleic Acids Res. 2018. PMID: 29106614 Free PMC article.
Designing and encoding models for synthetic biology.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N. Endler L, et al. Among authors: rodriguez n. J R Soc Interface. 2009 Aug 6;6 Suppl 4(Suppl 4):S405-17. doi: 10.1098/rsif.2009.0035.focus. Epub 2009 Apr 1. J R Soc Interface. 2009. PMID: 19364720 Free PMC article. Review.
1,238 results