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Results: 1 to 20 of 62

1.

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Review.

2.

Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model.

Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N.

PLoS One. 2015 Jan 28;10(1):e0116616. doi: 10.1371/journal.pone.0116616. eCollection 2015.

3.

Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

Lai M, Brun D, Edelstein SJ, Le Novère N.

PLoS Comput Biol. 2015 Jan 22;11(1):e1004063. doi: 10.1371/journal.pcbi.1004063. eCollection 2015 Jan.

4.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

5.

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.

BMC Bioinformatics. 2014 Dec 14;15(1):369. doi: 10.1186/s12859-014-0369-z.

6.

BioModels: ten-year anniversary.

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D542-8. doi: 10.1093/nar/gku1181. Epub 2014 Nov 20.

7.

The EBI RDF platform: linked open data for the life sciences.

Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.

Bioinformatics. 2014 May 1;30(9):1338-9. doi: 10.1093/bioinformatics/btt765. Epub 2014 Jan 11.

8.

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.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.

9.

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.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

10.

Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum.

Mattioni M, Le Novère N.

PLoS One. 2013 Jul 3;8(7):e66811. doi: 10.1371/journal.pone.0066811. Print 2013.

11.

Cooperative binding.

Stefan MI, Le Novère N.

PLoS Comput Biol. 2013;9(6):e1003106. doi: 10.1371/journal.pcbi.1003106. Epub 2013 Jun 27.

12.

The systems biology simulation core algorithm.

Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A.

BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55.

13.

Structure, function, and behaviour of computational models in systems biology.

Knüpfer C, Beckstein C, Dittrich P, Le Novère N.

BMC Syst Biol. 2013 May 31;7:43. doi: 10.1186/1752-0509-7-43.

14.

Towards the collaborative curation of the registry underlying Identifiers.org.

Juty N, Le Novère N, Hermjakob H, Laibe C.

Database (Oxford). 2013 Apr 12;2013:bat017. doi: 10.1093/database/bat017. Print 2013.

15.

A community-driven global reconstruction of human metabolism.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.

16.

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations.

von Eichborn J, Dunkel M, Gohlke BO, Preissner SC, Hoffmann MF, Bauer JM, Armstrong JD, Schaefer MH, Andrade-Navarro MA, Le Novere N, Croning MD, Grant SG, van Nierop P, Smit AB, Preissner R.

Nucleic Acids Res. 2013 Jan;41(Database issue):D834-40. doi: 10.1093/nar/gks1040. Epub 2012 Nov 11.

17.

LibKiSAO: a Java library for Querying KiSAO.

Zhukova A, Adams R, Laibe C, Le Novère N.

BMC Res Notes. 2012 Sep 24;5:520. doi: 10.1186/1756-0500-5-520.

18.

Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII.

Li L, Stefan MI, Le Novère N.

PLoS One. 2012;7(9):e43810. doi: 10.1371/journal.pone.0043810. Epub 2012 Sep 4.

19.

Qualitative translation of relations from BioPAX to SBML qual.

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A.

Bioinformatics. 2012 Oct 15;28(20):2648-53. doi: 10.1093/bioinformatics/bts508. Epub 2012 Aug 24.

20.

The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models.

Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ.

J Biol Rhythms. 2012 Aug;27(4):328-32. doi: 10.1177/0748730412451077.

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