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Results: 1 to 20 of 110

1.

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N.

CPT Pharmacometrics Syst Pharmacol. 2015 Jun;4(6):316-9. doi: 10.1002/psp4.57. Epub 2015 Jun 15.

2.

BioModels: Content, Features, Functionality, and Use.

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.

CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26.

3.

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.

Bioinformatics. 2015 Jun 16. pii: btv341. [Epub ahead of print]

4.

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.

5.

Quantitative and logic modelling of molecular and gene networks.

Le Novère N.

Nat Rev Genet. 2015 Mar;16(3):146-58. doi: 10.1038/nrg3885. Epub 2015 Feb 3. Review.

PMID:
25645874
6.

SPARQL-enabled identifier conversion with Identifiers.org.

Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.

Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31.

7.

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.

8.

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.

9.

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.

10.

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;15:369. doi: 10.1186/s12859-014-0369-z.

11.

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.

12.

BioModels linked dataset.

Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C.

BMC Syst Biol. 2014 Aug 15;8:91. doi: 10.1186/s12918-014-0091-5.

13.

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.

14.

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.

15.

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.

16.

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.

17.

Cooperative binding.

Stefan MI, Le Novère N.

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

18.

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.

19.

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.

20.

Controlled annotations for systems biology.

Juty N, Laibe C, Le Novère N.

Methods Mol Biol. 2013;1021:227-45. doi: 10.1007/978-1-62703-450-0_12.

PMID:
23715988
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