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Results: 1 to 20 of 98

1.

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.

PMID:
24413672
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24321545
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
24180668
[PubMed - in process]
Free Article
4.

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.

PMID:
23843966
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Cooperative binding.

Stefan MI, Le Novère N.

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

PMID:
23843752
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23826941
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23721297
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
9.

Supporting SBML as a model exchange format in software applications.

Keating SM, Le Novère N.

Methods Mol Biol. 2013;1021:201-25. doi: 10.1007/978-1-62703-450-0_11.

PMID:
23715987
[PubMed - indexed for MEDLINE]
10.

BioModels Database: a repository of mathematical models of biological processes.

Chelliah V, Laibe C, Le Novère N.

Methods Mol Biol. 2013;1021:189-99. doi: 10.1007/978-1-62703-450-0_10.

PMID:
23715986
[PubMed - indexed for MEDLINE]
11.

Using chemical kinetics to model biochemical pathways.

Le Novère N, Endler L.

Methods Mol Biol. 2013;1021:147-67. doi: 10.1007/978-1-62703-450-0_8.

PMID:
23715984
[PubMed - indexed for MEDLINE]
12.

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.

PMID:
23584831
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Cooperativity of allosteric receptors.

Edelstein SJ, Le Novère N.

J Mol Biol. 2013 May 13;425(9):1424-32. doi: 10.1016/j.jmb.2013.03.011. Epub 2013 Mar 21. Review.

PMID:
23523898
[PubMed - indexed for MEDLINE]
Free Article
14.

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.

PMID:
23455439
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
23143269
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
23006857
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
22962589
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
22923304
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
22855577
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

Mattioni M, Cohen U, Le Novère N.

Front Neuroinform. 2012 Jun 6;6:20. doi: 10.3389/fninf.2012.00020. eCollection 2012.

PMID:
22685429
[PubMed]
Free PMC Article

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