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Items: 1 to 20 of 126

1.

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.

BMC Bioinformatics. 2016 Apr 5;17:154. doi: 10.1186/s12859-016-1000-2.

2.

The evolution of standards and data management practices in systems biology.

Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053. No abstract available.

3.

Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine.

Pir P, Le Novère N.

Methods Mol Biol. 2016;1386:331-50. doi: 10.1007/978-1-4939-3283-2_15.

PMID:
26677190
4.

Enabling surface dependent diffusion in spatial simulations using Smoldyn.

Seeliger C, Le Novère N.

BMC Res Notes. 2015 Dec 8;8(1):752. doi: 10.1186/s13104-015-1723-6.

5.

SBOL Visual: A Graphical Language for Genetic Designs.

Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM.

PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015 Dec.

6.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271.

PMID:
26528569
7.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.

J Integr Bioinform. 2015 Sep 4;12(2):270. doi: 10.2390/biecoll-jib-2015-270.

PMID:
26528568
8.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

Mi H, Schreiber F, Moodie S, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger A.

J Integr Bioinform. 2015 Sep 4;12(2):265. doi: 10.2390/biecoll-jib-2015-265.

PMID:
26528563
9.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie S, Schreiber F, Villéger A.

J Integr Bioinform. 2015 Sep 4;12(2):264. doi: 10.2390/biecoll-jib-2015-264.

PMID:
26528562
10.

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

Moodie S, Le Novère N, Demir E, Mi H, Villéger A.

J Integr Bioinform. 2015 Sep 4;12(2):263. doi: 10.2390/biecoll-jib-2015-263.

PMID:
26528561
11.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Bergmann FT, Cooper J, Le Novère N, Nickerson D, Waltemath D.

J Integr Bioinform. 2015 Sep 4;12(2):262. doi: 10.2390/biecoll-jib-2015-262.

PMID:
26528560
12.

COMBINE Archive Specification Version 1.

Bergmann FT, Rodriguez N, Le Novère N.

J Integr Bioinform. 2015 Sep 4;12(2):261. doi: 10.2390/biecoll-jib-2015-261.

PMID:
26528559
13.

Specifications of Standards in Systems and Synthetic Biology.

Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S.

J Integr Bioinform. 2015 Sep 4;12(2):258. doi: 10.2390/biecoll-jib-2015-258.

PMID:
26528556
14.

Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

15.

Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop.

Kiselev VY, Juvin V, Malek M, Luscombe N, Hawkins P, Le Novère N, Stephens L.

Nucleic Acids Res. 2015 Nov 16;43(20):9663-79. doi: 10.1093/nar/gkv1015. Epub 2015 Oct 12.

16.

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.

17.

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.

18.

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 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.

19.

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.

20.

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.

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