Publications

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Hucka M, Hoops S, Keating S, Le Novère N, Sahle S, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nat Precedings 2008;
Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 [Internet]. Journal of Integrative Bioinformatics 2019;:Online advance publication.Available from: https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2019-0021/jib-2019-0021.xml?format=INT
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol 2010;8:140.
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. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics 2015;12(2):271.
Hucka M, Nickerson DPhillip, Bader G, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJohn, Schreiber F, Waltemath D, Le Novère N. Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative [Internet]. Frontiers in Bioengineering and Biotechnology 2015;3:19.Available from: http://journal.frontiersin.org/Journal/10.3389/fbioe.2015.00019/
Hucka M, Finney A, Hoops S, Keating S, Le Novère N. Systems biology markup language (SBML) Level 2: structures and facilities for model definitions. Nature Precedings 2007;
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. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics 2018;15(1):20170080.
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. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Journal of Integrative Bioinformatics 2018;15(1):10170081.
Hucka M, Finney A., Le Novère N. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. [Internet]. Nat Precedings 2006;Available from: http://sbml.org/documents/sbml-level-2/version-2/revision-1/sbml-level-2-version-2-rev1.pdf
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga YK, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008;26(10):1155-60.
Henkel R, Endler L, Peters A, Le Novère N, Waltemath D. Ranked retrieval of Computational Biology models. BMC Bioinformatics 2010;11:423.
Henkel R, Le Novère N, Wolkenhauer O, Waltemath D. Considerations of graph-based concepts to manage of computational biology models and associated simulations. INFORMATIK 2012 2012;
Hastings J, Mains A, Artal-Sanz M, Bergmann S, Braeckman BP, Bundy J, Cabreiro F, Dobson P, Ebert P, Hattwell J, Hefzi H, Houtkooper RH, Jelier R, Joshj C, Kothamachu VB, Lewis N, Lourenco ABastos, Nie Y, Norvaisas P, Pearce J, Riccio C, Rodriguez N, Santermans T, Scarcia P, Shirra HJoachim, Sheng M, Smith R, Suriyalaksh M, Towbin B, Tuli MAnn, Van Weeghel M, Weinkove D, Zecic A, Zimmerman J, Le Novère N, Kaleta C, Witting M, Casanueva O. WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series [Internet]. Worm 2017;6(2):e1373939.Available from: http://www.tandfonline.com/doi/full/10.1080/21624054.2017.1373939
Hastings J, Le Novere N, Ceusters W, Mulligan K, Smith B. Wanting what we don’t want to want: Representing addiction in interoperable bio-ontologies [Internet]. In: Proceedings of the 3rd International Conference on Biomedical Ontology. 2012Available from: http://ceur-ws.org/Vol-897/session3-paper12.pdf
Hastings J, Mains A, Virk B, Rodriguez N, Murdoch S, Pearce J, Bergmann S, Le Novère N, Casanueva O. Multi-omics and genome-scale modeling reveal a metabolic shift during C. elegans aging [Internet]. Frontiers in Molecular Biosciences 2019;Available from: https://www.frontiersin.org/articles/10.3389/fmolb.2019.00002/