Publications

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2018
Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling M, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Le Novère N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology [Internet]. BiorXiv 2018;:246470 .Available from: https://www.biorxiv.org/content/early/2018/01/23/246470
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. Journal of Integrative Bioinformatics 2018;15(1):20180013.
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.
2015
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 K, Pettit J-B, Rodriguez N, Schubert M, Wimalaratne S, Zhou Y, Hermjakob H, Le Novère N, Laibe C. BioModels: ten year anniversary [Internet]. Nucleic Acids Research 2015;Available from: http://nar.oxfordjournals.org/content/early/2014/11/20/nar.gku1181.abstract
Naldi A, Monteiro PT, Müssel C, Albert R, Barberis M, Calzone L, Chasapi A, Cokelaer T, Crespo I, Dorier J, Dräger A, Hernandez C, Hucka M, de Jong H, Keating SM, Klamt S, Klarner H, Laubenbacher R, Le Novère N, Niknejad A, Rodriguez N, Siebert H, Stoll G, Zañudo JGT, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics 2015;31(7):1154-1159.
Ebrahim A, almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RMT, Fong SS, Hatzimanakis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SYup, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Niels LK, Nogales J, Noronha A, Pal C, Palsson BØ, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do Genome-scale Models Need Exact Solvers or Clearer Standards?. Molecular Systems Biology 2015;11(10)
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. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics 2015;
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/
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kornmeier B, Le Novère N, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2015;12(2):258.
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.
2011
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N. Controlled vocabularies and semantics in systems biology. Mol Syst Biol 2011;7:543.
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics 2011;27(15):2167-8.
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2011;5(2):230-42.
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol 2011;7(4):e1001122.
Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol 2011;5:198.
2010
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010;4:92.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung K-H, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010;28(9):935-42.
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol 2010;8:140.