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
Lieven C, Beber MEmanuel, Olivier BG, Bergmann FT, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BElisabeth, Edirisinghe JN, Fleming RMT, Garcia-Jimenez B, van Helvoirt W, Henry C, Hermjakob H, Herrgård MJ, Kim HUk, King Z, Koehorst JJan, Klamt S, Klipp E, Lakshmanan M, Le Novère N, Lee D-Y, Lee SYup, Lee S, Lewis NE, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk J, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Resendis O, Palsson B, Papin JA, Patil KRaosaheb, Price ND, Richelle A, Rocha I, Schaap P, Sheriff RSMalik, Shoaie S, Sonnenschein N, Teusink B, Vilaca P, Vik JOlav, Wodke JA, Xavier JC, Yuan Q, Zakhartsev M, Cheng Z. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite. BiorXiv 2018;
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, 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.
2015
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, 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.