Publications

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2018
Boras V, Fucic A, Virag M, Gabric D, Blivajs I, Tomasovic-Longaric C, Rakusic Z, Bisof V, Le Novère N, Vrdoljak DV. Significance of stroma in biology of oral squamous cell carcinoma. Tumori 2018;104(1):9-14.
Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Lucian S, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of Integrative Bioinformatics 2018;15(1):20170086.
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.
Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novère N, Pocock M, Sauro H, Sexton JT, Stan G-B, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. Journal of Integrative Bioinformatics 2018;15:20170074.
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.
Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MManuela, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms [Internet]. NPJ Systems Biology and Applications 2018;4:21.Available from: https://www.nature.com/articles/s41540-018-0059-y
Fucic A, Aghajanyan A, Culig Z, Le Novère N. Systems Oncology: Bridging Pancreatic and Castrate Resistant Prostate Cancer [Internet]. Pathology and Oncology Research 2018;Available from: https://link.springer.com/article/10.1007%2Fs12253-018-0467-8
2015
Quinn JYuan, Cox, III RSidney, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari A, McLaughlin JAlastair, Myers C, P U, Pocock M, Rodriguez C, Soldatova L, Stan G-B, Swainston N, Sauro HM, Wipat A. SBOL Visual: Standard Schematics for Synthetic Genetic Constructs. PLoS Biology 2015;13(12):e1002310.
Bergmann FT, Cooper J, Le Novère N, Nickerson DP, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of Integrative Bioinformatics 2015;12(2):262.
Wimalaratne SM, Bolleman J, Juty N, Katayam T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. SPARQL-enabled identifier conversion with Identifiers.org. Bioinformatics 2015;
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.
Mi H, Schreiber F, Moodie SL, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger AC. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. Journal of Integrative Bioinformatics 2015;12:266.
Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie SL, Schreiber F, Villéger AC. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. Journal of Integrative Bioinformatics 2015;12(2):264.
Moodie SL, Le Novère N, Demir E, Mi H, Villéger AC. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. Journal of Integrative Bioinformatics 2015;12(2):263.
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.
Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel M, Le Novère N, Helikar T. The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. Journal of Integrative Bioinformatics 2015;12(2):270.
2013
Chaouiya C, Berenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, çalves 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. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology 2013;7(1):135.
Waltemath D, Le Novère N. Simulation Experiment Description Markup Language (SED-ML). In: Encyclopedia of computational neuroscience. 2013
Knüpfer C, Beckstein C, Dittrich P, Le Novère N. Structure, function, and behaviour of computational models in systems biology. BMC Syst Biol 2013;7:43.
Keating SM, Le Novère N. Supporting SBML as a model exchange format in software applications. Methods Mol Biol 2013;1021:201-25.
von Eichborn J, Dunkel M, Gohlke B, Preissner S, Hoffmann M, Bauer J, Armstrong JD, Schaefer M, Andrade M, Le Novère M, Croning M, Grant SGN, van Nierop P, Smit AB, Preissner R. SynSysNet: Integration of experimental data on synaptic protein-protein interactions with drug-target relations [Internet]. Nucleic Acids Res. 2013;41(D1):D834-D840.Available from: http://nar.oxfordjournals.org/content/41/D1/D834.full
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Drager A. The systems biology simulation core algorithm. BMC Systems Biology 2013;
2009
Dräger A, Planatscher H, Wouamba DMotsou, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics 2009;25(11):1455-6.
Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, Schürrle K, van Leeuwen I. SysBioMed report: advancing systems biology for medical applications. IET Syst Biol 2009;3(3):131-6.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol 2009;27(8):735-41.
Mi H, Schreiber F, Le Novére N, Moodie S, Sorokin A. Systems biology graphical notation: Activity flow language level 1. Nature Precedings 2009;
Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nat Precedings 2009;
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems biology graphical notation: process description language level 1. Nature Precedings 2009;