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Lloret-Villas A, Daudin R, Le Novère N. "Big Data" in neuroscience: open door to a more comprehensive and translational research [Internet]. Big Data Analytics 2016;1:5.Available from: http://bdataanalytics.biomedcentral.com/articles/10.1186/s41044-016-0005-1
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006;34(Database issue):D689-91.
Chelliah V, Juty N, Laibe C, Hermjakob H, Le Novère N. BioModels Database: a public repository for sharing models of biological processes. In: Encyclopedia of Computational Neuroscience. New York Heidelberg Dordrecht London : Springer-Verlag; 2015
Chelliah V, Laibe C, Le Novère N. BioModels Database, A Repository of Mathematical Models of Biological Processes. In: Encyclopedia of Systems Biology. Springer; 2013
Chelliah V, Laibe C, Le Novère N. BioModels Database: a repository of mathematical models of biological processes. Methods Mol Biol 2013;1021:189-99.
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.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne S, Hermjakob H, Le Novère N, Laibe C, Chelliah V. BioModels Database: content, features, functionality and use. CPT: Pharmacometrics & Systems Pharmacology 2015;2(4):1-14.
Glont M, Nguyen TV, Graesslin M, Raza A, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat M, Eils J, Eils R, Laibe C, Malik-Sheriff R, Chelliah V, Le Novère N, Hermjakob H. BioModels: Expanding horizons to include more modelling approaches and formats [Internet]. Nucleic Acids Research 2018;46(D1):D1248-D1253.Available from: https://academic.oup.com/nar/article/4584626
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C. BioModels linked dataset. BMC Syst Biol 2014;8:91.
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
Li C, Courtot M, Le Novère N, Laibe C. BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform 2010;11(3):270-7.
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.
Myers CJ, Bader G, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Nickerson DP, Schreiber F, Waltemath D. A brief history of COMBINE. Winter Simulation Conference 2017 2017;:884-895.
Tolle DP, Le Novère N. Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. BMC Syst Biol 2010;4:25.
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Li L, Stefan MI, Le Novère N. Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII. PLoS One 2012;7(9):e43810.
Schilstra MJ, Li L, Matthews J, Finney A, Hucka M, Le Novère N. CellML2SBML: conversion of CellML into SBML. Bioinformatics 2006;22(8):1018-20.
Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project [Internet]. BMC Systems Biology 2014;15:369 .Available from: http://arxiv.org/abs/1407.4992
Bergmann FT, Rodriguez N, Le Novère N. COMBINE archive specification Version 1. Journal of Integrative Bioinformatics 2015;12(2):261.
Beal J, Nguyen T, Gorochowski TE, Goñi-Moreno A, Scott-Brown J, McLaughlin JAlastair, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo-Hair S, Clancy K, Luna A, Le Novère N, Palchick Z, Pocock M, Sauro H, Sexton J, Tabor J, Voigt C, Zundel Z, Myers C, Wipat A. Communicating Structure and Function in Synthetic Biology Diagrams [Internet]. ACS Synthetic Biology 2019;8(8):1818-1825.Available from: https://pubs.acs.org/doi/10.1021/acssynbio.9b00139
Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming R, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R. Community-driven roadmap for integrated disease maps [Internet]. Briefings in Bioinformatics 2018;Available from: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby024/4982567
Guerlet G, Taly A, Prado de Carvalho L, Martz A, Jiang R, Specht A, Le Novère N, Grutter T. Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem Biophys Res Commun 2008;375(3):405-9.
Stefan MI, Edelstein SJ, Le Novère N. Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Syst Biol 2009;3:68.
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.
Juty N, Laibe C, Le Novère N. Controlled annotations for systems biology. Methods Mol Biol 2013;1021:227-45.
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.
Stefan MI, Le Novère N. Cooperative binding. PLoS Computational Biology 2013;9(6)
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.
Edelstein SJ, Le Novère N. Cooperativity of allosteric receptors. Journal of Molecular Biology 2013;425(9): 1424-1432.
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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
Dumontier M, Gray AJG, Marshall SM, Alexiev V, Ansell P, Bader GD, Baran J, Bolleman J, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz E, Gonzalez-Beltran A, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayam T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall C, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ 2016;4:e2331.
Nguyen A, Guedán A, Mousnier A, Swieboda D, Zhang Q, Horkai D, Le Novère N, Solari R, Wakelam MJO. Host lipidome analysis during rhinovirus replication in human bronchial epithelial cells identifies potential therapeutic targets. [Internet]. Journal of Lipid Research 2018;Available from: http://www.jlr.org/content/early/2018/06/26/jlr.M085910.abstract
Bargehr J, Ong LP, Colzani M, Davaapil H, Hofsteen P, Bhandari, iv S, Gambardella L, Le Novère N, Iyer D, Sampaziotis F, Weinberger F, Bertero A, Leonard A, Bernard WG, Martinson A, Figg N, Regnier M, Bennett MR, Murry CE, Sinha S. Human embryonic stem cell-derived epicardial cells augment cardiomyocyte-driven heart regeneration [Internet]. Nature Biotechnology 2019;37:895–906.Available from: https://www.nature.com/articles/s41587-019-0197-9
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McMurry J, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Hastings J, Haendel MA, Hermjakob H, Hériché J-K, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Mungall CJ, Rocca-Serra P, Sansone S-A, Sariyar M, Snoep JL, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams AR, Wolstencroft K, Goble C, Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact of life science data [Internet]. PLoS Biology 2017;15(6):e2001414.Available from: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414
Juty N, Le Novère N, Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res 2012;40(Database issue):D580-6.
Laibe C, Wimalaratne S, Juty N, Le Novère N, Hermjakob H. Identifiers.org: integration tool for heterogeneous datasets. 10th International workshop Data Integration in the Life Sciences 2014;
Villas ALloret i, Varusai TM, Juty N, Laibe C, Le Novère N, Hermjakob H, Chelliah V. The impact of mathematical modeling in understanding the mechanisms underlying neurodegeneration: evolving dimensions and future directions [Internet]. CPT: Pharmacometrics & Systems Pharmacology 2017;Available from: onlinelibrary.wiley.com/doi/10.1002/psp4.12155/full
Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V. The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: Pharmacometrics & Systems Pharmacology 2013;2:e54.
Mattioni M, Le Novère N. Integration of biochemical and electrical signaling - multiscale model of the medium spiny neuron of the striatum. PLoS ONE 2013;8(7):e66811.
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Pir P, Le Novère N. Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine. In: Methods Molecular Biology: Systems Medicine. Springer; 2016 p. 331-350.
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, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Lucian S, Zhang F, Eric B. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences 2013;9
Dumousseau M, Rodriguez N, Juty N, Le Novère N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics 2012;13:101.
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;
Tolle DP, Le Novère N. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Syst Biol 2010;4:24.
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.
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 2005;23(12):1509-15.
Laibe C, Le Novère N. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst Biol 2007;1:58.
Le Novère N. Model storage, exchange and integration. BMC Neurosci 2006;7 Suppl 1:S11.
Wittig MA, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, Van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis N, Schirra H-J, Kaleta C, Casanueva O. Modeling meets Metabolomics – The WormJam Consensus Model as basis for Metabolic Studies in the model organism Caenorhabditis elegans [Internet]. Frontiers in Molecular Biosciences 2018;5:96.Available from: https://www.frontiersin.org/articles/10.3389/fmolb.2018.00096/full
Lai M, Brun D, Edelstein S, Le Novère N. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions [Internet]. PLoS Computational Biology 2015;11(1):e1004063.Available from: http://arxiv.org/abs/1406.2195
Le Novère N, Donizelli M. The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). BMC Bioinformatics 2004;5:174.
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/
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Kiselev VY, Juvin V, Mouhannad M, Luscombe NM, Hawkins P, Le Novère N, Stephens LR. Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop [Internet]. Nucleic Acids Research 2015;43(20): 9663-9679.Available from: http://nar.oxfordjournals.org/content/43/20/9663.long
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NRode, Lavielle M, Mari A, Magni P, Bizzoto R, Smith M, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chenel M, Edwards D, Franklin C, Giorgina T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kobash N, Laibe C, Laveille C, Mentre F, Mezzalana E, Munafo A, Nordgren R, Nyberg HB, Para-Guillen ZP, Pasotti L, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Harnisch L, Karlsson M, Hermjakob H, Le Novère N. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT: Pharmacometrics & Systems Pharmacology 2015;6:316-319.
Waltemath D, Wolkenhauer O, Le Novère N, Dumontier M. Possibilities for Integrating Model-related Data in Computational Biology [Internet]. 9th International workshop Data Integration in the Life Sciences 2013;Available from: http://www.unbsj.ca/sase/csas/data/ws/dils2013/papers/DILS-SYS-EC-paper8.pdf
Knight-Schrijver V, Chelliah V, Cucurull-Sanchez L, Le Novère N. The promises of quantitative systems pharmacology modelling for drug development [Internet]. Computational and Structural Biotechnology Journal 2016;14:363–370.Available from: http://www.sciencedirect.com/science/article/pii/S2001037016300435
Taylor CF, Field D, Sansone S-A, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz P-A, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon A-M, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008;26(8):889-96.
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/
Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VYu, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Hawkins P, Clark J, Stephens LR. PTEN regulates PI(3,4)P2 signalling downstream of class I PI3K [Internet]. Molecular Cell 2017;68(3):566–580.Available from: http://www.sciencedirect.com/science/article/pii/S1097276517307025
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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.
Rodriguez N, Donizelli M, Le Novère N. SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). BMC Bioinformatics 2007;8:79.
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.
Pezze PDalle, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks [Internet]. BMC Systems Biology 2017;11:46.Available from: https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0423-3
Baldi BF, Hoyer C, Le Novère N. Schizophrenic: forever young?. Genome Med 2010;2(5):32.
Waltemath D, Le Novère N. Simulation Experiment Description Markup Language (SED-ML). In: Encyclopedia of computational neuroscience. 2013
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.
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.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 2012;28(15):2016-21.
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol 2010;8:140.
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.
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.
Stefan MI, Marshall DP, Le Novère N. Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII. PLoS One 2012;7(1):e29406.
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.
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.
Madsen C, Moreno AGoni, Palchick Z, P U, Roehner N, Bartley B, Bhatia S, Bhakta S, Bissel M, Clancy K, Cox RSidney, Gorochowski T, Grünberg R, Luna A, McLaughlin J, Nguyen T, Le Novère N, Pocock M, Sauro H, Scott-Brown J, 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 2.1 [Internet]. Journal of Integrative Bioinformatics 2019;:Online advance publication.Available from: https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0101/jib-2018-0101.xml?format=INT
Baig H, Fontanarossa P, Kulkarni V, McLaughlin J, Vaidyanathan P, Bartley B, Bhatia S, Bhakta S, Bissel M, Clancy K, Cox RSidney, Moreno AGoni, Gorochowski T, Grünberg R, Luna A, Madsen C, Mısırlı G, Nguyen T, Le Novère N, Palchick Z, Pocock M, Roehner N, Sauro H, Scott-Brown J, Sexton JT, Stan G-B, Tabor JJ, Vilar MVazquez, Voigt CA, Wipat A, Zong D, Zundel Z, Beal J, Myers C. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.2. Journal of Integrative Bioinformatics 2020;17:20200014.
Rodriguez N, Pettit J-B, Pezze PDalle, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. The Systems Biology Format Converter. BMC Bioinformatics 2016;17:154.
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, 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, 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, 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.
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.
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