Publications

Export 166 results:
Author Title [ Type(Asc)] Year
Journal Article
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
Le Novère N, Endler L. Using chemical kinetics to model biochemical pathways. Methods Mol Biol 2013;1021:147-67.
Juty N, Le Novère N, Hermjakob H, Laibe C. Towards the collaborative curation of the registry underlying Identifiers.org. Databases 2013;
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PEPinto, Cantarelli M, Chew YHoon, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gómez HF, Hahn J, Hameri T, Gardiol DFHernande, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knüpfer C, König M, Lee D, Lloret-Villas A, Mandrik N, J Medley K, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song J-H, Theile T, Tokic M, Tomar N, Touré V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. Toward Community Standards and Software for Whole-Cell Modeling [Internet]. IEEE Transactions on Biomedical Engineering 2016;63(10):2007 - 2014.Available from: http://ieeexplore.ieee.org/abstract/document/7489010/
Díaz-Muñoz MD, Kiselev VYu, Le Novère N, Curk T, Ule J, Turner M. Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells [Internet]. Nature Communications 2017;8:530.Available from: https://www.nature.com/articles/s41467-017-00454-2
Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H. Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology 2011;7:e1002202.
Pezze PDalle, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PRazquin, van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Hahn U, Horvatovich P, Shanley DP, Thedieck K. A systems study reveals concurrent activation of AMPK and mTOR by amino acids [Internet]. 2016;7:13254 - .Available from: http://dx.doi.org/10.1038/ncomms13254
Guimera AMartinez, Welsh C, Pezze PDalle, Fullard N, Nelson G, Roger MF, Przyborski SA, Shanley DP. Systems modelling ageing: from single senescent cells to simple multi-cellular models [Internet]. Essays In Biochemistry 2017;61(3):369.Available from: http://essays.biochemistry.org/content/61/3/369.abstract
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;
Le Novère N, Oellrich A. Systems Biology Markup Language (SBML) Level 3 Proposal: multistate components [Internet]. 2007;Available from: http://www.ebi.ac.uk/ lenov/PUBLIS/Lenov2007c.pdf
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.
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, 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, 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
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 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.
Le Novère N, Moodie S, Sorokin A, Hucka M, Schreiber F, Demir E, Mi H, Matsuoka Y, Wegner K, Kitano H. Systems biology graphical notation: process diagram level 1. 2008;
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.
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nat Precedings 2011;
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nat Precedings 2010;
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems biology graphical notation: process description language level 1. Nature Precedings 2009;
Le Novère N, Demir E, Mi H, Moodie S, Villeger A. Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2). Nat Precedings 2011;
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.
Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nat Precedings 2010;
Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nat Precedings 2009;
Mi H, Schreiber F, Le Novére N, Moodie S, Sorokin A. Systems biology graphical notation: Activity flow language level 1. Nature Precedings 2009;
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.
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.
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.
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.
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.
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
Keating SM, Le Novère N. Supporting SBML as a model exchange format in software applications. Methods Mol Biol 2013;1021:201-25.
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.
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.
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.
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.
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;
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol 2010;8:140.
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.
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.
Waltemath D, Bergmann FT, Adams R, Le Novère N. Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1. Nat Precedings 2011;
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.
Le Novère N, Finney A. A simple scheme for annotating SBML with references to controlled vocabularies and database entries [Internet]. 2005;Available from: http://www.ebi.ac.uk/ lenov/PUBLIS/Lenov2005d.pdf
Boras V, Fusic 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.
Baldi BF, Hoyer C, Le Novère N. Schizophrenic: forever young?. Genome Med 2010;2(5):32.
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
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.
Rodriguez N, Donizelli M, Le Novère N. SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). BMC Bioinformatics 2007;8:79.
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.
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, Swainston N, Lister A, Bergmann F, Henkel R, Hoops S, Hucka M, Juty N, Keating S, Knuepfer C, others. SBML Level 3 Package Proposal: Annot. Nature Precedings 2011;
Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W. Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol 2011;7:512.
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.
Musante V, Li L, Kanyo J, Lam TT, Colangelo CM, Cheng SK, Brody H, Greengard P, Le Novère N, Nairn AC. Reciprocal regulation of ARPP-16 by protein kinase A and MAST-3 kinase provides a cAMP-regulated switch in protein phosphatase 2A inhibition. eLife 2017;6:e24998.
Henkel R, Endler L, Peters A, Le Novère N, Waltemath D. Ranked retrieval of Computational Biology models. BMC Bioinformatics 2010;11:423.
Touré V, Le Novère N, Waltemath D, Wolkenhauer O. Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Computational Biology 2018;14(2): e1005740.
Le Novère N. Quantitative and logic modelling of gene and molecular networks. Nature Reviews Genetics 2015;16:146–158.
Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A. Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics 2012;28(20):2648-53.
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
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/
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.
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
Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J 2013;8(9):1017-34.
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.
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
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Drager A, Le Novère N. Path2Models: Large-scale generation of computational models from biochemical pathway map [Internet]. BMC Systems Biology 2013;7:116.Available from: http://arxiv.org/abs/1307.7005
Tolle DP, Le Novère N. Particle-based stochastic simulation in systems biology. Current Bioinformatics 2006;1:315–320.
Dräger A, Planatscher H, Wouamba DM, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. Oligomeric membrane receptors: linking structural dynamics and functional kinetics. SBML2LATEX: Conversion of SBML files into human-readable reports 2009;25:1455-1456.
Edelstein SJ, Changeux J-P. Oligomeric membrane receptors: linking structural dynamics and functional kinetics. Biophys J 2010;98:2045-2052.
Schapira AHV, Bezard E, Brotchie J, Calon F, Collingridge GL, Ferger B, Hengerer B, Hirsch E, Jenner P, Le Novère N, Obeso JA, Schwarzschild MA, Spampinato U, Davidai G. Novel pharmacological targets for the treatment of Parkinson's disease. Nat Rev Drug Discov 2006;5(10):845-54.
Edelstein SJ. A Novel Equation for Cooperativity of the Allosteric State Function. Journal of Molecular Biology 2014;426:39-42.
Taly A, Delarue M, Grutter T, Nilges M, Le Novère N, Corringer P-J, Changeux J-P. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys J 2005;88(6):3954-65.
Mattioni M, Cohen U, Le Novère N. Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Front Neuroinform 2012;6:20.
Le Novère N. Neurological disease: are systems approaches the way forward?. Pharmacopsychiatry 2008;41 Suppl 1:S28-31.
Le Novère N, Donizelli M. The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). BMC Bioinformatics 2004;5:174.
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. Model storage, exchange and integration. BMC Neurosci 2006;7 Suppl 1:S11.
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 2013;587(17):2832-41.
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, 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.
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.
Tolle DP, Le Novère N. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Syst Biol 2010;4:24.
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.
Kettner C, Field D, Sansone S, Taylor C, Aerts J, Binns N, Blake A, Britten CM, Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop. Standards in Genomic Sciences 2010;3:259-266.
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
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.
Shimizu TS, Le Novère N. Looking inside the box: bacterial transistor arrays. Mol Microbiol 2008;69(1):5-9.
Le Novère N. The long journey to a Systems Biology of neuronal function. BMC Syst Biol 2007;1:28.
Roy RDutta, Rosenmund C, Edelstein SJ, Le Novère N. Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model [Internet]. PLoS ONE 2015;10(1):e0116616.Available from: http://arxiv.org/abs/1407.4750
Edelstein SJ, Stefan MI, Le Novère N. Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction. PLoS One 2010;5(1):e8449.
Zhukova A, Adams R, Laibe C, Le Novère N. LibKiSAO: a Java library for Querying KiSAO. BMC Res Notes 2012;5:520.
Donizelli M, Djite M-A, Le Novère N. LGICdb: a manually curated sequence database after the genomes. Nucleic Acids Res 2006;34(Database issue):D267-9.
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.
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;
Prevost MS, Moraga-Cid G, Van Renterghem C, Edelstein SJ, Changeux J-P, Corringer P-J. Intermediate closed state for glycine receptor function revealed by cysteine cross-linking. Proc Natl Acad Sci U S A 2013;110(42):17113-8.
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.
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ. The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. J Biol Rhythms 2012;27(4):328-32.
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.
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
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.
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
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.
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
Dean AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, J Burleigh G, Chanet B, Cooper LD, Courtot M, Csõsz S, Cui H, Dahdul W, Das S, T Dececchi A, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendle M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lapp H, Lawrence CJ, Le Novère N, Lecointre G, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, R Squires B, Thacker RW, Thessen A, Triana JFernandez, Vihinen M, Vize PD, Voget L, Wall CE, Walls RL, Westerfield M, Wharton RA, Wirkner CS, Wooley JB, Yoder MJ, Zorn AM, Mabee PM. Finding our way through phenotypes. PLoS Biology 2015;13(1): e1002033.
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep JL, Goble C. The evolution of standards and data management practices in systems biology [Internet]. Molecular Systems Biology 2015;11:851.Available from: http://msb.embopress.org/content/11/12/851
Seeliger C, Le Novère N. Enabling surface dependent diffusion in spatial simulations using Smoldyn. BMC Research Notes 2015;8:752.
Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM. The EBI RDF platform: linked open data for the life sciences. Bioinformatics 2014;30(9):1338-9.
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)
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N. Designing and encoding models for synthetic biology. J R Soc Interface 2009;6 Suppl 4:S405-17.
Poitevin F, Edelstein SJ. Derivation of the Crick-Wyman equation for allosteric proteins defining the difference between the number of binding sites and the Hill coefficient. Journal Of Molecular Biology 2013;425(9):1497–1499.
Le Novère N, Li L, Girault J-A. DARPP-32: molecular integration of phosphorylation potential. Cell Mol Life Sci 2008;65(14):2125-7.
Fernandez E, Schiappa R, Girault J-A, Le Novère N. DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2006;2(12):e176.
Edelstein SJ, Le Novère N. Cooperativity of allosteric receptors. Journal of Molecular Biology 2013;425(9): 1424-1432.
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.
Stefan MI, Le Novère N. Cooperative binding. PLoS Computational Biology 2013;9(6)
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.
Juty N, Laibe C, Le Novère N. Controlled annotations for systems biology. Methods Mol Biol 2013;1021:227-45.
Alcasabas AA, de Clare M, Pir P, Oliver SG. Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids. BMC Genomics 2013;14:744.
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.
Changeux J-P, Edelstein SJ. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 2011;3:19.
Changeux J-P, Edelstein S. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 2011;3:19.
Stefan MI, Edelstein SJ, Le Novère N. Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Syst Biol 2009;3:68.
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.
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
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Goryanin I, Gudmundsson S, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, Van Beek H, Weichart D, Nielsen JB, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism. Nat Biotechnol 2013;31(5):419-425.
Bergmann FT, Rodriguez N, Le Novère N. COMBINE archive specification Version 1. Journal of Integrative Bioinformatics 2015;12(2):261.
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
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.
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.
Tolle DP, Le Novère N. Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. BMC Syst Biol 2010;4:25.
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.
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.
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
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C. BioModels linked dataset. BMC Syst Biol 2014;8:91.
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
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.
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.
Chelliah V, Laibe C, Le Novère N. BioModels Database: a repository of mathematical models of biological processes. Methods Mol Biol 2013;1021:189-99.
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.
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
Stefan MI, Edelstein SJ, Le Novère N. An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proc Natl Acad Sci U S A 2008;105(31):10768-73.
Edelstein SJ. Allosteric interactions after 50 years. Journal Of Molecular Biology 2013;425(9):1391–1395.
Wolkenhauer O, Fell D, De Meyts P, Blüthgen N, Herzel H, Le Novère N, Höfer T, van Leeuwen I. Advancing systems biology for medical applications. ESF science policy briefing 2008;
Le Novère N, Courtot M, Laibe C. Adding semantics in kinetics models of biochemical pathways [Internet]. Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations 2007;:137–153.Available from: http://www.beilstein-institut.de/index.php?id=196

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