Publications

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B. F. Baldi, Hoyer, C., and Le Novère, N., Schizophrenic: forever young?, Genome Med, vol. 2, no. 5, p. 32, 2010.
R. Beeri, Le Novère, N., Mervis, R., Huberman, T., Grauer, E., Changeux, J. P., and Soreq, H., Enhanced hemicholinium binding and attenuated dendrite branching in cognitively impaired acetylcholinesterase-transgenic mice., J Neurochem, vol. 69, no. 6, pp. 2441-51, 1997.
F. T. Bergmann, Rodriguez, N., and Le Novère, N., COMBINE archive specification Version 1, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 261, 2015.
F. T. Bergmann, Cooper, J., Le Novère, N., Nickerson, D. P., and Waltemath, D., Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 262, 2015.
F. T. Bergmann, Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., Olivier, B. G., Rodriguez, N., Sauro, H. M., Scharm, M., Soiland-Reyes, S., Waltemath, D., Yvon, F., and Le Novère, N., COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project, BMC Systems Biology, vol. 15, p. 369 , 2014.
A. Bessis, Salmon, A. M., Zoli, M., Le Novère, N., Picciotto, M., and Changeux, J. P., Promoter elements conferring neuron-specific expression of the beta 2-subunit of the neuronal nicotinic acetylcholine receptor studied in vitro and in transgenic mice., Neuroscience, vol. 69, no. 3, pp. 807-19, 1995.
F. Büchel, Wrzodek, C., Mittag, F., Dräger, A., Eichner, J., Rodriguez, N., Le Novère, N., and Zell, A., Qualitative translation of relations from BioPAX to SBML qual., Bioinformatics, vol. 28, no. 20, pp. 2648-53, 2012.
F. Büchel, 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, D. B., Müller, W., Mendes, P., Zell, A., Chaouiya, C., Saez-Rodriguez, J., Schreiber, F., Laibe, C., Drager, A., and Le Novère, N., Path2Models: Large-scale generation of computational models from biochemical pathway map, BMC Systems Biology, vol. 7, p. 116, 2013.
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N. Champtiaux, Gotti, C., Cordero-Erausquin, M., David, D. J., Przybylski, C., Léna, C., Clementi, F., Moretti, M., Rossi, F. M., Le Novère, N., McIntosh, M. J., Gardier, A. M., and Changeux, J. - P., Subunit composition of functional nicotinic receptors in dopaminergic neurons investigated with knock-out mice., J Neurosci, vol. 23, no. 21, pp. 7820-9, 2003.
J. P. Changeux, Bertrand, D., Corringer, P. J., Dehaene, S., Edelstein, S., Léna, C., Le Novère, N., Marubio, L., Picciotto, M., and Zoli, M., Brain nicotinic receptors: structure and regulation, role in learning and reinforcement., Brain Res Brain Res Rev, vol. 26, no. 2-3, pp. 198-216, 1998.
J. - P. Changeux and Edelstein, S., Conformational selection or induced fit? 50 years of debate resolved., F1000 Biol Rep, vol. 3, p. 19, 2011.
J. - P. Changeux and Edelstein, S. J., Conformational selection or induced fit? 50 years of debate resolved, F1000 Biol Rep, vol. 3, p. 19, 2011.
J. P. Changeux, Bessis, A., Bourgeois, J. P., Corringer, P. J., Devillers-Thiery, A., Eiselé, J. L., Kerszberg, M., Léna, C., Le Novère, N., Picciotto, M., and Zoli, M., Nicotinic receptors and brain plasticity., Cold Spring Harb Symp Quant Biol, vol. 61, pp. 343-62, 1996.
C. Chaouiya, Keating, S. M., Berenguier, D., Naldi, A., Thieffry, D., van Iersel, M., Le Novère, N., and Helikar, T., The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 270, 2015.
C. Chaouiya, Berenguier, D., Keating, S. M., Naldi, A., van Iersel, M. P., Rodriguez, N., Dräger, A., Büchel, F., Cokelaer, T., Kowal, B., Wicks, B., çalves, E., Dorier, J., Page, M., Monteiro, P. T., von Kamp, A., Xenarios, I., de Jong, H., Hucka, M., Klamt, S., Thieffry, D., Le Novère, N., Saez-Rodriguez, J., and Helikar, T., SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools, BMC Systems Biology, vol. 7, no. 1, p. 135, 2013.
V. Chelliah, 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., and Laibe, C., BioModels: ten year anniversary, Nucleic Acids Research, 2015.
V. Chelliah, Endler, L., Juty, N., Laibe, C., Li, C., Rodriguez, N., and Le Novère, N., Data Integration and Semantic Enrichment of Systems Biology Models and Simulations, in 6th International workshop Data Integration in the Life Sciences, 2009, vol. 5647, pp. 5–15.
V. Chelliah, Laibe, C., and Le Novère, N., BioModels Database, A Repository of Mathematical Models of Biological Processes, in Encyclopedia of Systems Biology, Springer, 2013.
V. Chelliah, Juty, N., Laibe, C., Hermjakob, H., and 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.
V. Chelliah, Laibe, C., and Le Novère, N., BioModels Database: a repository of mathematical models of biological processes., Methods Mol Biol, vol. 1021, pp. 189-99, 2013.
L. M. Cordero-Erausquin, Marubio, L. M., Arroyo-Jimenez, M. M. M., Le Novère, N., Huchet, M., Léna, C., and Changeux, J. P., Characterization of mice lacking the nicotinic receptor alpha4 subunit, Journal of Physiology-Paris, vol. 92, pp. 423–423, 1998.
P. J. Corringer, Le Novère, N., and Changeux, J. P., Nicotinic receptors at the amino acid level., Annu Rev Pharmacol Toxicol, vol. 40, pp. 431-58, 2000.
V. Courtois, Chatelain, G., Han, Z. - Y., Le Novère, N., Brun, G., and Lamonerie, T., New Otx2 mRNA isoforms expressed in the mouse brain., J Neurochem, vol. 84, no. 4, pp. 840-53, 2003.
M. Courtot, Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., Hoops, S., Keating, S., Kell, D. B., Kerrien, S., Lawson, J., Lister, A., Lu, J., Machne, R., Mendes, P., Pocock, M., Rodriguez, N., Villeger, A., Wilkinson, D. J., Wimalaratne, S., Laibe, C., Hucka, M., and Le Novère, N., Controlled vocabularies and semantics in systems biology., Mol Syst Biol, vol. 7, p. 543, 2011.
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G. M. Dall'Olio, Marino, J., Schubert, M., Keys, K. L., Stefan, M. I., Gillespie, C. S., Poulain, P., Shameer, K., Sugar, R., Invergo, B. M., Jensen, L. J., Bertranpetit, J., and Laayouni, H., Ten Simple Rules for Getting Help from Online Scientific Communities, PLoS Computational Biology, vol. 7, p. e1002202, 2011.
A. R. Dean, Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., J Burleigh, G., Chanet, B., Cooper, L. D., Courtot, M., Csõsz, S., Cui, H., Dahdul, W., Das, S., T Dececchi, A., Dettai, A., Diogo, R., Druzinsky, R. E., Dumontier, M., Franz, N. M., Friedrich, F., Gkoutos, G. V., Haendle, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Köhler, S., Lapp, H., Lawrence, C. J., Le Novère, N., Lecointre, G., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Mikó, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramírez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., R Squires, B., Thacker, R. W., Thessen, A., Triana, J. Fernandez, Vihinen, M., Vize, P. D., Voget, L., Wall, C. E., Walls, R. L., Westerfield, M., Wharton, R. A., Wirkner, C. S., Wooley, J. B., Yoder, M. J., Zorn, A. M., and Mabee, P. M., Finding our way through phenotypes, PLoS Biology, vol. 13, no. 1, p. e1002033, 2015.
E. Demir, Cary, M. P., 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, A. C., 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, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., 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, P. D., Sander, C., and Bader, G. D., The BioPAX community standard for pathway data sharing., Nat Biotechnol, vol. 28, no. 9, pp. 935-42, 2010.
D. Dikicioglu, Pir, P., and Oliver, S. G., Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory., Biotechnol J, vol. 8, no. 9, pp. 1017-34, 2013.
M. Donizelli, Djite, M. - A., and Le Novère, N., LGICdb: a manually curated sequence database after the genomes., Nucleic Acids Res, vol. 34, no. Database issue, pp. D267-9, 2006.
A. Dräger, Planatscher, H., Wouamba, D. Motsou, Schröder, A., Hucka, M., Endler, L., Golebiewski, M., Müller, W., and Zell, A., SBML2L(A)T(E)X: conversion of SBML files into human-readable reports., Bioinformatics, vol. 25, no. 11, pp. 1455-6, 2009.
A. Dräger, Planatscher, H., Wouamba, D. M., Schröder, A., Hucka, M., Endler, L., Golebiewski, M., Müller, W., and Zell, A., Oligomeric membrane receptors: linking structural dynamics and functional kinetics, SBML2LATEX: Conversion of SBML files into human-readable reports, vol. 25, pp. 1455-1456, 2009.
A. Dräger, Rodriguez, N., Dumousseau, M., Dörr, A., Wrzodek, C., Le Novère, N., Zell, A., and Hucka, M., JSBML: a flexible Java library for working with SBML., Bioinformatics, vol. 27, no. 15, pp. 2167-8, 2011.
T. A. Duke, Le Novère, N., and Bray, D., Conformational spread in a ring of proteins: a stochastic approach to allostery., J Mol Biol, vol. 308, no. 3, pp. 541-53, 2001.
M. Dumontier, Gray, A. J. G., Marshall, S. M., Alexiev, V., Ansell, P., Bader, G. D., 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, S. M., and Yamaguchi, A., The health care and life sciences community profile for dataset descriptions, PeerJ, vol. 4, p. e2331, 2016.
M. Dumousseau, Rodriguez, N., Juty, N., and Le Novère, N., MELTING, a flexible platform to predict the melting temperatures of nucleic acids., BMC Bioinformatics, vol. 13, p. 101, 2012.
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A. Ebrahim, almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M. T., Fong, S. S., Hatzimanakis, V., Herrgård, M. J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S. Yup, Le Novère, N., Lerman, J. A., Lewis, N. E., Ma, D., Mahadevan, R., Maranas, C., Nagarajan, H., Navid, A., Nielsen, J., Niels, L. K., Nogales, J., Noronha, A., Pal, C., Palsson, B. Ø., Papin, J. A., Patil, K. R., Price, N. D., Reed, J. L., Saunders, M., Senger, R. S., Sonnenschein, N., Sun, Y., and Thiele, I., Do Genome-scale Models Need Exact Solvers or Clearer Standards?, Molecular Systems Biology, vol. 11, no. 10, 2015.
S. J. Edelstein, Allosteric interactions after 50 years, Journal Of Molecular Biology, vol. 425, no. 9, pp. 1391–1395, 2013.
S. J. Edelstein, A Novel Equation for Cooperativity of the Allosteric State Function, Journal of Molecular Biology, vol. 426, pp. 39-42, 2014.
S. J. Edelstein and Changeux, J. - P., Oligomeric membrane receptors: linking structural dynamics and functional kinetics, Biophys J, vol. 98, pp. 2045-2052, 2010.
S. J. Edelstein and Le Novère, N., Cooperativity of allosteric receptors, Journal of Molecular Biology, vol. 425, no. 9, pp. 1424-1432, 2013.
S. J. Edelstein, Stefan, M. I., and Le Novère, N., Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction., PLoS One, vol. 5, no. 1, p. e8449, 2010.
J. von Eichborn, Dunkel, M., Gohlke, B., Preissner, S., Hoffmann, M., Bauer, J., Armstrong, J. D., Schaefer, M., Andrade, M., Le Novère, M., Croning, M., Grant, S. G. N., van Nierop, P., Smit, A. B., and Preissner, R., SynSysNet: Integration of experimental data on synaptic protein-protein interactions with drug-target relations, Nucleic Acids Res., vol. 41, no. D1, pp. D834-D840, 2013.
L. Endler, Stefan, M. I., Edelstein, S. J., and Le Novère, N., Using chemical kinetics to model neuronal signalling pathways, in Computational Systems Neurobiology, N. Le Novère Springer Netherlands, 2012, pp. 81–117.
L. Endler, Rodriguez, N., Juty, N., Chelliah, V., Laibe, C., Li, C., and Le Novère, N., Designing and encoding models for synthetic biology., J R Soc Interface, vol. 6 Suppl 4, pp. S405-17, 2009.
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Z. - Y. Han, Zoli, M., Cardona, A., Bourgeois, J. - P., Changeux, J. - P., and Le Novère, N., Localization of [3H]nicotine, [3H]cytisine, [3H]epibatidine, and [125I]alpha-bungarotoxin binding sites in the brain of Macaca mulatta., J Comp Neurol, vol. 461, no. 1, pp. 49-60, 2003.
Z. Y. Han, Le Novère, N., Zoli, M., Hill, J. A., Champtiaux, N., and Changeux, J. P., Localization of nAChR subunit mRNAs in the brain of Macaca mulatta., Eur J Neurosci, vol. 12, no. 10, pp. 3664-74, 2000.
J. Hastings, Le Novere, N., Ceusters, W., Mulligan, K., and Smith, B., Wanting what we don’t want to want: Representing addiction in interoperable bio-ontologies, in Proceedings of the 3rd International Conference on Biomedical Ontology, 2012.
R. Henkel, Endler, L., Peters, A., Le Novère, N., and Waltemath, D., Ranked retrieval of Computational Biology models., BMC Bioinformatics, vol. 11, p. 423, 2010.
R. Henkel, Le Novère, N., Wolkenhauer, O., and Waltemath, D., Considerations of graph-based concepts to manage of computational biology models and associated simulations, INFORMATIK 2012. 2012.
M. J. Herrgård, Swainston, N., Dobson, P., Dunn, W. B., Arga, Y. K., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasić, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttilä, M., Klipp, E., Palsson, B. Ø., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., and Kell, D. B., A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology., Nat Biotechnol, vol. 26, no. 10, pp. 1155-60, 2008.
J. A. Hill, Le Novère, N., Zoli, M., and Changeux, J. - P., Ontogeny of nicotinic receptor subunit expression in cardiac autonomic circuit in rat, Circulation, vol. 90, p. 360, 1994.
M. Hucka, Finney A.,, and Le Novère, N., Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions., Nat Precedings, 2006.
M. Hucka, Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., Cuellar, A. A., Dronov, S., Gilles, E. D., Ginkel, M., Gor, V., Goryanin, I. I., Hedley, W. J., Hodgman, T. C., Hofmeyr, J. - H., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., Le Novère, N., Loew, L. M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E. D., Nakayama, Y., Nelson, M. R., Nielsen, P. F., Sakurada, T., Schaff, J. C., Shapiro, B. E., Shimizu, T. S., Spence, H. D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., and Wang, J., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models., Bioinformatics, vol. 19, no. 4, pp. 524-31, 2003.
M. Hucka and Le Novère, N., Software that goes with the flow in systems biology., BMC Biol, vol. 8, p. 140, 2010.
M. Hucka, Finney, A., Hoops, S., Keating, S., and Le Novère, N., Systems biology markup language (SBML) Level 2: structures and facilities for model definitions, Nature Precedings, 2007.
M. Hucka, Nickerson, D. Phillip, Bader, G., Bergmann, F. T., Cooper, J., Demir, E., Garny, A., Golebiewski, M., Myers, C. John, Schreiber, F., Waltemath, D., and Le Novère, N., Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative, Frontiers in Bioengineering and Biotechnology, vol. 3, p. 19, 2015.
M. Hucka, Hoops, S., Keating, S., Le Novère, N., Sahle, S., and Wilkinson, D. J., Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions, Nat Precedings, 2008.
M. Hucka, Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D., and Wilkinson, D. J., Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 271, 2015.
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S. M. Keating and Le Novère, N., Encoding Neuronal Models in SBML, in Computational Systems Neurobiology, N. Le Novère Springer Netherlands, 2012, pp. 459–488.
S. M. Keating and Le Novère, N., Supporting SBML as a model exchange format in software applications., Methods Mol Biol, vol. 1021, pp. 201-25, 2013.
R. Keller, Dörr, A., Tabira, A., Funahashi, A., Ziller, M. J., Adams, R., Rodriguez, N., Le Novère, N., Hiroi, N., Planatscher, H., Zell, A., and Drager, A., The systems biology simulation core algorithm, BMC Systems Biology, 2013.
C. Kettner, Field, D., Sansone, S., Taylor, C., Aerts, J., Binns, N., Blake, A., Britten, C. M., 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., and Whetzel, P. L., Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop, Standards in Genomic Sciences, vol. 3, pp. 259-266, 2010.
V. Y. Kiselev, Juvin, V., Mouhannad, M., Luscombe, N. M., Hawkins, P., Le Novère, N., and Stephens, L. R., Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop, Nucleic Acids Research, vol. 43, no. 20, pp. 9663-9679, 2015.
V. Knight-Schrijver, Chelliah, V., Cucurull-Sanchez, L., and Le Novère, N., The promises of quantitative systems pharmacology modelling for drug development, Computational and Structural Biotechnology Journal, vol. 14, pp. 363–370, 2016.
C. Knüpfer, Beckstein, C., Dittrich, P., and Le Novère, N., Structure, function, and behaviour of computational models in systems biology., BMC Syst Biol, vol. 7, p. 43, 2013.
D. Köhn and Le Novere, N., SED-ML–an XML format for the implementation of the MIASE guidelines, in Proceedings of the 6th conference on Computational Methods in Systems Biology, 2008, vol. 5307, pp. 176–190.
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B. Lacombe, Becker, D., Hedrich, R., DeSalle, R., Hollmann, M., Kwak, J. M., Schroeder, J. I., Le Novère, N., Nam, H. G., Spalding, E. P., Tester, M., Turano, F. J., Chiu, J., and Coruzzi, G., The identity of plant glutamate receptors., Science, vol. 292, no. 5521, pp. 1486-7, 2001.
M. Lai, Brun, D., Edelstein, S., and Le Novère, N., Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions, PLoS Computational Biology, vol. 11, no. 1, p. e1004063, 2015.
C. Laibe and Le Novère, N., MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology., BMC Syst Biol, vol. 1, p. 58, 2007.
C. Laibe, Wimalaratne, S., Juty, N., Le Novère, N., and Hermjakob, H., Identifiers.org: integration tool for heterogeneous datasets, 10th International workshop Data Integration in the Life Sciences. 2014.
N. Le Novère, Hucka, M., Anwar, N., Bader, G. D., Demir, E., Moodie, S., and Sorokin, A., Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)., Stand Genomic Sci, vol. 5, no. 2, pp. 230-42, 2011.
N. Le Novère, Corringer, P. J., and Changeux, J. P., Improved secondary structure predictions for a nicotinic receptor subunit: incorporation of solvent accessibility and experimental data into a two-dimensional representation., Biophys J, vol. 76, no. 5, pp. 2329-45, 1999.
N. Le Novère, Shimizu, T. S., and Finney, A., Systems Biology Markup Language (SBML) Level 3 Proposal: Multistate Features, 2002.
N. Le Novère, MELTING, computing the melting temperature of nucleic acid duplex., Bioinformatics, vol. 17, no. 12, pp. 1226-7, 2001.
N. Le Novère and Changeux, J. P., LGICdb: the ligand-gated ion channel database., Nucleic Acids Res, vol. 29, no. 1, pp. 294-5, 2001.
N. Le Novère, Zoli, M., and Changeux, J. P., Neuronal nicotinic receptor alpha 6 subunit mRNA is selectively concentrated in catecholaminergic nuclei of the rat brain., Eur J Neurosci, vol. 8, no. 11, pp. 2428-39, 1996.
N. Le Novère, Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J. L., Spence, H. D., and Wanner, B. L., Minimum information requested in the annotation of biochemical models (MIRIAM)., Nat Biotechnol, vol. 23, no. 12, pp. 1509-15, 2005.
N. Le Novère, Courtot, M., and Laibe, C., Adding semantics in kinetics models of biochemical pathways, Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations, pp. 137–153, 2007.
N. Le Novère, Quantitative and logic modelling of gene and molecular networks, Nature Reviews Genetics, vol. 16, pp. 146–158, 2015.
N. Le Novère, Model storage, exchange and integration., BMC Neurosci, vol. 7 Suppl 1, p. S11, 2006.
N. Le Novère, Moodie, S., Sorokin, A., Schreiber, F., and Mi, H., Systems Biology Graphical Notation: Entity Relationship language Level 1, Nat Precedings, 2009.
N. Le Novère and Finney, A., A simple scheme for annotating SBML with references to controlled vocabularies and database entries, 2005.
N. Le Novère and Tolle, D., Particle-based stochastic simulations, in Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks, 2005, pp. 41-45.
N. Le Novère, Grutter, T., and Changeux, J. - P., Models of the extracellular domain of the nicotinic receptors and of agonist- and Ca2+-binding sites., Proc Natl Acad Sci U S A, vol. 99, no. 5, pp. 3210-5, 2002.
N. Le Novère, Corringer, P. J., and Changeux, J. P., Predicted secondary structure of a nicotinic acetylcholine receptor subunit. Incorporation of predicted solvent accessibility and experimental data data into a two dimensional representation, Journal of Physiology-Paris, vol. 92, pp. 458–458, 1998.
N. Le Novère, Demir, E., Mi, H., Moodie, S., and Villeger, A., Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2), Nat Precedings, 2011.
N. Le Novère, Contribution à l'étude de la relation structure-fonction dans la famille des sous-unités des récepteurs nicotiniques de l'acétylcholine, 1998.
N. Le Novère, Realistic Models of Neurons Require Quantitative Information at the Single-cell Level, in Unravelling Single Cell Genomics, Dauphinot and Potier, Bontoux, 2010, pp. 45-53.
N. Le Novère, Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villeger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K., and Kitano, H., The Systems Biology Graphical Notation., Nat Biotechnol, vol. 27, no. 8, pp. 735-41, 2009.
N. Le Novère, Approches théoriques et pratiques en hybridation in situ et autoradiographie réceptorielle, Annales de l'Institut Pasteur/Actualites, vol. 9, pp. 259–270, 1998.
N. Le Novère, Li, L., and Girault, J. - A., DARPP-32: molecular integration of phosphorylation potential., Cell Mol Life Sci, vol. 65, no. 14, pp. 2125-7, 2008.
N. Le Novère, Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J. L., and Hucka, M., BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems., Nucleic Acids Res, vol. 34, no. Database issue, pp. D689-91, 2006.
N. Le Novère, Bessis, A., Léna, C., Picciotto, M., and Zoli, M., Le récepteur nicotinique neuronal de l'acétylcholine: du gène au tabagisme, MS. Médecine/sciences, vol. 9, pp. 41–49, 1993.
N. Le Novère, Neurological disease: are systems approaches the way forward?, Pharmacopsychiatry, vol. 41 Suppl 1, pp. S28-31, 2008.
N. Le Novère and Shimizu, T. S., STOCHSIM: modelling of stochastic biomolecular processes., Bioinformatics, vol. 17, no. 6, pp. 575-6, 2001.
N. Le Novère, Moodie, S., Sorokin, A., Schreiber, F., and Mi, H., Systems Biology Graphical Notation: Entity Relationship language Level 1, Nat Precedings, 2010.
N. Le Novère and Donizelli, M., The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)., BMC Bioinformatics, vol. 5, p. 174, 2004.
N. Le Novère and Endler, L., Using chemical kinetics to model biochemical pathways., Methods Mol Biol, vol. 1021, pp. 147-67, 2013.
N. Le Novère and Oellrich, A., Systems Biology Markup Language (SBML) Level 3 Proposal: multistate components, 2007.
N. Le Novère and Changeux, J. P., The Ligand Gated Ion Channel Database., Nucleic Acids Res, vol. 27, no. 1, pp. 340-2, 1999.
N. Le Novère and Changeux, J. P., Molecular evolution of the nicotinic acetylcholine receptor: an example of multigene family in excitable cells., J Mol Evol, vol. 40, no. 2, pp. 155-72, 1995.
N. Le Novère and Changeux, J. P., The Ligand Gated Ion Channel database: an example of a sequence database in neuroscience., Philos Trans R Soc Lond B Biol Sci, vol. 356, no. 1412, pp. 1121-30, 2001.
N. Le Novère, Zoli, M., and Changeux, J. P., Effects of nicotine injections on messenger RNAs encoding proteins involved in transmission in the mesostriatum dopaminergic system, Semaine des Hopitaux de Paris, vol. 70, pp. 403–403, 1994.
N. Le Novère, The long journey to a Systems Biology of neuronal function., BMC Syst Biol, vol. 1, p. 28, 2007.
N. Le Novère, Zoli, M., Léna, C., Ferrari, R., Picciotto, M. R., Merlo-Pich, E., and Changeux, J. P., Involvement of alpha6 nicotinic receptor subunit in nicotine-elicited locomotion, demonstrated by in vivo antisense oligonucleotide infusion., Neuroreport, vol. 10, no. 12, pp. 2497-501, 1999.
N. Le Novère, Moodie, S., Sorokin, A., Hucka, M., Schreiber, F., Demir, E., Mi, H., Matsuoka, Y., Wegner, K., and Kitano, H., Systems biology graphical notation: process diagram level 1, 2008.
N. Le Novère, La communication neuronale à l'ère post-génomique : le projet DopaNet, Biofutur, vol. 237, pp. 20-24, 2003.
N. Le Novère, Corringer, P. - J., and Changeux, J. - P., The diversity of subunit composition in nAChRs: evolutionary origins, physiologic and pharmacologic consequences., J Neurobiol, vol. 53, no. 4, pp. 447-56, 2002.
N. Le Novère, BioModels. net, tools and resources to support Computational Systems Biology, in 4th Workshop on Computation of Biochemical Pathways and Genetic Networks, 2005, pp. 69–74.
C. Léna, de Kerchove D'Exaerde, A., Cordero-Erausquin, M., Le Novère, N., del Mar Arroyo-Jimenez, M., and Changeux, J. P., Diversity and distribution of nicotinic acetylcholine receptors in the locus ceruleus neurons., Proc Natl Acad Sci U S A, vol. 96, no. 21, pp. 12126-31, 1999.
X. M. Li, Zoli, M., Finnman, U. B., Le Novère, N., Changeux, J. P., and Fuxe, K., A single (-)-nicotine injection causes change with a time delay in the affinity of striatal D2 receptors for antagonist, but not for agonist, nor in the D2 receptor mRNA levels in the rat substantia nigra., Brain Res, vol. 679, no. 1, pp. 157-67, 1995.
L. Li, Stefan, M. I., and Le Novère, N., Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII., PLoS One, vol. 7, no. 9, p. e43810, 2012.
C. Li, Courtot, M., Le Novère, N., and Laibe, C., BioModels.net Web Services, a free and integrated toolkit for computational modelling software., Brief Bioinform, vol. 11, no. 3, pp. 270-7, 2010.
C. Li, Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I., Snoep, J. L., Hucka, M., Le Novère, N., and Laibe, C., BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models., BMC Syst Biol, vol. 4, p. 92, 2010.
A. Lloret-Villas, Daudin, R., and Le Novère, N., "Big Data" in neuroscience: open door to a more comprehensive and translational research, Big Data Analytics, vol. 1, p. 5, 2016.
R. J. Lukas, Changeux, J. P., Le Novère, N., Albuquerque, E. X., Balfour, D. J., Berg, D. K., Bertrand, D., Chiappinelli, V. A., Clarke, P. B., Collins, A. C., Dani, J. A., Grady, S. R., Kellar, K. J., Lindstrom, J. M., Marks, M. J., Quik, M., Taylor, P. W., and Wonnacott, S., International Union of Pharmacology. XX. Current status of the nomenclature for nicotinic acetylcholine receptors and their subunits., Pharmacol Rev, vol. 51, no. 2, pp. 397-401, 1999.
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L. M. Marubio, del Mar Arroyo-Jimenez, M., Cordero-Erausquin, M., Léna, C., Le Novère, N., de Kerchove D'Exaerde, A., Huchet, M., Damaj, M. I., and Changeux, J. P., Reduced antinociception in mice lacking neuronal nicotinic receptor subunits., Nature, vol. 398, no. 6730, pp. 805-10, 1999.
M. Mattioni and Le Novère, N., Integration of biochemical and electrical signaling - multiscale model of the medium spiny neuron of the striatum, PLoS ONE, vol. 8, no. 7, p. e66811, 2013.
M. Mattioni, Cohen, U., and Le Novère, N., Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON., Front Neuroinform, vol. 6, p. 20, 2012.
H. Mi, Schreiber, F., Moodie, S. L., Czauderna, T., Demir, E., Haw, R., Luna, A., Le Novère, N., Sorokin, A., and Villéger, A. C., Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2, Journal of Integrative Bioinformatics, vol. 12, p. 266, 2015.
H. Mi, Schreiber, F., Le Novére, N., Moodie, S., and Sorokin, A., Systems biology graphical notation: Activity flow language level 1, Nature Precedings, 2009.
S. Moodie, Le Novère, N., Demir, E., Mi, H., and Schreiber, F., Systems Biology Graphical Notation: Process Description language Level 1, Nat Precedings, 2010.
S. Moodie, Le Novère, N., Demir, E., Mi, H., and Schreiber, F., Systems biology graphical notation: process description language level 1, Nature Precedings, 2009.
S. L. Moodie, Le Novère, N., Demir, E., Mi, H., and Villéger, A. C., Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 263, 2015.
S. Moodie, Le Novère, N., Demir, E., Mi, H., and Schreiber, F., Systems Biology Graphical Notation: Process Description language Level 1, Nat Precedings, 2011.
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P. Dalle Pezze and Le Novère, N., SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks, BMC Systems Biology, vol. 11, p. 46, 2017.
P. Dalle Pezze and Le Novère, N., SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks, BioRxiv, 2017.
M. R. Picciotto, Zoli, M., Léna, C., Bessis, A., Lallemand, Y., Le Novère, N., Vincent, P., Pich, E. M., Brûlet, P., and Changeux, J. P., Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain., Nature, vol. 374, no. 6517, pp. 65-7, 1995.
P. Pir and Le Novère, N., Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine, in Methods Molecular Biology: Systems Medicine, vol. 1386, Springer, 2016, pp. 331-350.
F. Poitevin and Edelstein, S. J., 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, vol. 425, no. 9, pp. 1497–1499, 2013.
M. S. Prevost, Moraga-Cid, G., Van Renterghem, C., Edelstein, S. J., Changeux, J. - P., and Corringer, P. - J., Intermediate closed state for glycine receptor function revealed by cysteine cross-linking., Proc Natl Acad Sci U S A, vol. 110, no. 42, pp. 17113-8, 2013.

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