Export 200 results:
Author Title [ Type(Desc)] Year
Book Chapter
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, in Encyclopedia of Systems Biology, Springer, 2013.
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.
F. Schreiber and Le Novère, N., Exchange Formats for Systems Biology: SBGN, in Encyclopedia of Systems Biology, 2013.
B. E. Shapiro, Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S. M., Novère, N., Matthews, J., and Schilstra, M. J., Introduction to Systems Biology, Humana Press, 2007, pp. 395–421.
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.
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.
B. E. Shapiro, Finney, A., Hucka, M., Borstein, B., Funahashi, A., Jouraki, A., Keating, S. M., Le Novère, N., Matthews, J. A., and Schilstra, M. J., SBML Models and MathSBML, S. Choi Humana Press, USA, 2007.
D. Waltemath and Le Novère, N., Simulation Experiment Description Markup Language (SED-ML), in Encyclopedia of computational neuroscience, 2013.
Tabac : comprendre la dépendance pour agir, INSERM Collective expertise, 2004.
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.
Conference Paper
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.
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.
N. Juty, Le Novère, N., Hermjakob, H., and Laibe, C., Delivering “Cool URIs” that do not change, in SWAT4LS 2012, 2012.
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.
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.
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.
Journal Article
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.
R. Ferrari, Le Novère, N., Picciotto, M. R., Changeux, J. P., and Zoli, M., Acute and long-term changes in the mesolimbic dopamine pathway after systemic or local single nicotine injections., Eur J Neurosci, vol. 15, no. 11, pp. 1810-8, 2002.
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.
O. Wolkenhauer, Fell, D., De Meyts, P., Blüthgen, N., Herzel, H., Le Novère, N., Höfer, T., and van Leeuwen, I., Advancing systems biology for medical applications., ESF science policy briefing, 2008.
S. J. Edelstein, Allosteric interactions after 50 years, Journal Of Molecular Biology, vol. 425, no. 9, pp. 1391–1395, 2013.
M. I. Stefan, Edelstein, S. J., and Le Novère, N., An allosteric model of calmodulin explains differential activation of PP2B and CaMKII., Proc Natl Acad Sci U S A, vol. 105, no. 31, pp. 10768-73, 2008.
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.
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.
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.
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.
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.
N. Juty, Ali, R., Glont, M., Keating, S., Rodriguez, N., Swat, M. J., Wimalaratne, S., Hermjakob, H., Le Novère, N., Laibe, C., and Chelliah, V., BioModels Database: content, features, functionality and use, CPT: Pharmacometrics & Systems Pharmacology, vol. 2, no. 4, pp. 1-14, 2015.
S. M. Wimalaratne, Grenon, P., Hermjakob, H., Le Novère, N., and Laibe, C., BioModels linked dataset., BMC Syst Biol, vol. 8, p. 91, 2014.
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.
C. Li, Courtot, M., Le Novère, N., and Laibe, C., Web Services, a free and integrated toolkit for computational modelling software., Brief Bioinform, vol. 11, no. 3, pp. 270-7, 2010.
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.
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.
D. P. Tolle and Le Novère, N., Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP., BMC Syst Biol, vol. 4, p. 25, 2010.
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.
M. J. Schilstra, Li, L., Matthews, J., Finney, A., Hucka, M., and Le Novère, N., CellML2SBML: conversion of CellML into SBML., Bioinformatics, vol. 22, no. 8, pp. 1018-20, 2006.
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.
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.
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.
I. Thiele, Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Goryanin, I., Gudmundsson, S., Hala, D., Hucka, M., Hull, D., Jameson, D., Jamshidi, N., Jonsson, J. J., Juty, N., Keating, S., Nookaew, I., Le Novère, N., Malys, N., Mazein, A., Papin, J. A., Price, N. D., Selkov, E., Sigurdsson, M. I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., Van Beek, H., Weichart, D., Nielsen, J. B., Westerhoff, H. V., Kell, D. B., Mendes, P., and Palsson, B. Ø., A community-driven global reconstruction of human metabolism, Nat Biotechnol, vol. 31, no. 5, pp. 419-425, 2013.
G. Guerlet, Taly, A., Prado de Carvalho, L., Martz, A., Jiang, R., Specht, A., Le Novère, N., and Grutter, T., Comparative models of P2X2 receptor support inter-subunit ATP-binding sites., Biochem Biophys Res Commun, vol. 375, no. 3, pp. 405-9, 2008.
M. I. Stefan, Edelstein, S. J., and Le Novère, N., Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters., BMC Syst Biol, vol. 3, p. 68, 2009.
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 and Edelstein, S., Conformational selection or induced fit? 50 years of debate resolved., F1000 Biol Rep, vol. 3, p. 19, 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. 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.
A. A. Alcasabas, de Clare, M., Pir, P., and Oliver, S. G., Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids., BMC Genomics, vol. 14, p. 744, 2013.
U. C. Rogner, Spyropoulos, D. D., Le Novère, N., Changeux, J. P., and Avner, P., Control of neurulation by the nucleosome assembly protein-1-like 2., Nat Genet, vol. 25, no. 4, pp. 431-5, 2000.
N. Juty, Laibe, C., and Le Novère, N., Controlled annotations for systems biology., Methods Mol Biol, vol. 1021, pp. 227-45, 2013.
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.
M. I. Stefan and Le Novère, N., Cooperative binding, PLoS Computational Biology, vol. 9, no. 6, 2013.
A. Naldi, Monteiro, P. T., 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, S. M., Klamt, S., Klarner, H., Laubenbacher, R., Le Novère, N., Niknejad, A., Rodriguez, N., Siebert, H., Stoll, G., Zañudo, J. G. T., Kestler, H. A., Thieffry, D., Xenarios, I., Saez-Rodriguez, J., Helikar, T., and Chaouiya, C., Cooperative development of logical modelling standards and tools with CoLoMoTo, Bioinformatics, vol. 31, no. 7, pp. 1154-1159, 2015.
S. J. Edelstein and Le Novère, N., Cooperativity of allosteric receptors, Journal of Molecular Biology, vol. 425, no. 9, pp. 1424-1432, 2013.
E. Fernandez, Schiappa, R., Girault, J. - A., and Le Novère, N., DARPP-32 is a robust integrator of dopamine and glutamate signals., PLoS Comput Biol, vol. 2, no. 12, p. e176, 2006.
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.
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.
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.
M. Zoli, Le Novère, N., Hill, J. A., and Changeux, J. P., Developmental regulation of nicotinic ACh receptor subunit mRNAs in the rat central and peripheral nervous systems., J Neurosci, vol. 15, no. 3 Pt 1, pp. 1912-39, 1995.
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.
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.
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. Jupp, Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., Redaschi, N., Wimalaratne, S. M., Martin, M., Le Novère, N., Parkinson, H., Birney, E., and Jenkinson, A. M., The EBI RDF platform: linked open data for the life sciences., Bioinformatics, vol. 30, no. 9, pp. 1338-9, 2014.
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.
C. Seeliger and Le Novère, N., Enabling surface dependent diffusion in spatial simulations using Smoldyn, BMC Research Notes, vol. 8, p. 752, 2015.
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.
N. J. Stanford, Wolstencroft, K., Golebiewski, M., Kania, R., Juty, N., Tomlinson, C., Owen, S., Butcher, S., Hermjakob, H., Le Novère, N., Mueller, W., Snoep, J. L., and Goble, C., The evolution of standards and data management practices in systems biology, Molecular Systems Biology, vol. 11, p. 851, 2015.
C. Fruchart-Gaillard, Gilquin, B., Antil-Delbeke, S., Le Novère, N., Tamiya, T., Corringer, P. - J., Changeux, J. - P., Ménez, A., and Servent, D., Experimentally based model of a complex between a snake toxin and the alpha 7 nicotinic receptor., Proc Natl Acad Sci U S A, vol. 99, no. 5, pp. 3216-21, 2002.
J. Sallette, Bohler, S., Benoit, P., Soudant, M., Pons, S., Le Novère, N., Changeux, J. - P., and Corringer, P. J., An extracellular protein microdomain controls up-regulation of neuronal nicotinic acetylcholine receptors by nicotine., J Biol Chem, vol. 279, no. 18, pp. 18767-75, 2004.
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.
T. Grutter, Prado de Carvalho, L., Le Novère, N., Corringer, P. J., Edelstein, S., and Changeux, J. - P., An H-bond between two residues from different loops of the acetylcholine binding site contributes to the activation mechanism of nicotinic receptors., EMBO J, vol. 22, no. 9, pp. 1990-2003, 2003.
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.
J. McMurry, Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D. K., Gonzalez-Beltran, A., Gormanns, P., Hastings, J., Haendel, M. A., Hermjakob, H., Hériché, J. - K., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J., Laibe, C., Le Novère, N., Malone, J., Martin, M. J., McEntyre, J. R., Morris, C., Muilu, J., Müller, W., Mungall, C. J., Rocca-Serra, P., Sansone, S. - A., Sariyar, M., Snoep, J. L., Stanford, N. J., Soiland-Reyes, S., Swainston, N., Washington, N., Williams, A. R., Wolstencroft, K., Goble, C., and Parkinson, H., Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact, PLoS Biology, In Press.
N. Juty, Le Novère, N., and Laibe, C., and MIRIAM Registry: community resources to provide persistent identification., Nucleic Acids Res, vol. 40, no. Database issue, pp. D580-6, 2012.
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.
A. Lloret i Villas, Varusai, T. M., Juty, N., Laibe, C., Le Novère, N., Hermjakob, H., and Chelliah, V., The impact of mathematical modeling in understanding the mechanisms underlying neurodegeneration: evolving dimensions and future directions, CPT: Pharmacometrics & Systems Pharmacology, 2017.
I. Ajmera, Swat, M., Laibe, C., Le Novère, N., and Chelliah, V., The impact of mathematical modeling on the understanding of diabetes and related complications, CPT: Pharmacometrics & Systems Pharmacology, vol. 2, p. e54, 2013.
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.
R. R. Adams, Tsorman, N., Stratford, K., Akman, O. E., Gilmore, S., Juty, N., Le Novère, N., Millar, A. J., and Millar, A. J., 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, vol. 27, no. 4, pp. 328-32, 2012.
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. 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.
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.
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. Rodriguez, Thomas, A., Watanabe, L., Vazirabad, I. Y., Kofia, V., Gómez, H. F., Mittag, F., Matthes, J., Rudolph, J., Wrzodek, F., Netz, E., Diamantikos, A., Eichner, J., Keller, R., Wrzodek, C., Fröhlich, S., Lewis, N. E., Myers, C. J., Le Novère, N., Palsson, B. Ø., Hucka, M., and Dräger, A., JSBML 1.0: providing a smorgasbord of options to encode systems biology models, Bioinformatics, 2015.
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.
N. Le Novère, La communication neuronale à l'ère post-génomique : le projet DopaNet, Biofutur, vol. 237, pp. 20-24, 2003.
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.
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.
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.
A. Zhukova, Adams, R., Laibe, C., and Le Novère, N., LibKiSAO: a Java library for Querying KiSAO., BMC Res Notes, vol. 5, p. 520, 2012.
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.
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., 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.
R. Dutta Roy, Rosenmund, C., Edelstein, S. J., and Le Novère, N., Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model, PLoS ONE, vol. 10, no. 1, p. e0116616, 2015.
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.
N. Le Novère, The long journey to a Systems Biology of neuronal function., BMC Syst Biol, vol. 1, p. 28, 2007.
T. S. Shimizu and Le Novère, N., Looking inside the box: bacterial transistor arrays., Mol Microbiol, vol. 69, no. 1, pp. 5-9, 2008.
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.
D. Waltemath, Bergmann, F. T., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C., Golebiewski, M., Hucka, M., Juty, N., Krebs, O., Le Novère, N., Mi, H., Moraru, I. I., Myers, C. J., Nickerson, D., Olivier, B. G., Rodriguez, N., Schreiber, F., Lucian, S., Zhang, F., and Eric, B., Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE), Standards in Genomic Sciences, vol. 9, 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.
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.
N. Le Novère, MELTING, computing the melting temperature of nucleic acid duplex., Bioinformatics, vol. 17, no. 12, pp. 1226-7, 2001.
D. P. Tolle and Le Novère, N., Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes., BMC Syst Biol, vol. 4, p. 24, 2010.
D. Waltemath, Adams, R., Beard, D. A., Bergmann, F. T., Bhalla, U. S., Britten, R., Chelliah, V., Cooling, M. T., Cooper, J., Crampin, E. J., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C., Miller, A. K., Moraru, I., Nickerson, D., Nielsen, P., Nikolski, M., Sahle, S., Sauro, H. M., Schmidt, H., Snoep, J. L., Tolle, D., Wolkenhauer, O., and Le Novère, N., Minimum Information About a Simulation Experiment (MIASE)., PLoS Comput Biol, vol. 7, no. 4, p. e1001122, 2011.
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.
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.
K. Smallbone, Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., Pir, P., Simeonidis, E., Spasić, I., Wishart, J., Weichart, D., Hayes, N. W., Jameson, D., Broomhead, D. S., Oliver, S. G., Gaskell, S. J., McCarthy, J. E. G., Paton, N. W., Westerhoff, H. V., Kell, D. B., and Mendes, P., A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes., FEBS Lett, vol. 587, no. 17, pp. 2832-41, 2013.
N. Le Novère, Model storage, exchange and integration., BMC Neurosci, vol. 7 Suppl 1, p. S11, 2006.
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.
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.
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.
T. S. Shimizu, Le Novère, N., Levin, M. D., Beavil, A. J., Sutton, B. J., and Bray, D., Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis., Nat Cell Biol, vol. 2, no. 11, pp. 792-6, 2000.
N. Le Novère and Donizelli, M., The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)., BMC Bioinformatics, vol. 5, p. 174, 2004.
U. C. Rogner, Spyropoulos, D. D., Le Novère, N., Changeux, J. - P., and Avner, P., Mutation of the murine X-linked gene NAP1L2 by homologous recombination, Eur J Neurosci, vol. 12, p. S247, 2000.
N. Le Novère, Neurological disease: are systems approaches the way forward?, Pharmacopsychiatry, vol. 41 Suppl 1, pp. S28-31, 2008.
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.
J. Sallette, Bohler, S., Benoit, P., Soudant, M., Pons, S., Le Novère, N., Changeux, J. P., and Corringer, P. J., Neuronal nicotinic receptors subtypes: Mechanism of up-regulation by chronic exposure to nicotine, Journal of Neuropsychopharmacology, vol. 7, p. S44, 2004.
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.
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.
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.
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.
A. Taly, Delarue, M., Grutter, T., Nilges, M., Le Novère, N., Corringer, P. - J., and Changeux, J. - P., Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism., Biophys J, vol. 88, no. 6, pp. 3954-65, 2005.
S. J. Edelstein, A Novel Equation for Cooperativity of the Allosteric State Function, Journal of Molecular Biology, vol. 426, pp. 39-42, 2014.
A. H. V. Schapira, Bezard, E., Brotchie, J., Calon, F., Collingridge, G. L., Ferger, B., Hengerer, B., Hirsch, E., Jenner, P., Le Novère, N., Obeso, J. A., Schwarzschild, M. A., Spampinato, U., and Davidai, G., Novel pharmacological targets for the treatment of Parkinson's disease., Nat Rev Drug Discov, vol. 5, no. 10, pp. 845-54, 2006.
S. J. Edelstein and Changeux, J. - P., Oligomeric membrane receptors: linking structural dynamics and functional kinetics, Biophys J, vol. 98, pp. 2045-2052, 2010.
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.
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.
D. P. Tolle and Le Novère, N., Particle-based stochastic simulation in systems biology, Current Bioinformatics, vol. 1, pp. 315–320, 2006.
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.
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.
M. J. Swat, Moodie, S., Wimalaratne, S. M., Kristensen, N. Rode, 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, A. C., Kaye, R., Keizer, R., Kloft, C., Kobash, N., Laibe, C., Laveille, C., Mentre, F., Mezzalana, E., Munafo, A., Nordgren, R., Nyberg, H. B., Para-Guillen, Z. P., Pasotti, L., Plan, E., Ribba, B., Smith, G., Trocóniz, I. F., Yvon, F., Harnisch, L., Karlsson, M., Hermjakob, H., and Le Novère, N., Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development, CPT: Pharmacometrics & Systems Pharmacology, vol. 6, pp. 316-319, 2015.
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.
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.
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.
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.
C. F. Taylor, Field, D., Sansone, S. - A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C. A., Binz, P. - A., Bogue, M., Booth, T., Brazma, A., Brinkman, R. R., Michael Clark, A., Deutsch, E. W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J. M., Hardy, N. W., Hermjakob, H., Julian, R. K., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Le Novère, N., Leebens-Mack, J., Lewis, S. E., Lord, P., Mallon, A. - M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J. M., Robertson, D. G., Rocca-Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo-Lopez, J., Scheuermann, R. H., Schober, D., Smith, B., Snape, J., Stoeckert, C. J., Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J., and Wiemann, S., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project., Nat Biotechnol, vol. 26, no. 8, pp. 889-96, 2008.
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.
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.
N. Le Novère, Quantitative and logic modelling of gene and molecular networks, Nature Reviews Genetics, vol. 16, pp. 146–158, 2015.
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.
T. Grutter, Le Novère, N., and Changeux, J. - P., Rational understanding of nicotinic receptors drug binding., Curr Top Med Chem, vol. 4, no. 6, pp. 645-50, 2004.
V. Musante, Li, L., Kanyo, J., Lam, T. T., Colangelo, C. M., Cheng, S. K., Brody, H., Greengard, P., Le Novère, N., and Nairn, A. C., Reciprocal regulation of ARPP-16 by protein kinase A and MAST-3 kinase provides a cAMP-regulated switch in protein phosphatase 2A inhibition, eLife, vol. 6, p. e24998, 2017.
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. D. Díaz-Muñoz, Kiselev, V. Yu, Le Novère, N., Curk, T., Ule, J., and Turner, M., Regulation of mRNA translation and subcellular location controls protein synthesis of key modulators of the DNA damage response during B cell activation, Nature Communications, In Press.
D. Waltemath, Adams, R., Bergmann, F. T., Hucka, M., Kolpakov, F., Miller, A. K., Moraru, I. I., Nickerson, D., Sahle, S., Snoep, J. L., and Le Novère, N., Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language., BMC Syst Biol, vol. 5, p. 198, 2011.