Publications

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O. Wolkenhauer, Fell, D., De Meyts, P., Blüthgen, N., Herzel, H., Le Novère, N., Höfer, T., Schürrle, K., and van Leeuwen, I., SysBioMed report: advancing systems biology for medical applications., IET Syst Biol, vol. 3, no. 3, pp. 131-6, 2009.
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. M. Wimalaratne, Bolleman, J., Juty, N., Katayam, T., Dumontier, M., Redaschi, N., Le Novère, N., Hermjakob, H., and Laibe, C., SPARQL-enabled identifier conversion with Identifiers.org, Bioinformatics, 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.
D. Waltemath, Wolkenhauer, O., Le Novère, N., and Dumontier, M., Possibilities for Integrating Model-related Data in Computational Biology, 9th International workshop Data Integration in the Life Sciences. 2013.
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.
D. Waltemath, Bergmann, F. T., Adams, R., and Le Novère, N., Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1, Nat Precedings, 2011.
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.
D. Waltemath and Le Novère, N., Simulation Experiment Description Markup Language (SED-ML), in Encyclopedia of computational neuroscience, 2013.
D. Waltemath, Swainston, N., Lister, A., Bergmann, F., Henkel, R., Hoops, S., Hucka, M., Juty, N., Keating, S., Knuepfer, C., and others, SBML Level 3 Package Proposal: Annot, Nature Precedings, 2011.
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.
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V. Touré, Le Novère, N., Waltemath, D., and Wolkenhauer, O., Quick tips for creating effectiveand impactful biological pathways using the Systems Biology Graphical Notation, PLoS Computational Biology, In Press.
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. P. Tolle and Le Novère, N., Particle-based stochastic simulation in systems biology, Current Bioinformatics, vol. 1, pp. 315–320, 2006.
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.
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.
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.
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.
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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.
M. I. Stefan and Le Novère, N., Cooperative binding, PLoS Computational Biology, vol. 9, no. 6, 2013.
M. I. Stefan, Marshall, D. P., and Le Novère, N., Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII., PLoS One, vol. 7, no. 1, p. e29406, 2012.
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.
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. 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.
A. Sorokin, Le Novère, N., Luna, A., Czauderna, T., Demir, E., Haw, R., Mi, H., Moodie, S. L., Schreiber, F., and Villéger, A. C., Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 264, 2015.
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.
T. S. Shimizu and Le Novère, N., Looking inside the box: bacterial transistor arrays., Mol Microbiol, vol. 69, no. 1, pp. 5-9, 2008.
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.
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.
C. Seeliger and Le Novère, N., Enabling surface dependent diffusion in spatial simulations using Smoldyn, BMC Research Notes, vol. 8, p. 752, 2015.
M. Schulz, Krause, F., Le Novère, N., Klipp, E., and Liebermeister, W., Retrieval, alignment, and clustering of computational models based on semantic annotations., Mol Syst Biol, vol. 7, p. 512, 2011.
F. Schreiber and Le Novère, N., Exchange Formats for Systems Biology: SBGN, in Encyclopedia of Systems Biology, 2013.
F. Schreiber, Bader, G. D., Golebiewski, M., Hucka, M., Kornmeier, B., Le Novère, N., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., and Weise, S., Specifications of Standards in Systems and Synthetic Biology, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 258, 2015.
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.
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.
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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.
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.
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.
P. Dalle Pezze, Ruf, S., Sonntag, A. G., Langelaar-Makkinje, M., Hall, P., Heberle, A. M., Navas, P. Razquin, van Eunen, K., Tölle, R. C., Schwarz, J. J., Wiese, H., Warscheid, B., Deitersen, J., Stork, B., Fäßler, E., Schäuble, S., Hahn, U., Horvatovich, P., Shanley, D. P., and Thedieck, K., A systems study reveals concurrent activation of AMPK and mTOR by amino acids, vol. 7, p. 13254 - , 2016.
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.
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C. J. Myers, Bader, G., Gleeson, P., Golebiewski, M., Hucka, M., Le Novère, N., Nickerson, D. P., Schreiber, F., and Waltemath, D., A brief history of COMBINE, Winter Simulation Conference 2017. In Press.
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.
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, Nat Precedings, 2011.
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.
H. Mi, Schreiber, F., Le Novére, N., Moodie, S., and Sorokin, A., Systems biology graphical notation: Activity flow language level 1, Nature Precedings, 2009.
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.
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 of life science data, PLoS Biology, vol. 15, no. 6, p. e2001414, 2017.
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.
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.
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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.
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.
N. Le Novère, The long journey to a Systems Biology of neuronal function., BMC Syst Biol, vol. 1, p. 28, 2007.
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, 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, 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, Moodie, S., Sorokin, A., Schreiber, F., and Mi, H., Systems Biology Graphical Notation: Entity Relationship language Level 1, Nat Precedings, 2010.
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 and Finney, A., A simple scheme for annotating SBML with references to controlled vocabularies and database entries, 2005.
N. Le Novère, Model storage, exchange and integration., BMC Neurosci, vol. 7 Suppl 1, p. S11, 2006.
N. Le Novère and Oellrich, A., Systems Biology Markup Language (SBML) Level 3 Proposal: multistate components, 2007.
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, Quantitative and logic modelling of gene and molecular networks, Nature Reviews Genetics, vol. 16, pp. 146–158, 2015.
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.
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 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, 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, Neurological disease: are systems approaches the way forward?, Pharmacopsychiatry, vol. 41 Suppl 1, pp. S28-31, 2008.
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 Donizelli, M., The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)., BMC Bioinformatics, vol. 5, p. 174, 2004.
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, 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, 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.
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.
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.
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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.
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.
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.
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.
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.
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.
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.
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.
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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.
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 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, Finney A.,, and Le Novère, N., Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions., Nat Precedings, 2006.
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.
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.
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.
J. Hastings, Mains, A., Artal-Sanz, M., Bergmann, S., Braeckman, B. P., Bundy, J., Cabreiro, F., Dobson, P., Ebert, P., Hattwell, J., Hefzi, H., Houtkooper, R. H., Jelier, R., Joshj, C., Kothamachu, V. B., Lewis, N., Lourenco, A. Bastos, Nie, Y., Norvaisas, P., Pearce, J., Riccio, C., Rodriguez, N., Santermans, T., Scarcia, P., Shirra, H. Joachim, Sheng, M., Smith, R., Suriyalaksh, M., Towbin, B., Tuli, M. Ann, Van Weeghel, M., Weinkove, D., Zecic, A., Zimmerman, J., Le Novère, N., Kaleta, C., Witting, M., and Casanueva, O., WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series, Worm, 2017.
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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.
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.
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.
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.
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.
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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.
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.
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.
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.
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.
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. D. Díaz-Muñoz, Kiselev, V. Yu, Le Novère, N., Curk, T., Ule, J., and Turner, M., Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells, Nature Communications, vol. 8, 2017.
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.
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.
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.
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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.
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, 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., Methods Mol Biol, vol. 1021, pp. 189-99, 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, Laibe, C., and Le Novère, N., BioModels Database, A Repository of Mathematical Models of Biological Processes, in Encyclopedia of Systems Biology, Springer, 2013.
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.
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.
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.

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