Publications

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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.
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
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.
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.
M. Glont, Nguyen, T. V., Graesslin, M., Raza, A., Schramm, J., Wimalaratne, S. M., Kothamachu, V. B., Rodriguez, N., Swat, M., Eils, J., Eils, R., Laibe, C., Malik-Sheriff, R., Chelliah, V., Le Novère, N., and Hermjakob, H., BioModels: Expanding horizons to include more modelling approaches and formats, Nucleic Acids Research, In Press.
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., BioModels.net 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.
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.
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.
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.
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.
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.
C. Seeliger and Le Novère, N., Enabling surface dependent diffusion in spatial simulations using Smoldyn, BMC Research Notes, vol. 8, p. 752, 2015.
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. 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.
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 of life science data, PLoS Biology, vol. 15, no. 6, p. e2001414, 2017.
N. Juty, Le Novère, N., and Laibe, C., Identifiers.org and MIRIAM Registry: community resources to provide persistent identification., Nucleic Acids Res, vol. 40, no. Database issue, pp. D580-6, 2012.
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.
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.
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.
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. 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.
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.
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.
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.
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 Donizelli, M., The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)., BMC Bioinformatics, vol. 5, p. 174, 2004.
N. Le Novère, Neurological disease: are systems approaches the way forward?, Pharmacopsychiatry, vol. 41 Suppl 1, pp. S28-31, 2008.
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.
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.
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.
S. J. Edelstein and Changeux, J. - P., Oligomeric membrane receptors: linking structural dynamics and functional kinetics, Biophys J, vol. 98, pp. 2045-2052, 2010.
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.
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.
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.
M. Malek, Kielkowska, A., Chessa, T., Anderson, K. E., Barneda, D., Pir, P., Nakanishi, H., Eguchi, S., Koizumi, A., Sasaki, J., Juvin, V., Kiselev, V. Yu, Niewczas, I., Gray, A., Valayer, A., Spensberger, D., Imbert, M., Felisbino, S., Habuchi, T., Beinke, S., Cosulich, S., Le Novère, N., Sasaki, T., Hawkins, P., Clark, J., and Stephens, L. R., PTEN regulates PI(3,4)P2 signalling downstream of class I PI3K, Molecular Cell, In Press.
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.
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.
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.
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.
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.
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.
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.
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.
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.
N. Rodriguez, Donizelli, M., and Le Novère, N., SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML)., BMC Bioinformatics, vol. 8, p. 79, 2007.
J. Yuan Quinn, Cox, III, R. Sidney, Adler, A., Beal, J., Bhatia, S., Cai, Y., Chen, J., Clancy, K., Galdzicki, M., Hillson, N. J., Le Novère, N., Maheshwari, A., McLaughlin, J. Alastair, Myers, C., P, U., Pocock, M., Rodriguez, C., Soldatova, L., Stan, G. - B., Swainston, N., Sauro, H. M., and Wipat, A., SBOL Visual: Standard Schematics for Synthetic Genetic Constructs, PLoS Biology, vol. 13, no. 12, p. e1002310, 2015.
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.
B. F. Baldi, Hoyer, C., and Le Novère, N., Schizophrenic: forever young?, Genome Med, vol. 2, no. 5, p. 32, 2010.
V. Boras, Fusic, A., Virag, M., Gabric, D., Blivajs, I., Tomasovic-Longaric, C., Rakusic, Z., Bisof, V., Le Novère, N., and Vrdoljak, D. V., Significance of stroma in biology of oral squamous cell carcinoma, Tumori, 2017.
N. Le Novère and Finney, A., A simple scheme for annotating SBML with references to controlled vocabularies and database entries, 2005.
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.
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.
M. P. van Iersel, Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M. I., Mi, H., Moodie, S. L., Kitano, H., Le Novère, N., and Schreiber, F., Software support for SBGN maps: SBGN-ML and LibSBGN., Bioinformatics, vol. 28, no. 15, pp. 2016-21, 2012.
M. Hucka and Le Novère, N., Software that goes with the flow in systems biology., BMC Biol, vol. 8, p. 140, 2010.
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.
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. 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.
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.
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.
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.
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.
N. Rodriguez, Pettit, J. - B., Pezze, P. Dalle, Li, L., Henry, A., van Iersel, M. P., Jalowicki, G., Kutmon, M., Natarajan, K. N., Tolnay, D., Stefan, M. I., Evelo, C. T., and Le Novère, N., The Systems Biology Format Converter, BMC Bioinformatics, vol. 17, p. 154, 2016.
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.
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.
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.
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.
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, Moodie, S., Sorokin, A., Schreiber, F., and Mi, H., Systems Biology Graphical Notation: Entity Relationship language Level 1, Nat 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, 2011.
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.
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.
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, 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, Finney A.,, and Le Novère, N., Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions., Nat Precedings, 2006.
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.
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.
N. Le Novère and Oellrich, A., Systems Biology Markup Language (SBML) Level 3 Proposal: multistate components, 2007.

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