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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.
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, Juty, N., Laibe, C., Hermjakob, H., and Le Novère, N., BioModels Database: a public repository for sharing models of biological processes, in Encyclopedia of Computational Neuroscience, New York Heidelberg Dordrecht London : Springer-Verlag, 2015.
V. Chelliah, Laibe, C., and Le Novère, N., BioModels Database: a repository of mathematical models of biological processes., Methods Mol Biol, vol. 1021, pp. 189-99, 2013.
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. 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.
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, 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.
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.
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.
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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.
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.
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.
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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.
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.
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.
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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.
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.
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.
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.
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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, 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.
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D. P. Tolle and Le Novère, N., Particle-based stochastic simulation in systems biology, Current Bioinformatics, vol. 1, pp. 315–320, 2006.
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.
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. 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. 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.
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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.
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.
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.
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.
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.
D. Waltemath and Le Novère, N., Simulation Experiment Description Markup Language (SED-ML), in Encyclopedia of computational neuroscience, 2013.
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.
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.
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.
S. Moodie, Le Novère, N., Demir, E., Mi, H., and Schreiber, F., Systems Biology Graphical Notation: Process Description language Level 1, Nat Precedings, 2010.
S. Moodie, Le Novère, N., Demir, E., Mi, H., and Schreiber, F., Systems biology graphical notation: process description language level 1, Nature Precedings, 2009.
S. L. Moodie, Le Novère, N., Demir, E., Mi, H., and Villéger, A. C., Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3, Journal of Integrative Bioinformatics, vol. 12, no. 2, p. 263, 2015.
S. Moodie, Le Novère, N., Demir, E., Mi, H., and Schreiber, F., Systems Biology Graphical Notation: Process Description language Level 1, Nat Precedings, 2011.
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, 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, 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, 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.
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.
A. Martinez Guimera, Welsh, C., Pezze, P. Dalle, Fullard, N., Nelson, G., Roger, M. F., Przyborski, S. A., and Shanley, D. P., Systems modelling ageing: from single senescent cells to simple multi-cellular models, Essays In Biochemistry, vol. 61, no. 3, p. 369, 2017.
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.

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