Complete list of publications

Another page is dedicated to what I believe are my most important publications. As of February 2014, Google Scholar says citation count ~12000; h-index=46.

Libre Access
Gratis Access
[peer-reviewed journals] [peer-reviewed proceedings] [non peer-reviewed] [technical reports]

Publications in peer-reviewed journals

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  1. Dutta Roy R., Rosenmund C., Edelstein S.J., Le Novère N. Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model Submitted (2014)
    [arXiv]

  2. Bergmann F et al. COMBINE archive: One File To Share Them All Submitted (2014)
    [arXiv]

  3. Lai M., Brun D., Edelstein S.J., Le Novère N. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions Submitted (2014)
    [arXiv]

  4. Wimalaratne S.M., Grenon P., Hermjakob H., Le Novère N., Laibe C. BioModels Linked Dataset BMC Systems Biology (2014) 8: 91
    [PubMed] [BMC Bioinformatics] [DOI] [PDF version]

  5. Jupp S., 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., Jenkinson A.M. The EBI RDF Platform: Linked Open Data for the Life Sciences. Bioinformatics (2014) 30: 1338-1339
    [PubMed] [Bioinformatics] [DOI] [Pubmed Central] [PDF version]

  6. Chaouiya C., Berenguier D., Keating S.M., Naldi A., van Iersel M.P., Rodriguez N., Dräger A., Büchel F., Cokelaer T., Kowal B., Wicks B., Gonçalves 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., Helikar T. SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology (2013) 7:135
    [PubMed] [BMC Systems Biology] [DOI] [Pubmed Central] [arXiv] [PDF version]

  7. Büchel F., 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., Dräger A., Le Novère N. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology (2013) 7: 116
    [PubMed] [BMC Systems Biology] [DOI] [arXiv] [PDF version]

  8. Ajmera I., Swat M., Laibe C., Le Novère N., Chelliah V. The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e54
    [PubMed] [NPG] [DOI] [PDF version]

  9. Keller R., Dörr A., Tabira A., Funahashi A., Ziller M.J., Adams R., Rodriguez N., Le Novère N., Hiroi N., Planatscher H., Zell A., Drager A. The systems biology simulation core algorithm. BMC Systems Biology (2013) 7: 55
    [PubMed] [DOI] [BMC Systems Biology] [Pubmed Central] [PDF version]

  10. Mattioni M., Le Novère N. Integration of biochemical and electrical signaling - multiscale model of the medium spiny neuron of the striatum. PLoS ONE (2013) 8(7): e66811
    [PubMed] [PLoS] [DOI] [Pubmed Central] [PDF version]

  11. Stefan M.I., Le Novère N. Cooperative binding PLoS Computational Biology (2013) 9(6): e1003106.
    [PubMed] [DOI] [PLoS] [Pubmed Central] [PDF version]

  12. Knüepfer C, Beckstein C, Dittrich P, Le Novère N. Structure, function, and behaviour of computational models in systems biology BMC Systems Biology (2013) 7(1):43.
    [PubMed] [DOI] [BMC Systems Biology] [PDF version]

  13. Edelstein S.J., Le Novère N. Cooperativity of allosteric receptors Journal of Molecular Biology (2013) 425(9):1424-32
    [PubMed] [DOI] [ScienceDirect] [PDF version]

  14. Thiele I., 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., Palsson B.Ø. A community-driven global reconstruction of human metabolism. Nature Biotechnology (2013) 31: 419–425
    [PubMed] [DOI] [NPG] [PDF version]

  15. von Eichborn J., Dunkel M., Gohlke B., Preissner S., Hoffmann M., Bauer J., Armstrong J.D., Schaefer M., Andrade M., Le Novère N., Croning M., Grant S.G.N., van Nierop P., Smit A.B., Preissner R. SynSysNet: Integration of experimental data on synaptic protein-protein interactions with drug-target relations. Nucleic Acids Research (2013), 41(D1):D834-D840
    [PubMed] [DOI] [NAR] [Pubmed Central] [PDF version]

  16. Zhukova A., Adams R., Laibe C., Le Novère N. LibKiSAO: a Java Library for Querying KiSAO. BMC Research Notes (2012), 5: 520
    [PubMed] [DOI] [BMC Research Notes] [Pubmed Central] [PDF version]

  17. Li L., Stefan M.I., Le Novère N. Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII. PLoS ONE (2012), 7(9): e43810
    [PubMed] [DOI] [PLoS] [Pubmed Central] [PDF version]

  18. Büchel F., Wrzodek C., Mittag F., Dräger A, Eichner J., Rodriguez N., Le Novère N., Zell A. Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics (2012), 28(20): 2648-2653
    [PubMed] [DOI] [Bioinformatics] [Pubmed Central] [PDF version]

  19. Adams R R, Tsorman N, Stratford K, Akman O, Gilmore S, Juty N, Le Novère N, and Millar A. The Input Signal Step Function (ISSF): A Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models. Journal of Biological Rhythms (2012), 27: 328-332
    [PubMed] [DOI] [Pubmed Central] [PDF version]

  20. Dumousseau M., Rodriguez N., Juty N., Le Novère N. MELTING, a flexible platform to predict the melting temperatures of nucleic acids. BMC Bioinformatics (2012), 13:101.
    [PubMed] [DOI] [BMC Bioinformatics] [Pubmed Central] [PDF version][Supp 1][Supp 2][Supp 3]

  21. Mattioni M., Cohen U., Le Novère N. Neuronvisio: a Graphical User Interface with 3D capabilities for NEURON. Frontiers in Neuroinformatics (2012), 6:20
    [PubMed] [DOI] [Frontiers] [Pubmed Central] [PDF version]

  22. van Iersel M.P., 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., Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (2012), 28: 2016-2021
    [PubMed] [DOI] [Bioinformatics] [Pubmed Central] [PDF version]

  23. Stefan M.I., Marshall D.P., Le Novère N. Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII. PLoS ONE (2012), 7(1): e29406
    [PubMed] [DOI] [PLoS] [Pubmed Central] [PDF version]

  24. Juty N., Le Novère N., Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Research (2012), 40: D580-D586
    [PubMed] [DOI] [NAR] [Pubmed Central] [PDF version]

  25. Waltemath D., Adams R., Bergmann F.T., Hucka M., Kolpakov F., Miller A.K., Moraru I.I., Nickerson D., Sahle S., Snoep J.L., Le Novère N. Reproducible computational biology experiments with SED-ML -- The Simulation Experiment Description Markup Language. BMC Systems Biology (2011), 5:198
    [PubMed] [DOI] [BMC Syst Biol] [Pubmed Central] [PDF version]

  26. Courtot M., 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., Le Novère N. Controlled vocabularies and semantics in Systems Biology. Molecular Systems Biology (2011), 7: 543
    [PubMed] [DOI] [MSB] [Pubmed Central] [PDF version]

  27. Schulz M., Krause F., Le Novère N., Klipp E., Liebermeister W. Retrieval, alignment, and clustering of computational models based on semantic annotations. Molecular Systems Biology (2011), 7: 512
    [PubMed] [DOI] [MSB] [Pubmed Central] [PDF version][PDF version]

  28. Dräger A., Rodriguez N., Dumousseau M., Dörr A., Wrzodek C., Le Novère N., Zell A., Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics (2011), 27: 2167-2168
    [PubMed] [DOI] [Bioinformatics] [Pubmed Central] [PDF version]

  29. Waltemath D., Adams R., Beard D.A., Bergmann F.T., Bhalla U.S, Britten R., Chelliah V., Cooling M.T., Cooper J., Crampin E., Garny A., Hoops S., Hucka M., Hunter P., Klipp E., Laibe C., Miller A., Moraru I., Nickerson D., Nielsen P., Nikolski M., Sahle S., Sauro H.M., Schmidt H., Snoep J.L., Tolle D., Wolkenhauer O., Le Novère N. Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology (2011), 7(4): e1001122
    [PubMed] [DOI] [PLoS] [Pubmed Central] [PDF version][Supplementary information 1][Supplementary information 2]

  30. Demir E, Cary MP, 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 AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinathrao 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, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Carrillo M, Cheung KH, 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 KH, Rzhetsky A, Schachter V, Sobral BS, 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 PD, Sander C, Bader GD. BioPAX – A Community Standard for Pathway Data Sharing. Nature Biotechnology (2010), 28: 935–942
    [PubMed] [DOI] [Nature Biotechnology] [Pubmed Central] [PDF version]

  31. Henkel R., Endler L., Le Novère N., Peters A., Waltemath D. Ranked Retrieval of Computational Biology Models. BMC Bioinformatics (2010), 11:423
    [PubMed] [DOI] [BMC Bioinformatics] [Pubmed Central] [PDF version]

  32. Li C., 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., Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology (2010), 4: 92
    [PubMed] [DOI] [BMC Systems Biology] [Pubmed Central] [PDF version]

  33. Li C., Courtot M., Laibe C., Le Novère N. BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Briefings in Bioinformatics (2010), 11: 270-277
    [PubMed] [DOI] [Pubmed Central] [PDF version]

  34. Tolle D.P., Le Novère N. Brownian Diffusion of AMPA Receptors Is Sufficient to Explain Fast Onset of LTP. BMC Systems Biology (2010), 4: 25
    [PubMed] [DOI] [BMC Systems Biology] [Pubmed Central] [PDF version]

  35. Tolle D.P., Le Novère N. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Systems Biology (2010), 4: 24
    [PubMed] [DOI] [BMC Systems Biology] [Pubmed Central] [PDF version]

  36. Edelstein S.J., Stefan M.I, Le Novère N. Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction. PLoS One (2010), 5(1): e8449
    [PubMed] [DOI] [PLoS ONE] [Pubmed Central] [PDF version]

  37. Le Novère N., Hucka M., Mi H., Moodie S., Shreiber F., Sorokin A., Demir E., Wegner K., Aladjem M., Wimalaratne S., Bergman F.T., Gauges R., Ghazal P., Kawaji H., Li L., Matsuoka Y., Villéger A., Boyd S.E., Calzone L., Courtot M., Dogrusoz U., Freeman T., Funahashi A., Ghosh S., Jouraku A., Kim S., Kolpakov F., Luna A., Sahle S., Schmidt E., Watterson S., Goryanin I., Kell D.B., Sander C., Sauro H., Snoep J.L., Kohn K., Kitano H. The Systems Biology Graphical Notation. Nature Biotechnology (2009), 27: 735-741
    [PubMed] [DOI] [NBT Free access] [PDF version] [Supplementary info]

  38. Stefan M.I., Edelstein S.J., Le Novère N. Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Systems Biology (2009), 3: 68
    [PubMed] [DOI] [Pubmed Central] [BioMedCentral] [PDF version]

  39. Endler L., Rodriguez N., Juty N., Chelliah V., Laibe C., Li L., Le Novère N. Designing and encoding models for Synthetic Biology. Journal of the Royal Society Interface (2009), 6: S405-S417.
    [PubMed] [DOI] [RSIF Free Access] [PDF version]

  40. Wolkenhauer O., Fell D., De Meyts P., Blüthgen N., Herzel H., Le Novère N., Höfer T., Schürrle K., van Leeuwen I. Advancing systems biology for medical applications. IET Systems Biology (2009), 3: 131-136.
    [PubMed] [DOI] [PDF version]

  41. Herrgård M.J., Swainston N., Dobson P., Dunn W.B., Arga K.Y., 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., Kırdar B., Penttilä M., Klipp E., Palsson B.Ø., Sauer U., Oliver S.G., Mendes P., Nielsen J., Kell D.B. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology (2008), 26: 1155-1160.
    [PubMed] [DOI] [PDF version]

  42. Guerlet G., Taly A., Prado de Carvahlo L., Marz A., Jiang R., Specht A., Le Novère N., Grutter T. Comparative models of P2X2 receptor support inter-subunit ATP-binding sites Biochemical and Biophysical Research Communications (2008), 375: 405-409.
    [PubMed] [DOI] [PDF version]

  43. Taylor C.F., Field D., Sansone S.-A., Aerts J., Apweiler R., Ashburner M., Ball C.A., Binz P.-A., Bogue M., Brazma A., Brinkman R., Clark A.M., Deutsch E.W., Fiehn O., Fostel J., Ghazal P., Gibson F., Gray T., Grimes G., 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., Mallin 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., Rosenfeld H., Santoyo-Lopez J., Scheuermann R.H., Schober D., Smith B., Snape J., Sterk P., Tipton K., Untergasser A., Vandesompele J., Wiemann S. Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project. Nature Biotechnology (2008), 26: 889-896.
    [PubMed] [DOI] [PDF version]

  44. Stefan M.I., Edelstein S.J., Le Novère N. An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proceedings of the National Academy of Sciences USA (2008), 105: 10768-10773.
    On Oct 6th 2008, we discovered that the figures 3 and 4 of the published paper are not the right ones. They were erroneously inserted during the editing period, after the paper was accepted. Unfortunately, the published figures are far less convincing than the one you can obtain by running the model, as did the curators of BioModels Database. PNAS issued a correction and I created a PDF with the correct figures appended.
    [Supporting information] [PubMed] [DOI] [Pubmed Central] [PNAS Free Access] [Model in BioModels Database]

  45. Le Novère N., Li L., Girault J.-A. DARPP-32: Molecular integration of phosphorylation potential. Cellular and Molecular Life Sciences (2008), 65: 2125-2127.
    [PubMed] [DOI] [PDF version]

  46. Laibe C., Le Novère N. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Systems Biology (2007), 1: 58.
    [PubMed] [DOI] [BioMedCentral] [Pubmed Central] [PDF version]

  47. Rodriguez N., Donizelli M., Le Novère N. SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML). BMC Bioinformatics (2007), 8:79.
    [PubMed] [DOI] [BioMedCentral] [Pubmed Central] [PDF version]

  48. Fernandez E., Schiappa R., Girault J.A., Le Novère N. DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Computational Biology (2006), 2(12): e176.
    [PubMed] [DOI] [PLoS] [Pubmed Central] [PDF version] [Model A in BioModels Database] [Model B in BioModels Database]

  49. Schapira A.H.V., 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., Davidai G. Novel pharmacological targets for the treatment of Parkinson's disease. Nature Reviews Drug Discovery (2006), 5: 845-854.
    [PubMed] [DOI] [PDF version]

  50. Tolle D., Le Novère N. Particle-based Stochastic Simulation in Systems Biology. Current Bioinformatics (2006), 1: 315-320.
    [PDF version]

  51. Schilstra M.J., Li L., Matthews J., Finney A., Hucka M., Le Novère N. CellML2SBML: Conversion of CellML into SBML. Bioinformatics (2006), 18: 1018-1020.
    [PubMed] [DOI] [Bioinformatics Free access] [PDF version]

  52. Donizelli M., Djite M.A., Le Novère N. LGICdb. A manually curated sequence database after the genomes. Nucleic Acids Research (2006), 34: D267-D269.
    [PubMed] [DOI] [Pubmed Central] [NAR] [PDF version]

  53. Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems. Nucleic Acids Research (2006), 34: D689-D691.
    [PubMed] [DOI] [NAR] [Pubmed Central] [PDF version]

  54. Le Novère N., 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., Wanner B.L. Minimum Information Requested In the Annotation of biochemical Models (MIRIAM). Nature Biotechnology (2005), 23: 1509-1515.
    [PubMed] [DOI] [PDF version]

  55. Taly A., Delarue M., Grutter T., Nilges M., Le Novère N., Corringer P.-J., Changeux J.-P. (2005) Normal mode analysis suggest a quaternary twist model for the nicotinic receptor gating mechanism. Biophysical Journal (2005), 88: 3954-3965.
    [PubMed] [DOI] [Pubmed Central] [PDF version] [Movie 1: lateral view] [Movie 2: superior view]

  56. Le Novère N., Donizelli M. The Molecular Pages of the Mesotelencephalic Dopamine Consortium (DopaNet). BMC bioinformatics (2004), 5: 174.
    [PubMed] [DOI] [BioMedCentral] [Pubmed Central] [PDF version]

  57. Sallette J., Bohler S., Benoit P., Soudant M., Pons S., Le Novère N., Changeux J.-P., Corringer P.-J. An extracellular microdomain controls up-regulation of neuronal nicotinic acetylcholine receptors by nicotine. Journal of Biological Chemistry (2004), 279: 18767-18775.
    [PubMed] [DOI] [JBC Free Access] [PDF version]

  58. Grutter T., Le Novère N., Changeux J.-P. Rational understanding of nicotinic receptors drug binding. Current Topics in Medicinal Chemistry (2004), 4: 645-651.
    [PubMed] [DOI] [PDF version]

  59. Champtiaux N., Gotti C., Cordero-Erausquin M., David D., Przybylski C., Léna C., Clementi F., Moretti M., Rossi F.M., Le Novère N., McInstosh J.M., Gardier A.M., Changeux J.-P. Subunit composition of functional nicotinic receptors in dopaminergic neurons investigated with knock-out mice. Journal of Neuroscience (2003), 23:7820-7829.
    [PubMed] [J Neurosci Free access] [PDF version]

  60. Han Z.-Y., Zoli M., Cardona A., Bourgeois J.-P., Changeux J.-P., Le Novère N. Localization of [3H]-nicotine, [3H]-cytisine, [3H]-epibatidine and [125I]-α-bungarotoxin binding sites in the brain of Macaca Mulatta. Journal of Comparative Neurology (2003), 461(1):49-60.
    [PubMed] [DOI] [PDF version]

  61. Grutter T., Prado de Carvalho L., Le Novère N., Corringer P.-J., Edelstein S., Changeux J.-P. An interaction between two residues from different loops of the acetylcholine-binding site contributes to the activation mechanism of nicotinic receptors. EMBO Journal (2003), 22:1990-2003.
    [PubMed] [DOI] [Pubmed Central] [EMBO J Free access] [PDF version] [Movie: superposition of wild-type nAChR α7 (in yellow, critical residues in orange) and G152K-P193I mutant (in green, critical residues in blue)]

  62. Courtois V., Chatelain G., Han Z.-Y., Le Novère N., Brun G., Lamonerie T. New Otx2 mRNA isoforms expressed in the mouse brain. Journal of Neurochemistry (2003), 84: 840-853.
    [PubMed] [DOI] [PDF version]

  63. Hucka M., Bolouri H., Finney A., Sauro H.M., Doyle J.C., Kitano H., and the rest of the Systems Biology Software Developer's Forum: Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Ginkel M., Gor V., Goryanin I.I., Hedley W.J., Hodgman T.C., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novère N., Loew L.M., Lucio D., Mendes P., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics (2003), 19: 524-531.
    [PubMed] [DOI] [Bioinformatics Free access] [PDF version]

  64. Fruchart-Gaillard C., Gilquin B., Antil-Delbeke S., Le Novère N., Tamiya T., Corringer P.-J., Changeux J.-P., Ménez A., Servent D. Experimentally-based model of a complex between a snake toxin and the α7 nicotinic receptor. Proceedings of the National Academy of Science USA (2002), 99: 3216-3221.
    [PubMed] [DOI] [Pubmed Central] [PNAS Free Access] [PDF version] [model of α-conotoxine bound to chick (α7)2]

  65. Le Novère N., Grutter T., Changeux J.-P. Models of the extracellular domain of the nicotinic receptors and of agonist and Ca++ binding sites. Proceedings of the National Academy of Sciences USA (2002), 99: 3210-3215.
    [PubMed] [DOI] [Pubmed Central] [PNAS Free Access] [PDF version] [model of Torpedo (α1)2β1γδ] [model of rat (α4)2(β2)3] [model of chick (α7)5] [model of acetylcholine bound to chick (α7)2] [model of nicotine bound to chick (α7)2] [model of epibatidine bound to chick (α7)2]

  66. Le Novère N., Corringer P.-J., Changeux J.-P. The diversity of subunit composition in nAChRs: evolutionary origins, physiological and pharmacological consequences Journal of Neurobiology (2002), 53: 447-456.
    [PubMed] [DOI] [J Neurobiol Free access] [PDF version]

  67. Ferrari R., Le Novère N., Picciotto M.R., Changeux J.-P., Zoli M. Acute and long-term changes in the mesolimbic dopamine pathway after systemic or local single nicotine injections. European Journal of Neuroscience (2002), 15: 1810-1818.
    [PubMed] [DOI] [PDF version]

  68. Le Novère N. MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics (2001), 17: 1226-1227.
    [
    PubMed] [DOI] [Bioinformatics Free access] [PDF version]

  69. Le Novère N., Shimizu T.S. StochSim: Modelling of stochastic biomolecular processes. Bioinformatics (2001), 17: 575-576.
    [PubMed] [DOI] [Bioinformatics Free access] [PDF version]

  70. Le Novère N., Changeux J.-P. LGICdb: the ligand-gated ion channel database. Nucleic Acids Research (2001), 29: 294-295.
    [PubMed] [DOI] [Pubmed Central] [NAR] [PDF version]

  71. Le Novère N., Changeux J.-P. The Ligand Gated Ion Channel database (LGICdb), an example of a sequence database in neuroscience. Phylosophical Transactions of the Royal Society (2001), 356:1121-1130.
    [PubMed] [DOI] [Pubmed Central] [PTRS Free Access] [PDF version]

  72. Duke T.A.J., Le Novère N., Bray D. Conformational spread in a ring of proteins: a stochastic approach to allostery. Journal of Molecular Biology (2001), 308:541-553.
    [PubMed] [DOI] [PDF version]

  73. Corringer P.J., Le Novère N., Changeux J.P. Nicotinic Receptors at the Amino Acid Level. Annual Reviews of Pharmacology and Toxicology (2000), 40: 431-458.
    [PubMed] [DOI] [PDF version]

  74. Han Z.-Y., Le Novère N., Zoli M., Champtiaux N., Hill J.A., Changeux J.-P. localization of nAChR subunit mRNAs in the brain of Macaca mulatta. European Journal of Neuroscience (2000), 12: 3664-3674.
    [PubMed] [DOI] [PDF version]

  75. Shimizu T.S., Le Novère N., Levin M.D., Beavil A.J., Sutton B.J., Bray D. Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis. Nature Cell Biology (2000), 2: 792-796.
    [PubMed] [DOI] [PDF version] [interaction between cheA and cheW][interaction between cheW and TSR][the elementary unit of the chemosome: (cheA)3(cheW)3(TSR)6][A "complete" minichemosome: (cheA)6(cheW)3(TSR)6][The complete cell of the lattice: (cheA)24(cheW)18(TSR)36]

  76. Rogner U.C., Spyropoulos D.D., Le Novère N., Changeux J.-P., Avner, P. Control of neurulation by the nucleosomal assembly protein 1l2. Nature genetics (2000), 25: 431-435.
    [PubMed] [DOI] [PDF version]

  77. Le Novère N., Zoli M., Léna C., Ferrari R., Picciotto M.R., Merlo-Pich E., Changeux J.P. Involvement of α6 nicotinic receptor subunit in nicotine-elicited locomotion, demonstrated by in vivo antisense oligonucleotide infusion. NeuroReport (1999), 10(12): 2497-2501.
    [PubMed] [HTML version] [PDF version]

  78. Le Novère N., Corringer P.J. and Changeux J.P. Improved secondary structure predictions for a nicotinic receptor subunit.Incorporation of solvent accessibility and experimental data into a 2D representation. Biophysical Journal (1999), 76: 2329-2345.
    [PubMed] [DOI] [Pubmed Central] [Biophys J Free Access] [PDF version]

  79. Le Novère N., Changeux J.P. The Ligand Gated Ion Channel database. Nucleic Acids Research (1999) 27: 340-342.
    [PubMed] [DOI] [Pubmed Central] [NAR] [PDF version]

  80. Lukas R.J., Changeux J.P., Le Novère N., Albuquerque E.X., Balfour D.J.K., Berg D.K., Bertrand D., Chiappinelli V.A., Clarke P.B.S., Collins A.C., Dani J.A., Grady S.R., Kellar K.J., Lindstrom J.M., Marks M.J., Quik M., Taylor P.W., Wonnacott S. International Union of Pharmacology.XX. Current status of the nomenclature for nicotinic acetylcholine receptors and their subunits. Pharmacological reviews (1999), 51: 397-401.
    [PubMed] [Pubmed Central] [Pharm Rev Free Access] [PDF version]

  81. Léna C., de Kerchove d'Exaerde A., Cordero-Erausquin M., Le Novère N.,Arroyo-Jimenez M.M., Changeux J.-P. Diversity and distribution of nicotinic acetylcholine receptors in the locus ceruleus neurons. Proceedings of the National Academy of Sciences USA (1999), 96: 12127-12131.
    [PubMed] [DOI] [Pubmed Central] [PNAS Free Access] [PDF version]

  82. Marubio L.M., Arroyo-Jimenez M.M., Cordero-Erausquin M., Léna C., Le Novère N., de Kerchove d'Exaerde A., Huchet M., Damaj M.I. and Changeux J.P. Reduced antinociception in mice lacking neuronal nicotinic receptor subunits. Nature (1999), 398: 805-810.
    [PubMed] [DOI] [PDF version]

  83. Changeux J.-P., Bertrand D., Corringer P.-J., Dehaene S., Edelstein S., Léna C., Le Novère N., Marubio L., Picciotto M., Zoli M. Brain nicotinic receptors: structure and regulation, role in learning and reinforcement. Brain Research Reviews (1998), 26: 198-216.
    [PubMed] [DOI] [PDF version]

  84. Beeri R., Le Novère N., Mervis R., Huberman T., Grauer E., Changeux J.-P., Soreq H. Enhanced hemicholinium binding and attenuated dendrite branching in cognitively impaired acetylcholinesterase-transgenic mice. Journal of Neurochemistry (1997), 68: 2441-2451.
    [PubMed] [PDF version]

  85. Le Novère N., Zoli M., Changeux J.P. Neuronal nicotinic receptor α6 subunit mRNA is selectively concentrated in catecholaminergic nuclei of the rat brain. European Journal of Neuroscience (1996), 8: 2428-2439.
    [PubMed] [DOI] [HTML version][PDF version]

  86. Changeux J.-P., Bessis A., Bourgeois J.-P., Corringer P.-J., Devillers-Thiéry A., Eiselé J.-L., Kerszberg M., Léna C., Le Novère, Picciotto M.R., Zoli M. Nicotinic receptors and brain plasticity. Cold Spring Harbor Symposia in Quantitative Biology (1996), LXI: 343-362.
    [PubMed]

  87. Le Novère N., Changeux J.P. Molecular evolution of the nicotinic acetylcholine receptor: an example of multigene family in excitable cells. Journal of Molecular Evolution (1995) 40: 155-172.
    This is the original phylogeny article. However a revisited and extended view of the nAChR subunit genes phylogeny can be found here.
    [PubMed] [DOI] [Postscript version][PDF version]

  88. Zoli M., Le Novère N., Hill J.-A., Changeux J.-P. Developmental regulation of nicotinic ACh receptor subunit mRNAs in the rat central and peripheral nervous systems. Journal of Neuroscience (1995), 15: 1912-1939.
    [PubMed] [J Neurosci Free access] [PDF version]

  89. Bessis A., Salmon A.-M., Zoli M., Le Novère N., Picciotto M.R., Changeux J.P. Promoter elements conferring neuron-specific expression of the beta2 subunit of the neuronal nicotinic acetylcholine receptor studied in vitro and in transgenic mice. Neuroscience (1995), 69: 807-819.
    [PubMed] [DOI] [PDF version]

  90. Li X.-M., Zoli M., Finnman U.-B., Le Novère N., Changeux J.-P., Fuxe K. A single (-)--nicotine injection causes change with a time delay in the affinity of striatal D2 receptors for antagonist, but not for agonist, nor in the D2 receptor mRNA levels in the rat substantia nigra. Brain Research (1995), 679: 157-167.
    [PubMed] [DOI] [PDF version]

  91. Picciotto M.R., Zoli M., Léna C., Bessis A., Lallemand Y., N. Le Novère, Vincent P., Merlo-Pich E., Brûlet P., Changeux J.-P. Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature (1995), 374: 65-67.
    [PubMed] [DOI] [PDF version]

  92. Le Novère N., Bessis A., Léna C., Picciotto M., Zoli M. Le récepteur nicotinique neuronal de l'acétylcholine: Du gène au tabagisme. médecine/sciences (1993), 9: 41-49.
    [PDF version]

Publications in peer-reviewed conference proceedings

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  1. Laibe C., Wimalaratne S., Juty N., Le Novère N., Hermjakob H. Identifiers.org: integration tool for heterogeneous datasets Proceedings of the 10th International workshop Data Integration in the Life Sciences (2014)
    [PDF version]

  2. Waltemath D., Wolkenhauer O., Le Novère N., Dumontier M. Possibilities for Integrating Model-related Data in Computational Biology Proceedings of the 9th International workshop Data Integration in the Life Sciences (2013)
    [PDF version]

  3. Juty N., Le Novère N., Hermjakob H., Laibe C. Towards the collaborative curation of the registry underlying Identifiers.org Database (2013) 2013:bat017
    [DOI] [PDF version]

  4. Juty N., Le Novère N., Hermjakob H., Laibe C. Delivering “Cool URIs” that do not change Proceedings of SWAT4LS 2012. (2012), CEUR Workshop Proceedings 952
    [CEUR-WS] [PDF version]

  5. Henkel R., Le Novère N., Wolkenhauer O., Waltemath D. Considerations of graph-based concepts to manage of computational biology models and associated simulations Proceedings of INFORMATIK 2012. (2012), Published
    [PDF version]

  6. Hastings J., Le Novère N., Ceusters W., Mulligan K., Smith B. Wanting what we don’t want to want: Representing addiction in interoperable bio-ontologies. Proceedings of the 3rd International Conference on Biomedical Ontology. (2012), CEUR Workshop Proceedings 897
    [CEUR-WS] [PDF version]

  7. Köhn D.,Le Novère N. SED-ML - An XML Format for the Implementation of the MIASE Guidelines. Proceedings of the 6th conference on Computational Methods in Systems Biology (2008), Heiner M and Uhrmacher AM eds, Lecture Notes in Bioinformatics, 5307: 176-190.
    [DOI] [PDF version]

  8. Le Novère N. Neurologic diseases: are systems approaches the way forward? Pharmacopsychiatry (2008), 41: S28-S31.
    [PubMed] [DOI] [proofs PDF version]

  9. Le Novère N., Courtot M., Laibe C. Adding semantics in kinetics models of biochemical pathways. Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations (2007), 137-153. Available at http://www.beilstein-institut.de/index.php?id=196
    [PDF version]

  10. Le Novère N. Model storage, exchange and integration. BMC Neuroscience (2006), 7: S11.
    [PubMed] [DOI] [Pubmed Central] [BioMedCentral] [PDF version]

  11. Hill JA, Le Novère N, Zoli M, Changeux J-P. Ontogeny of nicotinic receptor subunit expression in cardiac autonomic circuit in rat. Circulation (1994), 90 part 2: 360.

  12. Le Novère N, Zoli M, Changeux J-P. Effets de l'injection de nicotine sur les ARNs messagers codant pour des protéines caractéristiques de la transmission dans le système dopaminergique mésostrié. Semaine des hôpitaux de Paris (1994), 70: 403.
    [PDF version]

Book chapters, editorials, publications in non peer-reviewed journals and conference proceedings etc.

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  1. Waltemath D., Le Novère N. Simulation Experiment Description Markup Language (SED-ML) Encyclopedia of Computational Neuroscience, Springer (2013) ISBN 978-1-4419-9864-4
    [DOI]

  2. Waltemath D., 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., Myers‎ C.J., Nickerson D., Olivier B., Rodriguez N., Schreiber F., Smith L., Zhang F., Bonnet E. COMBINE 2013: meeting report SIGS (2013) 9(3)
    [DOI] [SIGS]

  3. Le Novère N. Normes pour l’échange des modèles en biologie des systèmes. Habilitation thesis, University Bordeaux II Victor Segalen (2013).
    [PDF version]

  4. Chelliah V., Laibe C., Le Novère N. BioModels Database: a repository of mathematical models of biological processes Encyclopedia of Systems Biology, Springer (2013) ISBN 978-1-4419-9864-4

  5. Schreiber F., Le Novère N. Exchange Formats for Systems Biology: SBGN Encyclopedia of Systems Biology, Springer (2013) ISBN 978-1-4419-9864-4

  6. Keating S.M., Le Novère N. Supporting SBML as a Model Exchange Format in Software Applications Methods in Molecular Biology 1021. In silico Systems Biology (2013), 201-225
    [PubMed] [DOI] [PDF version]

  7. Chelliah V., Laibe C., Le Novère N. BioModels Database: a repository of mathematical models of biological processes Methods in Molecular Biology 1021. In silico Systems Biology (2013), pp 189-199
    [PubMed] [DOI] [PDF version]

  8. Juty, N., Laibe C., Le Novère N. Controlled annotations for Systems Biology Methods in Molecular Biology 1021. In silico Systems Biology (2013), pp 227-245
    [PubMed] [DOI] [PDF version]

  9. Le Novère N., Endler L. Using chemical kinetics to model biochemical pathways Methods in Molecular Biology 1021. In silico Systems Biology (2013), pp 147-167
    [PubMed] [DOI] [PDF version]

  10. Keating S., Le Novère N. Encoding neuronal models in SBML. Computational Systems Neurobiology, Le Novère ed, Springer (2012) pp 459-488 ISBN-13: 978-9400738577
    [PDF version]

  11. Endler L., Stefan M.I., Edelstein S., Le Novère N. Using chemical kinetics to model neuronal signalling pathways. Computational Systems Neurobiology, Le Novère ed, Springer (2012) pp 81-117 ISBN-13: 978-9400738577
    [PDF version]

  12. Le Novère N., Hucka M., Anwar N., Bader G., Demir E., Moodie S., Sorokin A. Meeting report from the first meetings of the Computational Modelling in Biology Network (COMBINE) SIGS (2011) 5(2):577
    [PubMed] [Pubmed Central] [SIGS]

  13. Hucka M., Le Novère N. Sofware that goes with the flow in systems biology. BMC Biology (2010) 8: 140
    [PubMed] [Pubmed Central] [BioMedCentral] [PDF version]

  14. Le Novère N. Realistic models of neuron require quantitative information at the single-cell level. (2010), in Unravelling Single Cell Genomics, Bontoux, Dauphinot and Potier eds, pp 45-53.

  15. Baldi B.F., Hoyer C., Le Novère N. Schizophrenic: Forever young? Genome Medecine (2010), 2: 32
    [PubMed] [Pubmed Central] [BioMedCentral] [PDF version]

  16. Chelliah V., Endler L., Juty N., Laibe C.,Li C., Rodriguez N., Le Novère N. Data Integration and Semantic Enrichment of Systems Biology Models and Simulations. 6th International workshop Data Integration in the Life Sciences, Lecture Notes in Bioinformatics (2009), 5647: 5-15.
    [PDF version]

  17. Schimizu T.S.S., Le Novère N. Looking inside the box: bacterial transistor arrays. Molecular Microbiology (2008), 69: 5-9
    [PubMed] [DOI] [Mol Microbiol Free Access] [PDF version]

  18. Shapiro B. E., Finney A., Hucka M., Borstein B., Funahashi A., Jouraki A., Keating S.M., Le Novère N., Matthews J.A. Schilstra M.J. SBML Models and MathSBML. Introduction to Systems Biology (2007), Humana Press, USA. ISBN-10: 1588297063, ISBN-13:978-1588297068.

  19. Le Novère N. The long journey to a Systems Biology of neuronal function. BMC Systems Biology (2007), 1: 28.
    [PubMed] [DOI] [Pubmed Central] [BioMedCentral] [PDF version]

  20. Le Novère N. BioModels.net, tools and resources to support Computational Systems Biology. Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks (2005), Logos, Berlin, pp. 69-74.
    [PDF version]

  21. Le Novère N., Tolle D. Particle-based stochastic simulations. Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks (2005), Logos, Berlin, pp. 41-45.
    [PDF version]

  22. Sallette J., Bohler S., Benoit P., Soudant M., Pons S., Le Novère N., Changeux J.P., Corringer P.J. Neuronal nicotinic receptors subtypes: Mechanism of up-regulation by chronic exposure to nicotine International Journal of Neuropsychopharmacology (2004), 24th CINP Congress, 7: S44

  23. Le Novère N. La communication neuronale à l'ère post-génomique : le projet DopaNet. Biofutur (2003), 237: 20-24..

  24. Lacombe B, Becker D, Hedrich R, DeSalle R, Hollmann M, Kwak JM, Schroeder JI, Le Novère N, Nam HG, Spalding EP, Tester M, Turano FJ, Chiu J, Coruzzi G. On the identity of plant glutamate receptors. Science (2001), 292: 1486-1487.
    [PubMed] [DOI]

  25. Rogner U.C., Spyropoulos D.D., Le Novère N., Changeux J.-P., Avner, P. Mutation of the murine X-linked gene NAP1L2 by homologous recombination. European Journal of Neuroscience (2000), 12: S247.

  26. Cordero-Erausquin M., Marubio L.M., Arroyo-Jimenez M.M.M., Le Novère N., Huchet M., Léna C, Changeux J.-P. Characterization of mice lacking the nicotinic receptor α4 subunit. Journal of Physiology-Paris (1998), 92: 423.

  27. Le Novère N., Corringer P.-J., Changeux J.-P. Predicted secondary structure of a nicotinic acetylcholine receptor subunit. Incorporation of predicted solvent accessibility and experimental data into a two dimensional representation. Journal of Physiology-Paris (1998), 92: 458.

  28. Le Novère N. Contribution à l'étude de la relation structure-fonction dans la famille des sous-unités des récepteurs nicotiniques de l'acétylcholine. PhD thesis, University Paris VI Pierre and Marie Curie (1998). [HTML version] [postscript version] The postscript version contains the text with embedded figures. In addition you need those additionnal figures (Be careful, this last file is very large!)

  29. Le Novère N Approches théoriques et pratiques en hybridation in situ et autoradiographie réceptorielle. Annales de l'Institut Pasteur / actualités (1998) 9 : 259-270.
    [postscript version with heavy figures]

Technical reports

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  1. Le Novère N., Demir E., Mi H., Moodie S., Villeger A. Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2) Nature Precedings (2011), DOI:10.1038/npre.2011.5902.1 [This is Level 1 Version 1.2]
    [PDF version]

  2. Waltemath D., Bergmann F.T., Adams R., Le Novère N. Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1 Nature Precedings (2011), DOI:10.1038/npre.2011.5846.1
    [PDF version]

  3. Moodie S., Le Novère N., Demir E., Mi H., Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nature Precedings (2011), DOI:10.1038/npre.2011.3721.3 [This is Level 1 Version 1.3]
    [PDF version]

  4. Waltemath D., Swainston N., Lister A., Bergmann F., Henkel R., Hoops S., Hucka M., Juty N., Keating S., Knüpfer C., Krause F., Laibe C., Liebermeister W., Lloyd C., Misirli G., Schulz M., Taschuk M., Le Novère N. SBML Level 3 Package Proposal: Annotation. Nature Precedings (2011), DOI:10.1038/npre.2011.5610.1.

  5. Le Novère N., Moodie S., Sorokin A., Schreiber F., Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nature Precedings (2010), DOI:10.1038/npre.2010.3719.2 [This is Level 1 Version 1.1]
    [PDF version]

  6. Moodie S., Le Novère N., Demir E., Mi H., Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nature Precedings (2010), DOI:10101/npre.2010.3721.2 [This is Level 1 Version 1.2]
    [PDF version]

  7. Mi H., Schreiber F., Le Novère N., Moodie S., Sorokin A. Systems Biology Graphical Notation: Activity Flow language Level 1. Nature Precedings (2009), DOI:10.1038/npre.2009.3724.1
    [PDF version]

  8. Le Novère N., Moodie S., Sorokin A., Schreiber F., Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nature Precedings (2009), DOI:10.1038/npre.2009.3719.1
    [PDF version]

  9. Moodie S., Le Novère N., Sorokin A., Schreiber F., Mi. H. Systems Biology Graphical Notation: Process Description language Level 1. Nature Precedings (2009), DOI:10.1038/npre.2009.3721.1 [This is Level 1 Version 1.1]
    [PDF version]

  10. Wolkenhauer O., Fell D., De Meyts P., Blüthgen N., Herzel H., Le Novère N., Höfer T., van Leeuwen I. Advancing systems biology for medical applications. ESF science policy briefing (2008), 35.
    [PDF version]

  11. Hucka M., Hoops S., Keating S., Le Novère N., Sahle S., Wilkinson D.J. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Precedings (2008), doi:10.1038/npre.2008.2715.1 [This is Level 2 Version 4]
    [PDF version. ]

  12. Le Novère N., Moodie S., Sorokin A., Hucka M., Schreiber F., Demir E., Mi H., Matsuoka Y, Wegner K., Kitano H. Systems Biology Graphical Notation: Process Diagram Level 1. Nature Precedings (2008), DOI:10101/npre.2008.2320.1
    [PDF version]

  13. Le Novère N., Oellrich A. Systems Biology Markup Language (SBML) Level 3 Proposal: multistate components. (2007)
    [PDF version]

  14. Hucka M., Finney A., Hoops S., Keating S.,Le Novère N. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Precedings (2007), doi:10101/npre.2007.58.1 [This is Level 2 Version 3]
    [PDF version of release 2][PDF version of release 1]

  15. Hucka M., Finney A., Le Novère N. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. http://sbml.org/documents/ [This is Level 2 Version 2]
    [
    PDF version]

  16. Le Novère N., Finney A. A simple scheme for annotating SBML with references to controlled vocabularies and database entries. (2005)
    [PDF version]

  17. Le Novère N. Effets cellulaire de la nicotine. In: Tabac : comprendre la dépendance pour agir (2004) INSERM Collective expertise.
    [PDF version] [Synthese and recommendations of the expertise]

  18. Le Novère N., Thomas Simon Shimizu, Andrew Finney Systems Biology Markup Language (SBML) Level 3 Proposal: Multistate Features. (2002)
    [PDF version]