Complete list of publications

As of September 2024, Google Scholar says citation count >29700; h-index=76.

Libre Access

Gratis Access

Publications in peer-reviewed journals

130. Deslande M., Puig-Castellví F., Castro I, Pacheco-tapia R, Leloire A, Andrikopoulos P., Toussaint B., Oger F., Gambardella N., Lefebvre P., Raverdy V., Caiazzo R., Lassailly G., Derhourhi M., Amanzougarene S., Staels B., Pattou F., Froguel P., Bonnefond A. Intrahepatic hippurate mediates microbiome protection in metabolic dysfunction-associated steatotic liver disease submitted.
     

129. Montalban E., Giralt A., Taing L., Nakamura Y., Schut E.H.S., Pelosi A., Brown M., de Pins B., Valjent E., Martin M., Nairn A.C., Greengard P., Flajolet M., Hervé D., Gambardella N., Roussarié J.-P., Girault J.-A. Operant training for highly palatable food alters translating mRNA in nucleus accumbens D2 neurons and reveals a modulatory role of Neurochondrin. Biological Psychiatry (2023), 95:926-937
     [Biol Psy] [DOI] []

128. Montalban E., Giralt A., Taing L., Schut E.H.S., Supiot L.F., Castell L., Nakamura Y., de Pins B., Pelosi A., Goutebroze L., Tuduri P., Wang W., Neiburga K.D., Vestito L., Castel J., Luquet S., Nairn A.C., Hervé D., Heintz N., Martin C., Greengard P., Valjent E., Meye F.J., Gambardella N., Roussarié J.-P., Girault J.-A. Translational profiling of mouse dopaminoceptive neurons reveals a role of PGE2 in dorsal striatum. Molecular Psychiatry (2022), 27:2068–2079
     [PubMed] [Pubmed Central] [Molecular Psychiatry [DOI] []

127. Dalle Pezze P., Karanasios E., Kandia V., Manifava M., Walker S.A., Gambardella Le Novère N., Ktistakis N.T. ATG13 dynamics in non-selective autophagy and mitophagy: insights from live imaging studies and mathematical modelling. Autophagy (2020), 11(5): 1131-1141
     [PubMed] [Pubmed Central] [Autophagy] [DOI] []

126. Li L., Lai M., Cole S., Le Novère N., Edelstein S. Neurogranin Stimulates Ca2+/Calmodulin-dependent Kinase II by Suppressing Calcineurin Activity at Specific Calcium Spike Frequencies. PLoS Computational Biology (2020), 16(2): e1006991
     [PubMed] [Pubmed Central] [PLoS] [DOI] []

125. Gambardella L., McManus S., Moignard V., Sebukhan D., Delaune A., Andrews S., Bernard W.G., Morrison M.A., Riley R.P., Göttgens B., Gambardella Le Novère N., Sinha S. BNC1 regulates cell heterogeneity in human pluripotent stem cell derived-epicardium. Development (2019), 146: dev174441
     [PubMed] [Pubmed Central] [Development] [DOI] []

124. Bargehr J., Ong L.P., Colzani M., Davaapil H., Hofsteen P., Bhandari. S., Gambardella L., Le Novère N., Iyer D., Sampaziotis F., Weinberger F., Bertero A., Leonard A., Bernard W.G., Martinson A., Figg N., Regnier M., Bennett M.R., Murry C.E., Sinha S. Human embryonic stem cell-derived epicardial cells augment cardiomyocyte-driven heart regeneration. Nature Biotechnology (2019), 37(8):895-906
     [PubMed] [Pubmed Central] [NPG] [DOI] []

123. Hastings J., Mains A., Virk B., Rodriguez N., Murdoch C., Pearce J., Bergman S., Le Novère N., Casanueva O. Multi-omics and genome-scale modeling reveal a metabolic shift during C. elegans aging. Frontiers in Molecular Biosciences (2019) 6: 2.
     [PubMed] [Frontiers] [Pubmed Central] [DOI] []

122. Witting M.A., Hastings J., Rodriguez N., Joshi C., Hattwell J., Ebert P., van Weeghel M., Gao A., Wakelam M., Houtkooper R., Mains A., Le Novère N., Sadykoff S., Schroeder F., Lewis N., Shirra H.-J., Kaleta C., Casanueva O. Modeling meets Metabolomics – The WormJam Consensus Model as basis for Metabolic Studies in the model organism Caenorhabditis elegans. Frontiers in Molecular Biosciences (2018) 5: 96
     [PubMed] [Frontiers] [Pubmed Central] [DOI] []

121. Fucic A., Aghajanyan A., Culig Z., Le Novère N. Systems Oncology: Bridging Pancreatic and Castrate Resistant Prostate Cancer. Pathology and Oncology Research (2018) 25(4): 1269–1277
     [PubMed] [Springer] [DOI] []

120. Nguyen A., Guedán A., Mousnier A., Swieboda D., Zhang Q., Horkai D., Le Novère N., Solari R., Wakelam M.J.O. Host lipidome analysis during rhinovirus replication in HBECs identifies potential therapeutic targets. Journal of Lipid Research (2018) 59(9): 1571-1684
     [PubMed] [JLR] [Pubmed Central] [DOI] []

119. Mazein A., Ostaszewski M., Kuperstein I., Watterson S., Le Novère N., Lefaudeux D., De Meulder B., Pellet J., Balaur I., Saqi M., Nogueira M.M., He F., Parton A., Lemonnier N., Gebel S., Hainaut P., Ollert M., Dogrusoz U., Barillot E., Zinovyev A., Schneider R., Balling R., Auffray C. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. NPJ Systems Biology and Applications (2018) 4: 21
     [PubMed] [NPJ] [Pubmed Central] [DOI] []

118. Ostaszewski M., Gebel S., Kuperstein I., Mazein A., Zinovyev A., Dogrusoz U., Hasenauer J., Fleming R.M.T., Le Novère N., Gawron P., Ligon T., Niarakis A., Nickerson D., Weindl D., Balling R., Barillot E., Auffray C., Schneider R. Community-driven roadmap for integrated disease maps. Briefings in Bioinformatics (2018) 20(2): 659–670
     [PubMed] [Brief Bioinfo] [Pubmed Central] [DOI] []

117. Glont M., 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., Hermjakob H. BioModels: Expanding horizons to include more modelling approaches and formats. Nucleic Acids Research (2018) 46(D1): D1248-D1253
     [PubMed] [NAR] [Pubmed Central] [DOI] []

116. Malek M., Kielkowska A., Chessa T., Anderson K.E., Barneda D., Pir P., Nakanishi H., Eguchi S., Koizumi A., Sasaki J., Juvin V., Kiselev V.Y., 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., Stephens L.R. PTEN regulates PI(3,4)P2 signalling downstream of class I PI3K. Molecular Cell (2017) 68(3): 566–580
     [PubMed] [Cell Press] [Pubmed Central] [DOI] [][Extended model description]

115. Boras V., Fusic A., Virag M., Gabric D., Blivajs I., Tomasovic-Longaric C., Rakusic Z., Bisof V., Le Novère N., Vrdoljak D.V. Significance of stroma in biology of oral squamous cell carcinoma. Tumori (2017) 104(1): 9-14
     [PubMed] [Tumori] [DOI] []

114. Díaz-Muñoz M.D., Kiselev V.Y., Le Novère N., Curk T., Ule J., Turner M. Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells. Nature Communications (2017) 8: 530
     [PubMed] [NPG] [DOI] [Pubmed Central] []

113. McMurry J., 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., Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact. PLoS Biology (2017) 15(6): e2001414
     [PubMed] [PLoS] [Pubmed Central] [DOI] []

112. Musante V., Li L., Kanyo J., Lam T.T., Colangelo C.M., Cheng S.K., Brody H., Greengard P., Le Novère N., Nairn A.C. Reciprocal regulation of ARPP-16 by PKA and MAST-3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. eLife (2017) 6: e24998
     [PubMed] [eLife] [DOI] [Pubmed Central] []

111. Dalle Pezze P., Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology (2017) 11(1): 46
     [PubMed] [Wiley] [Pubmed Central] [DOI] []

110. Lloret i Villas A., Varusai T. M., Juty N., Laibe C., Le Novère N., Hermjakob H., Chelliah, V. The impact of mathematical modeling in understanding the mechanisms underlying neurodegeneration: evolving dimensions and future directions. CPT: Pharmacometrics & Systems Pharmacology (2016), 6:73–86
     [PubMed] [Wiley] [Pubmed Central] [DOI] []

109. Knight-Schrijver V., Chelliah V., Cucurull-Sanchez L., Le Novère N. The promises of quantitative systems pharmacology modelling for drug development. Computational and Structural Biotechnology Journal (2016), 14: 363–370
     [PubMed] [DOI] [CSBJ] [Pubmed Central] []

108. Dumontier M., Gray A.J.G., Marshall M.S., Alexiev V., Ansell P., Bader G.D., Baran J., Bolleman J.T., Callahan A., Cruz-Toledo J., Gaudet P., Gombocz E., Gonzalez-Beltran A., Groth P., Haendel M., Ito M., Jupp S., Juty N., Katayama T., Kobayashi N., Krishnaswami K., Laibe C., Le Novère N., Lin S., Malone J., Miller M., Mungall C.J., Rietveld L., Wimalaratne S.M., Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ (2016), 4:e2331
     [PubMed] [DOI] [Pubmed Central] [PeerJ] []

107. Rodriguez N., Pettit J.B., Dalle Pezze P., Li L., Henry A., van Iersel M.P., Jalowicki G., Kutmon M., Natarajan K. N., Tolnay D., Stefan M.I., Evelo C.T., Le Novère N. The Systems Biology Format Converter. BMC Bioinformatics (2016) 17(1):154
     [PubMed] [Pubmed Central] [DOI] [BMC Bioinformatics] []

106. Stanford N.J., Wolstencroft K., Golebiewski M., Kania R., Juty N., Tomlinson C., Owen S., Butcher S., Hermjakob H., Le Novère N., Mueller W., Snoep J.L., Goble C. The evolution of standards and data management practices in systems biology. Molecular Systems Biology (2015) 11: 851.
     [PubMed] [Pubmed Central] [DOI] [Molecular Systems Biology] []

105. Seeliger C., Le Novère N. Enabling surface dependent diffusion in spatial simulations using Smoldyn. BMC Research Notes (2015) 8(1):752.
     [PubMed] [Pubmed Central] [DOI] [BioMed Central] []

104. Quinn J.Y., Cox R.S. 3rd, Adler A., Beal J., Bhatia S., Cai Y., Chen J., Clancy K., Galdzicki M., Hillson N.J., Le Novère N., Maheshwari A.J., McLaughlin J.A., Myers C.J., P U., Pocock M., Rodriguez C., Soldatova L., Stan G.B., Swainston N., Wipat A., Sauro H.M. SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biology (2015) 13(12):e1002310
     [PubMed] [DOI] [Pubmed Central] [PLoS] []

103. Ebrahim A., Almaas E., Bauer E., Bordbar A., Burgard A.P., Chang R.L., Dräger A., Famili I., Feist A.M., Fleming R.M., Fong S.S., Hatzimanikatis V., Herrgård M.J., Holder A., Hucka M., Hyduke D., Jamshidi N., Lee S.Y., Le Novère N., Lerman J.A., Lewis N.E., Ma D., Mahadevan R., Maranas C., Nagarajan H., Navid A., Nielsen J., Nielsen L.K., Nogales J., Noronha A., Pal C., Palsson B.O., Papin J.A., Patil K.R., Price N.D., Reed J.L., Saunders M., Senger R.S., Sonnenschein N., Sun Y., Thiele I. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology (2015) 11(10):831
     [PubMed] [DOI] [Pubmed Central] [MSB] []

102. Kiselev V.Y., Juvin V., Mouhannad M., Luscombe N.M., Hawkins P., Le Novère N., Stephens L.R. Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop. Nucleic Acids Research (2015) 43 (20): 9663-9679
     [PubMed] [DOI] [Pubmed Central] [NAR] [] [Supp mat][Plot mRNA expression][Ismara analysis]

101. Rodriguez N., 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., Dräger A. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics (2015) 31(20):3383-3366
     [PubMed] [DOI] [Pubmed Central] [Bioinformatics] []

100. Swat M.J., Moodie S., Wimalaratne S.M., Kristensen N.R., Lavielle M., Mari A., Magni P., Bizzotto R., Pasotti L, Mezzalana E, Smith M. K., Comets E., Sarr C., Terranova N., Blaudez E., Chan P., Chard J., Chatel K., Chenel M., Edwards D., Franklin C, Giorgino T., Glont M., Girard P., Grenon P., Harling K., Hooker A.C, Kaye R., Keizer R., Kloft C., Kok, J. N., Kokash N., Laibe C., Laveille C., Lestini G., Mentré 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., Le Novère N. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT: Pharmacometrics & Systems Pharmacology (2015) 6: 316-319
     [PubMed] [DOI] [Pubmed Central] [Wiley] []

99. Juty N., Ali R., Glont M., Keating S., Rodriguez N., Swat M.J., Wimalaratne S., Hermjakob H., Le Novère N., Laibe C., Chelliah V. BioModels Database: Content, Features, Functionality, and Use. CPT: Pharmacometrics & Systems Pharmacology (2015) 2(4): 55-68
    [PubMed] [DOI] [Pubmed Central] [Wiley] []

98. Hucka M., Nickerson D.P., Bader G., Bergmann F.T., Cooper J., Demir E., Garny A., Golebiewski M., Myers C.J., Schreiber F., Waltemath D., Le Novère, N. Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative. Frontiers in Bioengineering and Biotechnology (2015) 3:19
    [PubMed] [FrontiersIn] [DOI] [Pubmed Central] []

97. Le Novère N. Quantitative and logic modelling of gene and molecular networks. Nature Reviews Genetics (2015) 16: 146–158
    [PubMed] [NPG] [DOI] [Pubmed Central] [] [Model for Box2 as a COMBINE archive] [Model for Box3 as a COMBINE archive]

96. Wimalaratne S.M., Bolleman J., Juty N., Katayam T., Dumontier M., Redaschi N., Le Novère N., Hermjakob H., Laibe C. SPARQL-enabled identifier conversion with Identifiers.org. Bioinformatics (2015) 31(11): 1875-1877
    [PubMed] [Bioinformatics] [DOI] [Pubmed Central] []

95. Dutta Roy R., Rosenmund C., Edelstein S.J., Le Novère N. Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model. PLoS ONE (2015) 10(1): e0116616
    [PubMed] [PLoS ONE] [DOI] [Pubmed Central] [arXiv] []

94. Naldi A., 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., Chaouiya, C. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics (2015) 31(7): 1154-1159
    [PubMed] [Bioinformatics] [DOI] []

93. Lai M., Brun D., Edelstein S.J., Le Novère N. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PLoS Computational Biology (2015) 10(1):e0116616
    [PubMed] [PLoS Computational Biology] [DOI] [Pubmed Central] [arXiv] []

92. Deans A.R., Lewis S.E., Huala E., Anzaldo S.S., Ashburner M., Balhoff J.P., Blackburn D.C., Blake J.A., Burleigh J.G., Chanet B., Cooper L.D., Courtot M., Csõsz S., Cui H., Dahdul W., Das S., Dececchi T.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., Squires R.B., Thacker R.W., Thessen A., Fernandez-Triana J., 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., Mabee P.M. Finding our way through phenotypes. PLoS Biology (2015) 13(1): e1002033
    [PubMed] [PLoS Biology] [DOI] [Pubmed Central] []

91. Chelliah V., Juty N., Ajmera I., Raza A., 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., Laibe C. BioModels: ten year anniversary. Nucleic Acids Research (2015) 43 (D1): D542-D548
    [PubMed] [NAR] [DOI] [Pubmed Central] []

90. Bergmann F.T., 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., Le Novère N. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Systems Biology (2014) 15:369
    [PubMed] [BMC Bioinformatics] [DOI] [Pubmed Central] [arXiv] []

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

88. 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] []

87. 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] []

86. 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] [Pubmed Central] [BMC Systems Biology] [DOI] [arXiv] []

85. 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] [CPT:PSP] [Pubmed Central] [DOI] []

84. 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] []

83. 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] [] []

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

81. Knüpfer 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] [Pubmed Central] []

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

79. 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] [Pubmed Central] []

78. 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] []

77. 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] []

76. 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] []

75. 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] []

74. 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] [J Biol Rhythms [Pubmed Central] []

73. 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] [][Supp 1][Supp 2][Supp 3] []

72. 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] []

71. 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] []

70. 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] []

69. 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] []

68. 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] []

67. 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] [] []

66. 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] [][]

65. 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] []

64. 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] [][Supplementary information 1][Supplementary information 2]

63. 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] []

62. 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] []

61. 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] []

60. 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] []

59. 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] []

58. 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] [] []

57. 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] []

56. 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] [] [Supplementary info]

55. 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] []

54. 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] [Pubmed Central] [DOI] [RSIF Free Access] []

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

52. 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] [Pubmed Central] [Nature Biotechnology] [DOI] []

51. 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] [BBRC] [DOI] []

50. 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] [Pubmed Central] [Nature Biotechnology] [DOI] []

49. 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 6^th 2008, we discovered that the figures 3 and 4 of the published paper were 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]
    

48. 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] []

47. 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] []

46. 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] []

45. 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] [] [Model A in BioModels Database] [Model B in BioModels Database]

44. 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] [Nat Rev Drug Discov] []

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

42. 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] []

41. 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] []

40. 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] []

39. 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] [Nat Biotechnol] []

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

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

36. 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] []

35. 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] []

34. 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] [DOI] [J Neurosci Free access] []

33. 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] []

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

31. 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] []

30. 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] []

29. 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] [] [model of α-conotoxine bound to chick (α7)₂]

28. 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] [] [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]

27. 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 (now Developmental Neurobiology) (2002), 53: 447-456.
    [PubMed] [DOI] [J Neurobiol Free access] []

26. 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] []

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

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

23. 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] []

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

21. 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] []

20. 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] []

19. 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] []

18. 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] [] [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]

17. 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] []

16. 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] [DOI] []

15. 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] [] []

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

13. 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] []

12. 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] []

11. 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] []

10. 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] []

9. 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] [DOI] []

8. 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][]

7. 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] [DOI]

6. 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][]

5. 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] [DOI] []

4. 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] []

3. 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] []

2. 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] []

1. 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.
   [iPubli] []

Publications in peer-reviewed conference proceedings

14. Myers C.J., Bader G., Gleeson P., Golebiewski M., Hucka M., Le Novère N., Nickerson D.P., Schreiber F., Waltemath D. A brief history of COMBINE. Winter Simulation Conference (2017), 884-895
    [DOI] []

13. Lloret-Villas A., Daudin R., Le Novère N. "Big Data" in neuroscience: open door to a more comprehensive and translational research. Big Data Analytics (2016), 1:5
    [] [DOI] [BioMed Central]

12. 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)
    []

11. 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)
    []

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

9. 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] []

8. 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
   []

7. 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 3^rd International Conference on Biomedical Ontology. (2012), CEUR Workshop Proceedings 897
   [CEUR-WS] []

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

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

4. 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.
   []

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

2. 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.
   

1. 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.
   []

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

43. Knight-Schrijver V.R., Cucurull-Sanchez L., Gambardella N. Is IL-6 a better drug target than IL-6Rα? A quantitative systems pharmacology perspective in the context of rheumatoid arthritis. To be submitted
    

42. Montalban E., Giralt A., Taing L., Nakamura Y., Schut E.H.S., Pelosi A., Brown M., de Pins B., Valjent E., Martin M., Nairn A.C., Greengard P., Flajolet M., Hervé D., Gambardella N., Roussarié J.-P., Girault J.-A. Operant training for highly palatable food alters translating mRNA in nucleus accumbens D2 neurons and reveals a modulatory role of Ncdn. BioRxiv (2023) 2023.03.07.531496v1.
    [BioRxiv] [DOI] []

41. Montalban E., Giralt A., Taing L., Nakamura Y., Martin C., de Pins B., Pelosi A., Goutebroze L., Castell L., Wang W., Neiburga K.L., Vestito L., Nairn A.C., Valjent E., Hervé D., Heintz N., Gambardella Le Novère N.,Greengard P., Roussarié J.-P., Girault J.-A. Translational profiling of mouse dopaminoceptive neurons reveals a role of PGE2 in dorsal striatum. BioRxiv (2020) 2020.09.02.279240.
    [BioRxiv] [DOI] []

40. Li L., Lai M., Cole S., Le Novère N., Edelstein S. Neurogranin Stimulates Ca2+/calmodulin-dependent Kinase II by Inhibiting Calcineurin at Specific Calcium Spike Frequencies. BioRxiv (2019) 2019/01/01/597278
    [BioRxiv] [DOI] []

39. Dalle Pezze P., Karanasios E., Kandia V., Walker S., Ktistakis N.T., Le Novère N. Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy. BioRxiv (2018) 2018/07/16/370114
    [BioRxiv] [DOI] []

38. Lieven C., Beber M.E., Olivier B.G., Bergmann F.T., Babaei P., Bartell J.A., Blank L.M., Chauhan S., Correia K., Diener C., Dräger A., Ebert B.E., Edirisinghe J.N., Fleming R.M.T., Garcia-Jimenez B., van Helvoirt W., Henry C., Hermjakob H., Herrgard M.J., Kim H.U., King Z., Koehorst J.J., Klamt S., Klipp E., Lakshmanan M., Le Novère N., Lee D.Y., Lee S.Y., Lee S., Lewis N.E., Ma H., Machado D., Mahadevan R., Maia P., Mardinoglu A., Medlock G.L., Monk J., Nielsen J., Nielsen L.K., Nogales J., Nookaew I., Resendis O., Palsson B., Papin J.A., Patil K.R., Price N.D., Richelle A., Rocha I., Schaap P., Sheriff R.S.M., Shoaie S., Sonnenschein N., Teusink B., Vilaca P., Vik J. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite. BioRxiv (2018) 2018/06/21/350991
    [BioRxiv] [DOI] []
    

37. Neal M.L., König M., Nickerson D., Mısırlı G., Kalbasi R., Dräger A., Atalag K., Chelliah V., Cooling M., Cook D.L., Crook S., de Alba M., Friedman S.H., Garny A., Gennari J.H., Gleeson P., Golebiewski M., Hucka M., Juty N., Le Novère N., Myers C., Olivier B.G., Sauro H.M., Scharm M., Snoep J.L., Touré V., Wipat A., Wolkenhauer O., Waltemath D. Harmonizing semantic annotations for computational models in biology. BioRxiv (2018) 01/23/246470
    [BioRxiv] [DOI] []

35. Touré V., Le Novère N., Waltemath D., Wolkenhauer O. Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Computational Biology (2018) 14(2): e1005740
    [PubMed] [PLoS] [DOI] []

36. Schreiber F., Bader G.D., Gleeson P., Golebiewski M., Hucka M., Keating S.M., Le Novère N., Myers C., Nickerson D., Sommer B., Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. Journal of Integrative Bioinformatics (2017) 15(1): 20180013
    [JIB] [DOI] []

34. Hastings J., Mains A., Artal-Sanz M., Bergmann S., Braeckman B.P., Bundy J., Cabreiro F., Dobson P., Ebert P., Hattwell J., Hefzi H., Houtkooper R.H., Jelier R., Joshj C., Kothamachu V.B., Lewis N., Bastos Lourenco A., Nie Y., Norvaisas P., Pearce J., Riccio C., Rodriguez N., Santermans T., Scarcia P., Shirra, H.J., Sheng M., Smith R., Suriyalaksh M., Towbin B., Tuli M.A., Van Weeghel M., Weinkove D., Zecic A., Zimmerman J., Le Novère N., Kaleta C., Witting M., Casanueva O. WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series. Worm (2017) 6(2): e1373939
    [Worm] [DOI] []

33. Schreiber F., Bader G.D., Gleeson P., Golebiewski M., Hucka M., Le Novère N., Myers C., Nickerson D., Sommer B., Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. Journal of Integrative Bioinformatics (2016) 13(3): 289
    [JIB] [DOI]

32. Pir P, Le Novère N. Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine. Methods in Molecular Biology 1386 (2016) 331-350
    [DOI] []

31. Schreiber F., Bader G.D., Golebiewski M., Hucka M., Kornmeier B., Le Novère N., Myers C., Nickerson D., Sommer B., Waltemath D., Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics (2015) 12(2): 258
    [JIB] [DOI] []

30. Chelliah V., Juty N., Laibe C., Hermjakob H., Le Novère N. BioModels Database: a public repository for sharing models of biological processes. Encyclopedia of Computational Neuroscience, Springer (2015) ISBN 978-1-4419-9864-4
    [Springer]

29. Waltemath D., Le Novère N. Simulation Experiment Description Markup Language (SED-ML). Encyclopedia of Computational Neuroscience, Springer (2014) ISBN 978-1-4419-9864-4
    [DOI]

28. 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] []

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

26. 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
    

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

24. 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] []

23. 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] []

22. 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] []

21. 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] []

20. 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
    []

19. 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
    []

18. 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] [DOI] [Pubmed Central] [SIGS] []

18. Hamilton D.J., Bergamino M., DeFelipe J., Le Novère N., Shepherd G.M., Witter M.P., Ascoli G.A. Machine-Readable Description of Neuron Types and Properties Frontiers in Neuroinformatics Conference Abstract: 4th INCF Congress of Neuroinformatics (2011) conf.fninf.2011.08.00102.
    [DOI]

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

16. 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. ISBN-10:1847559115 ISBN-13:978-1847559111

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

14. 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. ISBN:978-3-642-02879-3
    []

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

12. 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.
    

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

10. Le Novère N. BioModels.net, tools and resources to support Computational Systems Biology. Proceedings of the 4^th Workshop on Computation of Biochemical Pathways and Genetic Networks (2005), Logos, Berlin, pp. 69-74. ISBN-13:978-3832510183
    []

9. Le Novère N., Tolle D. Particle-based stochastic simulations. Proceedings of the 4^th Workshop on Computation of Biochemical Pathways and Genetic Networks (2005), Logos, Berlin, pp. 41-45. ISBN-13:978-3832510183
   []

8. 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, SP.36.01
   [DOI]

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

6. 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]

5. 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.
   

4. 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. [DOI]

3. 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. [DOI]

2. 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!)

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

Technical reports

37. Baig H., Fontanarossa P., Kulkarni V., McLaughlin J., Vaidyanathan P., Bartley B., Bhakta S., Bhatia S., Bissel M., Clancy K., Cox R.S., Moreno. A.G., Gorochowski T., Grünberg R., Lee J., Luna A., Madsen C., Mısırlı G., Nguyen T., Le Novère N., Palchick Z., Pocock M., Roehner N., Sauro H., Scott-Brown J., Sexton J.T., Stan G.-B., Tabor J.J., Vilar Vazquez M., Voigt C.A., Wipat A., Zong D., Zundel Z., Beal J., Myers C. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.3. Journal of Integrative Bioinformatics (2021) 18(3): 20200045
    [JIB] [DOI]

36. Baig H., Fontanarossa P., Kulkarni V., McLaughlin J., Vaidyanathan P., Bartley B., Bhatia S., Bhakta S., Bissel M., Clancy K., Cox R.S., Moreno. A.G., Gorochowski T., Grünberg R., Luna A., Madsen C., Mısırlı G., Nguyen T., Le Novère N., Palchick Z., Pocock M., Roehner N., Sauro H., Scott-Brown J., Sexton J.T., Stan G.-B., Tabor J.J., Vilar Vazquez M., Voigt C.A., Wipat A., Zong D., Zundel Z., Beal J., Myers C. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.2. Journal of Integrative Bioinformatics (2020) 17: 20200014
    [JIB] [DOI]

35. Madsen C., Moreno A.G., Palchick Z., P U., Roehner N., Bartley B., Bhatia S., Bhakta S., Bissell M., Clancy K., Cox R.S., Gorochowski T., Grünberg R., Luna A., McLaughlin J., Nguyen T., Le Novère N., Pocock M., Sauro H., Scott-Brown J., Sexton J.T., Stan G.-B., Tabor J.J., Voigt C.A., Zundel Z., Myers C., Beal J., Wipat A. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. Journal of Integrative Bioinformatics (2019) 16(2)20180101
    [JIB] [DOI]

34. Hucka M., Bergmann F.T., Chouiya C., Dräger A., Hoops S., Keating S.M., König M., Le Novère N., Myers C.J., Olivier B.G., Sahle S., Schaff J.C., Smith L.P., Waltemath D., Wilkinson D.J., Zhang F. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics (2019) 16(2) 20190021
    [JIB] [DOI]

33. Hucka M., 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., Wilkinson D.J. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Journal of Integrative Bioinformatics (2018) 15(1): 20170081
    [JIB] [DOI]

32. Hucka M., 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., Wilkinson D.J. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics (2018) 15(1): 20170080
    [JIB] [DOI]

31. Bergmann F.T., Cooper J., König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Lucian S, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of Integrative Bioinformatics (2018) 15(1): 20170086
    [JIB] [DOI]

30. Cox R.S., Madsen C., McLaughlin J., Nguyen T., Roehner N., Bartley B., Bhatia S., Bissell M., Clancy K., Gorochowski T., Grünberg R., Luna A., Le Novère N., Pocock M., Sauro H., Sexton J.T., Stan G.-B., Tabor J.J., Voigt C.A., Zundel Z., Myers C., Beal J., Wipat A. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. Journal of Integrative Bioinformatics (2018) 15(1): 20170074
    [JIB] [DOI]

29. Science Europe Career Pathways in Multidisciplinary Research: How to Assess the Contributions of Single Authors in Large Teams. Science Europe (2015)
    [Sci Eur]

28. Hucka M., 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., Wilkinson D.J. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics (2015) 12(2): 271
    [JIB] [DOI]

27. Chaouiya C., Keating S.M., Berenguier D., Naldi A., Thieffry D., van Iersel M.P., Le Novère N., Helikar T. The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. Journal of Integrative Bioinformatics (2015) 12(2): 270
    [JIB] [DOI]

26. Mi H., Schreiber F., Moodie S., Czauderna T., Demir E., Haw R., Luna A., Le Novère N., Sorokin A., Villéger A. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. Journal of Integrative Bioinformatics (2015) 12(2): 266
    [JIB] [DOI]

25. Sorokin A., Le Novère N., Luna A., Czauderna T., Demir E., Haw R., Mi H., Moodie S., Schreiber F., Villéger A. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. Journal of Integrative Bioinformatics (2015) 12(2): 264
    [JIB] [DOI]

24. Moodie S., Le Novère N., Demir E., Mi H., Villéger A. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. Journal of Integrative Bioinformatics (2015) 12(2): 263
    [JIB] [DOI]

23. Bergmann F.T., Cooper J., Le Novère N., Nickerson D., Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of Integrative Bioinformatics (2015) 12(2): 262
    [JIB] [DOI]

22. Bergmann F.T., Rodriguez N., Le Novère N. COMBINE archive specification Version 1 Journal of Integrative Bioinformatics (2015) 12(2): 261
    [JIB] [DOI]

21. Gray A.J.G., Dumontier M., Marshall M.S., Baran J., Ansell P., Bader G.D., Bando A., Callahan A., Cruz-Toledo J., Gombocz E., Gonzalez-Beltran A., Groth P., Haendel M., Ito M., Jupp S., Katayama T., Krishnaswami K., Kin S., Mungall C., Le Novère N., Laibe C, Juty N., Malone J., Rietveld L. Dataset Descriptions: HCLS Community Profile W3C Interest Group Notes 2014
    [W3C]

20. Moodie S., Swat M.J., Kristensen N.R., Le Novère N. PharmML: The Pharmacometrics Markup Language (version 0.2) (2013)
    []

19. 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]
    []

18. 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
    []

17. 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]
    []

16. 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.

15. 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]
    []

14. Oellrich A., Le Novère N. Multistate and Multicomponent Species (multi).
    (2010)
    []

13. 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]
    []

12. 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
    []

11. 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
    []

10. 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]
    []

9. 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.
   []

8. 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]
   [. ]

7. 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
   []

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

5. 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]
   [ release 2][ release 1]

4. 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]
   []

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

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

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