Publications

Export 171 results:
Author Title Type [ Year(Asc)]
2018
Glont M, Nguyen TV, Graesslin M, Raza A, Schramm J, Wimalaratne SM, Kothamachu VB, 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 [Internet]. Nucleic Acids Research 2018;46(D1):D1248-D1253.Available from: https://academic.oup.com/nar/article/4584626
Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming R, 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 [Internet]. Briefings in Bioinformatics 2018;Available from: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby024/4982567
Pezze PDalle, Karanasios E, Kandia V, Walker SA, Ktistakis NT, Le Novère N. Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy [Internet]. BiorXiv 2018;:370114.Available from: https://www.biorxiv.org/content/early/2018/07/16/370114
Nguyen A, Guedán A, Mousnier A, Swieboda D, Zhang Q, Horkai D, Le Novère N, Solari R, Wakelam MJO. Host lipidome analysis during rhinovirus replication in human bronchial epithelial cells identifies potential therapeutic targets. [Internet]. Journal of Lipid Research 2018;Available from: http://www.jlr.org/content/early/2018/06/26/jlr.M085910.abstract
Lieven C, Beber MEmanuel, Olivier BG, Bergmann FT, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BElisabeth, Edirisinghe JN, Fleming RMT, Garcia-Jimenez B, van Helvoirt W, Henry C, Hermjakob H, Herrgård MJ, Kim HUk, King Z, Koehorst JJan, Klamt S, Klipp E, Lakshmanan M, Le Novère N, Lee D-Y, Lee SYup, Lee S, Lewis NE, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk J, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Resendis O, Palsson B, Papin JA, Patil KRaosaheb, Price ND, Richelle A, Rocha I, Schaap P, Sheriff RSMalik, Shoaie S, Sonnenschein N, Teusink B, Vilaca P, Vik JOlav, Wodke JA, Xavier JC, Yuan Q, Zakhartsev M, Cheng Z. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite. BiorXiv 2018;
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.
Boras V, Fucic A, Virag M, Gabric D, Blivajs I, Tomasovic-Longaric C, Rakusic Z, Bisof V, Le Novère N, Vrdoljak DV. Significance of stroma in biology of oral squamous cell carcinoma. Tumori 2018;104(1):9-14.
Bergmann FT, 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.
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, 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 2018;15(1):20180013.
Cox RS, 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 JT, Stan G-B, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. Journal of Integrative Bioinformatics 2018;15:20170074.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics 2018;15(1):20170080.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Journal of Integrative Bioinformatics 2018;15(1):10170081.
Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MManuela, He F, Parton A, Lemonnier N, Gawron P, 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 [Internet]. NPJ Systems Biology and Applications 2018;4:21.Available from: https://www.nature.com/articles/s41540-018-0059-y
Fucic A, Aghajanyan A, Culig Z, Le Novère N. Systems Oncology: Bridging Pancreatic and Castrate Resistant Prostate Cancer [Internet]. Pathology and Oncology Research 2018;Available from: https://link.springer.com/article/10.1007%2Fs12253-018-0467-8
2017
Myers CJ, Bader G, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Nickerson DP, Schreiber F, Waltemath D. A brief history of COMBINE. Winter Simulation Conference 2017 2017;:884-895.
McMurry J, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Hastings J, Haendel MA, Hermjakob H, Hériché J-K, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Mungall CJ, Rocca-Serra P, Sansone S-A, Sariyar M, Snoep JL, Stanford NJ, Soiland-Reyes S, Swainston N, Washington N, Williams AR, Wolstencroft K, Goble C, Parkinson H. Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact of life science data [Internet]. PLoS Biology 2017;15(6):e2001414.Available from: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001414
Villas ALloret i, Varusai TM, 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 [Internet]. CPT: Pharmacometrics & Systems Pharmacology 2017;Available from: onlinelibrary.wiley.com/doi/10.1002/psp4.12155/full
Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VYu, 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 LR. PTEN regulates PI(3,4)P2 signalling downstream of class I PI3K [Internet]. Molecular Cell 2017;68(3):566–580.Available from: http://www.sciencedirect.com/science/article/pii/S1097276517307025
Musante V, Li L, Kanyo J, Lam TT, Colangelo CM, Cheng SK, Brody H, Greengard P, Le Novère N, Nairn AC. Reciprocal regulation of ARPP-16 by protein kinase A and MAST-3 kinase provides a cAMP-regulated switch in protein phosphatase 2A inhibition. eLife 2017;6:e24998.
Pezze PDalle, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks [Internet]. BMC Systems Biology 2017;11:46.Available from: https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0423-3
Guimera AMartinez, Welsh C, Pezze PDalle, Fullard N, Nelson G, Roger MF, Przyborski SA, Shanley DP. Systems modelling ageing: from single senescent cells to simple multi-cellular models [Internet]. Essays In Biochemistry 2017;61(3):369.Available from: http://essays.biochemistry.org/content/61/3/369.abstract
Díaz-Muñoz MD, Kiselev VYu, Le Novère N, Curk T, Ule J, Turner M. Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells [Internet]. Nature Communications 2017;8:530.Available from: https://www.nature.com/articles/s41467-017-00454-2
Hastings J, Mains A, Artal-Sanz M, Bergmann S, Braeckman BP, Bundy J, Cabreiro F, Dobson P, Ebert P, Hattwell J, Hefzi H, Houtkooper RH, Jelier R, Joshj C, Kothamachu VB, Lewis N, Lourenco ABastos, Nie Y, Norvaisas P, Pearce J, Riccio C, Rodriguez N, Santermans T, Scarcia P, Shirra HJoachim, Sheng M, Smith R, Suriyalaksh M, Towbin B, Tuli MAnn, 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 [Internet]. Worm 2017;6(2):e1373939.Available from: http://www.tandfonline.com/doi/full/10.1080/21624054.2017.1373939
2016
Lloret-Villas A, Daudin R, Le Novère N. "Big Data" in neuroscience: open door to a more comprehensive and translational research [Internet]. Big Data Analytics 2016;1:5.Available from: http://bdataanalytics.biomedcentral.com/articles/10.1186/s41044-016-0005-1
Dumontier M, Gray AJG, Marshall SM, Alexiev V, Ansell P, Bader GD, Baran J, Bolleman J, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz E, Gonzalez-Beltran A, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayam T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall C, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ 2016;4:e2331.
Pir P, Le Novère N. Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine. In: Methods Molecular Biology: Systems Medicine. Springer; 2016 p. 331-350.
Knight-Schrijver V, Chelliah V, Cucurull-Sanchez L, Le Novère N. The promises of quantitative systems pharmacology modelling for drug development [Internet]. Computational and Structural Biotechnology Journal 2016;14:363–370.Available from: http://www.sciencedirect.com/science/article/pii/S2001037016300435
Rodriguez N, Pettit J-B, Pezze PDalle, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. The Systems Biology Format Converter. BMC Bioinformatics 2016;17:154.
Pezze PDalle, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PRazquin, van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Hahn U, Horvatovich P, Shanley DP, Thedieck K. A systems study reveals concurrent activation of AMPK and mTOR by amino acids [Internet]. 2016;7:13254 - .Available from: http://dx.doi.org/10.1038/ncomms13254
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PEPinto, Cantarelli M, Chew YHoon, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gómez HF, Hahn J, Hameri T, Gardiol DFHernande, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knüpfer C, König M, Lee D, Lloret-Villas A, Mandrik N, J Medley K, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song J-H, Theile T, Tokic M, Tomar N, Touré V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. Toward Community Standards and Software for Whole-Cell Modeling [Internet]. IEEE Transactions on Biomedical Engineering 2016;63(10):2007 - 2014.Available from: http://ieeexplore.ieee.org/abstract/document/7489010/
2015
Chelliah V, Juty N, Laibe C, Hermjakob H, Le Novère N. BioModels Database: a public repository for sharing models of biological processes. In: Encyclopedia of Computational Neuroscience. New York Heidelberg Dordrecht London : Springer-Verlag; 2015
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, 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):1-14.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan K, Pettit J-B, Rodriguez N, Schubert M, Wimalaratne S, Zhou Y, Hermjakob H, Le Novère N, Laibe C. BioModels: ten year anniversary [Internet]. Nucleic Acids Research 2015;Available from: http://nar.oxfordjournals.org/content/early/2014/11/20/nar.gku1181.abstract
Bergmann FT, Rodriguez N, Le Novère N. COMBINE archive specification Version 1. Journal of Integrative Bioinformatics 2015;12(2):261.
Naldi A, Monteiro PT, 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 SM, Klamt S, Klarner H, Laubenbacher R, Le Novère N, Niknejad A, Rodriguez N, Siebert H, Stoll G, Zañudo JGT, Kestler HA, 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.
Ebrahim A, almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RMT, Fong SS, Hatzimanakis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SYup, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Niels LK, Nogales J, Noronha A, Pal C, Palsson BØ, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do Genome-scale Models Need Exact Solvers or Clearer Standards?. Molecular Systems Biology 2015;11(10)
Seeliger C, Le Novère N. Enabling surface dependent diffusion in spatial simulations using Smoldyn. BMC Research Notes 2015;8:752.
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep JL, Goble C. The evolution of standards and data management practices in systems biology [Internet]. Molecular Systems Biology 2015;11:851.Available from: http://msb.embopress.org/content/11/12/851
Dean AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, J Burleigh G, Chanet B, Cooper LD, Courtot M, Csõsz S, Cui H, Dahdul W, Das S, T Dececchi A, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendle M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lapp H, Lawrence CJ, Le Novère N, Lecointre G, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, R Squires B, Thacker RW, Thessen A, Triana JFernandez, Vihinen M, Vize PD, Voget L, Wall CE, Walls RL, Westerfield M, Wharton RA, Wirkner CS, Wooley JB, Yoder MJ, Zorn AM, Mabee PM. Finding our way through phenotypes. PLoS Biology 2015;13(1): e1002033.
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics 2015;
Roy RDutta, Rosenmund C, Edelstein SJ, Le Novère N. Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model [Internet]. PLoS ONE 2015;10(1):e0116616.Available from: http://arxiv.org/abs/1407.4750
Lai M, Brun D, Edelstein S, Le Novère N. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions [Internet]. PLoS Computational Biology 2015;11(1):e1004063.Available from: http://arxiv.org/abs/1406.2195
Kiselev VY, Juvin V, Mouhannad M, Luscombe NM, Hawkins P, Le Novère N, Stephens LR. Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop [Internet]. Nucleic Acids Research 2015;43(20): 9663-9679.Available from: http://nar.oxfordjournals.org/content/43/20/9663.long
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NRode, Lavielle M, Mari A, Magni P, Bizzoto R, Smith M, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chenel M, Edwards D, Franklin C, Giorgina T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kobash N, Laibe C, Laveille C, Mentre F, Mezzalana E, Munafo A, Nordgren R, Nyberg HB, Para-Guillen ZP, Pasotti L, Plan E, Ribba B, Smith G, Trocóniz IF, 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.
Hucka M, Nickerson DPhillip, Bader G, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJohn, Schreiber F, Waltemath D, Le Novère N. Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative [Internet]. Frontiers in Bioengineering and Biotechnology 2015;3:19.Available from: http://journal.frontiersin.org/Journal/10.3389/fbioe.2015.00019/
Le Novère N. Quantitative and logic modelling of gene and molecular networks. Nature Reviews Genetics 2015;16:146–158.
Quinn JYuan, Cox, III RSidney, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari A, McLaughlin JAlastair, Myers C, P U, Pocock M, Rodriguez C, Soldatova L, Stan G-B, Swainston N, Sauro HM, Wipat A. SBOL Visual: Standard Schematics for Synthetic Genetic Constructs. PLoS Biology 2015;13(12):e1002310.
Bergmann FT, Cooper J, Le Novère N, Nickerson DP, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of Integrative Bioinformatics 2015;12(2):262.
Wimalaratne SM, 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;
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kornmeier B, Le Novère N, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Weise S. Specifications of Standards in Systems and Synthetic Biology. Journal of Integrative Bioinformatics 2015;12(2):258.
Mi H, Schreiber F, Moodie SL, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger AC. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. Journal of Integrative Bioinformatics 2015;12:266.
Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie SL, Schreiber F, Villéger AC. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. Journal of Integrative Bioinformatics 2015;12(2):264.
Moodie SL, Le Novère N, Demir E, Mi H, Villéger AC. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. Journal of Integrative Bioinformatics 2015;12(2):263.
Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics 2015;12(2):271.
Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel M, 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.
2013
Edelstein SJ. Allosteric interactions after 50 years. Journal Of Molecular Biology 2013;425(9):1391–1395.
Chelliah V, Laibe C, Le Novère N. BioModels Database: a repository of mathematical models of biological processes. Methods Mol Biol 2013;1021:189-99.
Chelliah V, Laibe C, Le Novère N. BioModels Database, A Repository of Mathematical Models of Biological Processes. In: Encyclopedia of Systems Biology. Springer; 2013
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Goryanin I, Gudmundsson S, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, Van Beek H, Weichart D, Nielsen JB, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism. Nat Biotechnol 2013;31(5):419-425.
Alcasabas AA, de Clare M, Pir P, Oliver SG. Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids. BMC Genomics 2013;14:744.
Juty N, Laibe C, Le Novère N. Controlled annotations for systems biology. Methods Mol Biol 2013;1021:227-45.
Stefan MI, Le Novère N. Cooperative binding. PLoS Computational Biology 2013;9(6)
Edelstein SJ, Le Novère N. Cooperativity of allosteric receptors. Journal of Molecular Biology 2013;425(9): 1424-1432.
Poitevin F, Edelstein SJ. Derivation of the Crick-Wyman equation for allosteric proteins defining the difference between the number of binding sites and the Hill coefficient. Journal Of Molecular Biology 2013;425(9):1497–1499.
Schreiber F, Le Novère N. Exchange Formats for Systems Biology: SBGN. In: Encyclopedia of Systems Biology. 2013
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.
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.
Prevost MS, Moraga-Cid G, Van Renterghem C, Edelstein SJ, Changeux J-P, Corringer P-J. Intermediate closed state for glycine receptor function revealed by cysteine cross-linking. Proc Natl Acad Sci U S A 2013;110(42):17113-8.
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Lucian S, Zhang F, Eric B. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences 2013;9
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 2013;587(17):2832-41.
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 DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Drager A, Le Novère N. Path2Models: Large-scale generation of computational models from biochemical pathway map [Internet]. BMC Systems Biology 2013;7:116.Available from: http://arxiv.org/abs/1307.7005
Waltemath D, Wolkenhauer O, Le Novère N, Dumontier M. Possibilities for Integrating Model-related Data in Computational Biology [Internet]. 9th International workshop Data Integration in the Life Sciences 2013;Available from: http://www.unbsj.ca/sase/csas/data/ws/dils2013/papers/DILS-SYS-EC-paper8.pdf
Dikicioglu D, Pir P, Oliver SG. Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnol J 2013;8(9):1017-34.
Chaouiya C, Berenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, çalves E, Dorier J, Page M, Monteiro PT, 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(1):135.
Waltemath D, Le Novère N. Simulation Experiment Description Markup Language (SED-ML). In: Encyclopedia of computational neuroscience. 2013
Knüpfer C, Beckstein C, Dittrich P, Le Novère N. Structure, function, and behaviour of computational models in systems biology. BMC Syst Biol 2013;7:43.
Keating SM, Le Novère N. Supporting SBML as a model exchange format in software applications. Methods Mol Biol 2013;1021:201-25.
von Eichborn J, Dunkel M, Gohlke B, Preissner S, Hoffmann M, Bauer J, Armstrong JD, Schaefer M, Andrade M, Le Novère M, Croning M, Grant SGN, van Nierop P, Smit AB, Preissner R. SynSysNet: Integration of experimental data on synaptic protein-protein interactions with drug-target relations [Internet]. Nucleic Acids Res. 2013;41(D1):D834-D840.Available from: http://nar.oxfordjournals.org/content/41/D1/D834.full
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, 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;
Juty N, Le Novère N, Hermjakob H, Laibe C. Towards the collaborative curation of the registry underlying Identifiers.org. Databases 2013;
Le Novère N, Endler L. Using chemical kinetics to model biochemical pathways. Methods Mol Biol 2013;1021:147-67.
2012
Li L, Stefan MI, Le Novère N. Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII. PLoS One 2012;7(9):e43810.
Henkel R, Le Novère N, Wolkenhauer O, Waltemath D. Considerations of graph-based concepts to manage of computational biology models and associated simulations. INFORMATIK 2012 2012;
Juty N, Le Novère N, Hermjakob H, Laibe C. Delivering “Cool URIs” that do not change [Internet]. In: SWAT4LS 2012. 2012Available from: http://ceur-ws.org/Vol-952/paper_4.pdf
Keating SM, Le Novère N. Encoding Neuronal Models in SBML. In: Le Novère NComputational Systems Neurobiology. Springer Netherlands; 2012 p. 459–488.
Juty N, Le Novère N, Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res 2012;40(Database issue):D580-6.
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ. The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. J Biol Rhythms 2012;27(4):328-32.
Zhukova A, Adams R, Laibe C, Le Novère N. LibKiSAO: a Java library for Querying KiSAO. BMC Res Notes 2012;5:520.
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.
Mattioni M, Cohen U, Le Novère N. Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Front Neuroinform 2012;6:20.
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):2648-53.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 2012;28(15):2016-21.
Stefan MI, Marshall DP, Le Novère N. Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII. PLoS One 2012;7(1):e29406.
Endler L, Stefan MI, Edelstein SJ, Le Novère N. Using chemical kinetics to model neuronal signalling pathways. In: Le Novère NComputational Systems Neurobiology. Springer Netherlands; 2012 p. 81–117.
Hastings J, Le Novere N, Ceusters W, Mulligan K, Smith B. Wanting what we don’t want to want: Representing addiction in interoperable bio-ontologies [Internet]. In: Proceedings of the 3rd International Conference on Biomedical Ontology. 2012Available from: http://ceur-ws.org/Vol-897/session3-paper12.pdf
2011
Changeux J-P, Edelstein SJ. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 2011;3:19.
Changeux J-P, Edelstein S. Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 2011;3:19.
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 DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N. Controlled vocabularies and semantics in systems biology. Mol Syst Biol 2011;7:543.
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(15):2167-8.
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2011;5(2):230-42.
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol 2011;7(4):e1001122.
Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol 2011;5:198.
Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W. Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol 2011;7:512.
Waltemath D, Swainston N, Lister A, Bergmann F, Henkel R, Hoops S, Hucka M, Juty N, Keating S, Knuepfer C, others. SBML Level 3 Package Proposal: Annot. Nature Precedings 2011;
Waltemath D, Bergmann FT, Adams R, Le Novère N. Simulation Experiment Description Markup Language (SED-ML): Level 1 Version 1. Nat Precedings 2011;
Le Novère N, Demir E, Mi H, Moodie S, Villeger A. Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2). Nat Precedings 2011;
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nat Precedings 2011;
Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H. Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology 2011;7:e1002202.
2010
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010;4:92.
Li C, Courtot M, Le Novère N, Laibe C. BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Brief Bioinform 2010;11(3):270-7.
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, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung K-H, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow 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. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010;28(9):935-42.
Tolle DP, Le Novère N. Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. BMC Syst Biol 2010;4:25.
Edelstein SJ, Stefan MI, Le Novère N. Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction. PLoS One 2010;5(1):e8449.
Kettner C, Field D, Sansone S, Taylor C, Aerts J, Binns N, Blake A, Britten CM, Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop. Standards in Genomic Sciences 2010;3:259-266.
Tolle DP, Le Novère N. Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes. BMC Syst Biol 2010;4:24.
Edelstein SJ, Changeux J-P. Oligomeric membrane receptors: linking structural dynamics and functional kinetics. Biophys J 2010;98:2045-2052.
Henkel R, Endler L, Peters A, Le Novère N, Waltemath D. Ranked retrieval of Computational Biology models. BMC Bioinformatics 2010;11:423.
Le Novère N. Realistic Models of Neurons Require Quantitative Information at the Single-cell Level. In: Dauphinot, PotierUnravelling Single Cell Genomics. Bontoux; 2010 p. 45-53.
Baldi BF, Hoyer C, Le Novère N. Schizophrenic: forever young?. Genome Med 2010;2(5):32.
Hucka M, Le Novère N. Software that goes with the flow in systems biology. BMC Biol 2010;8:140.
Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nat Precedings 2010;
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nat Precedings 2010;
2009
Stefan MI, Edelstein SJ, Le Novère N. Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Syst Biol 2009;3:68.
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. In: 6th International workshop Data Integration in the Life Sciences. Springer; 2009 p. 5–15.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N. Designing and encoding models for synthetic biology. J R Soc Interface 2009;6 Suppl 4:S405-17.
Dräger A, Planatscher H, Wouamba DM, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. Oligomeric membrane receptors: linking structural dynamics and functional kinetics. SBML2LATEX: Conversion of SBML files into human-readable reports 2009;25:1455-1456.
Dräger A, Planatscher H, Wouamba DMotsou, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics 2009;25(11):1455-6.
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 Syst Biol 2009;3(3):131-6.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol 2009;27(8):735-41.
Mi H, Schreiber F, Le Novére N, Moodie S, Sorokin A. Systems biology graphical notation: Activity flow language level 1. Nature Precedings 2009;
Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nat Precedings 2009;
Moodie S, Le Novère N, Demir E, Mi H, Schreiber F. Systems biology graphical notation: process description language level 1. Nature Precedings 2009;
2008
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;
Stefan MI, Edelstein SJ, Le Novère N. An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proc Natl Acad Sci U S A 2008;105(31):10768-73.
Guerlet G, Taly A, Prado de Carvalho L, Martz A, Jiang R, Specht A, Le Novère N, Grutter T. Comparative models of P2X2 receptor support inter-subunit ATP-binding sites. Biochem Biophys Res Commun 2008;375(3):405-9.
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga YK, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008;26(10):1155-60.
Le Novère N, Li L, Girault J-A. DARPP-32: molecular integration of phosphorylation potential. Cell Mol Life Sci 2008;65(14):2125-7.
Shimizu TS, Le Novère N. Looking inside the box: bacterial transistor arrays. Mol Microbiol 2008;69(1):5-9.
Le Novère N. Neurological disease: are systems approaches the way forward?. Pharmacopsychiatry 2008;41 Suppl 1:S28-31.
Taylor CF, Field D, Sansone S-A, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz P-A, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon A-M, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008;26(8):889-96.
Köhn D, Le Novere N. SED-ML–an XML format for the implementation of the MIASE guidelines. In: Heiner M, Uhrmacher AMProceedings of the 6th conference on Computational Methods in Systems Biology. Springer Berlin/Heidelberg; 2008 p. 176–190.
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. 2008;
Hucka M, Hoops S, Keating S, Le Novère N, Sahle S, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nat Precedings 2008;
2007
Le Novère N, Courtot M, Laibe C. Adding semantics in kinetics models of biochemical pathways [Internet]. Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations 2007;:137–153.Available from: http://www.beilstein-institut.de/index.php?id=196

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