EBI Groups Computational Systems Neurobiology Publications

Publications of the group

Direct access to the publications for a given year: 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010

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: Free (Gratis) Access

2012

Mattioni M., Cohen U., Le Novère N.

A Graphical User Interface with 3D capabilities for NEURON

Frontiers in Neuroinformatics, accepted

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, accepted

Keating S., Le Novère N.

Encoding neuronal models in SBML.

Computational Systems Neurobiology, Le Novère ed, Springer, in the press

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, in the press

Dumousseau M., Rodriguez N., Nick Juty, Le Novère N. (2012)

MELTING, a flexible platform to predict the melting temperatures of nucleic acids.

BMC Bioinformatics, 13:101

[DOI] [BioMedCentral]

Villéger A.C., van Iersel M.P., 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. (2012)

Software support for SBGN maps: SBGN-ML and LibSBGN

Bioinformatics, Online publication

[Bioinformatics]

Stefan M., Marshall D., Le Novère N. (2012)

Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII

PLoS ONE, 7(1): e29406

[DOI] [PLoS]

Juty N., Le Novère N., Laibe C. (2012)

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

Nucleic Acids Research, 40: D580-D586

[citeXplore] [DOI] [NAR]

2011

Waltemath D., Adams R., Bergmann F.T., Hucka M., Kolpakov F., Miller A., Moraru I.I., Nickerson D., Snoep J., Le Novère N. (2011)

Reproducible computational biology experiments with SED-ML -- The Simulation Experiment Description Markup Language

BMC Systems Biology, 5:198

[DOI] [BioMedCentral]

Le Novère N., Hucka M., Anwar N., Bader G., Demir E., Moodie S., Sorokin A. (2011)

Meeting report from the first meetings of the Computational Modelling in Biology Network (COMBINE)

SIGS, 5(2):577

[DOI] [SIGS]

Dall'Olio1 G.M., Marino J., Schubert M., Keys K.L., Stefan M.I, Gillespie C.S., Poulain P., Shameer K., Sugar R., Invergo1 B.M, Jensen L.J, Bertranpetit J., Laayouni H. (2011)

Ten Simple Rules for Getting Help from Online Scientific Communities

PLoS Computational Biology, 7(9): e1002202

[citeXplore] [DOI] [PLoS] [Pubmed Central]

Changeux J.-P., Edelstein S.J. (2011)

Conformational selection or induced fit? 50 years of debate resolved.

F1000 Biol Rep., 3:19

[citeXplore] [DOI] [Pubmed Central]

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. (2011)

Controlled vocabularies and semantics in systems biology.

Molecular Systems Biology, 7:543

[citeXplore] [DOI] [MSB]

Schulz M., Krause F., Le Novère N., Klipp E., Liebermeister W. R (2011)

Retrieval, alignment, and clustering of computational models based on semantic annotations.

Molecular Systems Biology, 7: 512

[citeXplore] [DOI] [MSB] [Pubmed Central]

Dräger A., Rodriguez N., Dumousseau M., Dörr A., Wrzodek C., Le Novère N., Zell A., Hucka M. (2011)

JSBML: a flexible Java library for working with SBML.

Bioinformatics, 27: 2167-2168

[citeXplore] [DOI] [Bioinformatics] [Pubmed Central]

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., Schmidt H., Snoep J.L., Tolle D., Wolkenhauer O., Le Novère N. (2011)

Minimum Information About a Simulation Experiment (MIASE)

PLoS Computational Biology, 7(4): e1001122

[citeXplore] [DOI] [PLoS] [PubMed Central]

2010

Kettner C, Field D, Sansone S, Taylor C, Aerts J, Binns N, Blake A, Britten CM, Marco A, Fostel1 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 (2010)

Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop

Standards in Genomic Sciences, 3: 259-266

[citeXplore] [DOI] [SIGS] [PubMed Central]

Hucka M., Le Novère N. (2010)

Software that goes with the flow in systems biology

BMC Biology, 8: 140

[citeXplore] [DOI] [BioMedCentral] [PubMed Central]

Le Novère N., Moodie S., Sorokin A., Schreiber F., Mi H. (2010)

Systems Biology Graphical Notation: Entity Relationship language Level 1

Nature Precedings (this is Level 1 Version 1.1)

[PDF] [DOI]

Moodie S., Le Novère N., Demir E., Mi H., Schreiber F. (2010)

Systems Biology Graphical Notation: Process Description language Level 1

Nature Precedings (this is Level 1 Version 1.2)

[PDF] [DOI]

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, Reubenacker O, Samwald M, van Iersel M, WimalaratneS, 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 (2010)

BioPAX – A Community Standard for Pathway Data Sharing

Nature Biotechnology, 28: 935-942

[citeXplore] [DOI] [NPG] [PubMed Central]

Le Novère N. (2010)

Realistic models of neuron require quantitative information at the single-cell level

in Unravelling Single Cell Genomics, Bontoux et al eds, pp 45-53

Henkel R., Endler L., Le Novère N., Peters A., Waltemath D. (2010)

Ranked Retrieval of Computational Biology Models

BMC Bioinformatics, 11:423

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

Edelstein S.J., Changeux J.-P. (2010)

Oligomeric membrane receptors: linking structural dynamics and functional kinetics

Biophys J, 98: 2045-2052

[citeXplore] [DOI] [Biophys J] [Pubmed Central]

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. (2010)

BioModels Database, enhanced curated and annotated resource of published quantitative kinetic models.

BMC Systems Biology, 4:92

[DOI] [citeXplore] [BioMedCentral] [Pubmed Central]

Li C., Courtot M., Le Novère N., Laibe C. (2010)

BioModels.net Web Services, a free and integrated toolkit for computational modelling software

Briefings in Bioinformatics, 11: 270-277

[citeXplore] [DOI] [Pubmed Central]

Baldi B., Hoyer C., Le Novère N. (2010)

Schizophrenic: Forever young?

Genome Medecine, 2: 32

[citeXplore] [DOI] [Genome Medicine] [Pubmed Central]

Tolle D., Le Novère N. (2010)

Brownian Diffusion of AMPA Receptors Is Sufficient to Explain Fast Onset of LTP

BMC Systems Biology, 4: 25

[DOI] [citeXplore] [BioMedCentral] [Pubmed Central]

Tolle D., Le Novère N. (2010)

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

BMC Systems Biology, 4: 24

[DOI] [citeXplore] [BioMedCentral] [Pubmed Central]

Edelstein S.J., Stefan M.I., Le Novère N (2010).

Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction

PLoS ONE, 5(1): e8449

[citeXplore] [DOI] [PLoS] [Pubmed Central]

2009

Mi H., Schreiber F., Le Novère N., Moodies S., Sorokin A. (2009)

Systems Biology Graphical Notation: Activity Flow language Level 1

Nature Precedings (this is Level 1 Version 1)

[PDF] [DOI]

Le Novère N., Moodie S., Sorokin A., Schreiber F., Mi H. (2009)

Systems Biology Graphical Notation: Entity Relationship language Level 1

Nature Precedings (this is Level 1 Version 1)

[PDF] [DOI]

Moodie S., Le Novère N., Sorokin A., Mi H., Schreiber F. (2009)

Systems Biology Graphical Notation: Process Description language Level 1

Nature Precedings (this is Level 1 Version 1.1)

[PDF] [DOI]

Le Novère N., Hucka M., Mi H., Moodie S., Schreiber F., Sorokin A., Demir E., Wegner K., Aladjem M.I., Wimalaratne S.M., Bergman F.T., Gauges R., Ghazal P., Kawaji H., Li L., Matsuoka Y., 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., Wu G., Goryanin I., Kell D.B., Sander C., Sauro H., Snoep J.L., Kohn K., Kitano H. (2009)

The Systems Biology Graphical Notation

Nature Biotechnology, 27: 735-741

[citeXplore] [DOI] [NPG]

Chelliah V., Endler L., Juty N., Laibe C.,Li C., Rodriguez N., Le Novère N. (2009)

Data Integration and Semantic Enrichment of Systems Biology Models and Simulations

6th international workshop Data Integration in the Life Sciences, Lecture Notes in Bioinformatics, 5647: 5-15

Stefan M.I., Edelstein S.J., Le Novère N. (2009)

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

BMC Systems Biology, 3: 68

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

O. Wolkenhauer, D. Fell, P. De Meyts, N. Blüthgen, H. Herzel, N. Le Novère, T. Höfer, K. Schürrle, I. van Leeuwen (2009)

SysBioMed report: Advancing systems biology for medical applications.

IET Systems Biology, 3: 131-136

[citeXplore] [DOI]

Dräger A., Planatscher H, Wouamba DM, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. (2009)

SBML2LATEX: Conversion of SBML files into human-readable reports.

Bioinformatics, 25: 1455-1456

[citeXplore] [DOI] [Bioinformatics] [Pubmed Central]

Endler L., Rodriguez N., Juty N., Chelliah V., Laibe C., Li C., Le Novère N. (2009)

Designing and encoding models for Synthetic Biology

Journal of the Royal Society Interface, 6: S405-S417

[citeXplore] [DOI] [RSP] [Pubmed Central]

2008

O. Wolkenhauer, D. Fell, P. De Meyts, N. Blüthgen, H. Herzel, N. Le Novère, T. Höfer, I. van Leeuwen (2008)

Advancing systems biology for medical applications

ESF Science Policy Briefing, 35

[PDF]

Hucka M., Hoops S., Keating S., & Le Novère N., Sahle S., Wilkinson D.J. (2008)

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Nature Precedings (this is Level 2 Version 4)

[DOI] [SBML website]

Herrgård M.J., Swainston N., Dobson P., Dunn W.B., Arga K.V., 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., Spasic 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. (2008)

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Nature Biotechnology, 26: 1155-1160

[citeXplore] [DOI]

Dagmar Köhn, Le Novère N. (2008)

SED-ML - An XML Format for the Implementation of the MIASE Guidelines

6th conference on Computational Methods in Systems Biology, Heiner M and Uhrmacher AM eds, Lecture Notes in Bioinformatics, 5307: 176-190

Le Novère N. (2008)

Neurologic diseases: are systems approaches the way forward?

Pharmacopsychiatry, 41: S28-S31

[citeXplore] [DOI]

Le Novère N., Moodie S., Sorokin A., Hucka M., Schreiber F., Demir E., Mi H., Matsuoka Y, Wegner K., Kitano H. (2008)

Systems Biology Graphical Notation: Process Diagram Level 1

Nature Precedings (this is Level 1 Version 1)

[PDF] [DOI]

Guerlet G., Taly A., Prado de Carvahlo L., Marz A., Jiang R., Specht A., Le Novère N., Grutter T. (2008)

Comparative models of P2X2 receptor support inter-subunit ATP-binding sites

Biochemical and Biophysical Research Communications, 375(3): 405-409

[citeXplore] [DOI]

Taylor C.F., Field D., Sansone S.-A., Aerts J., Apweiler R., Ashburner M., Ball C.A., Binz P.-A., Bogue M., Booth T., Brazma A., Brinkman R.R., 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., Mallon A.-M., Marthandan N., Masuya H., McNally R., Mehrle A., Morrison N., Orchard S., Quackenbush J., Reecy J.M., Robertson D.G., Rocca-Serra P., Rodriguez H., Rosenfeld H., Santoyo-Lopez J., Scheuermann R.H., Schober D., Smith B., Snape J., Sterk P., Tipton K., Untergasser A., Vandesompele J., Wiemann S. (2008)

Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project.

Nature Biotechnology, 26: 889-896

[citeXplore] [DOI] [NPG] [Pubmed Central]

Stefan M.I., Edelstein S.J., Le Novère N. (2008)

An allosteric model of calmodulin explains differential activation of PP2B and CaMKII

Proceedings of the National Academy of Sciences USA, 105:10768-10773

[citeXplore] [DOI] [PNAS] [Pubmed Central]

Le Novère N., Li L., Girault J.-A. (2008)

DARPP-32: Molecular integration of phosphorylation potential

Cellular and Molecular Life Sciences, 65: 2125-2127

[citeXplore] [DOI]

Schimizu T.S.S., Le Novère N. (2008)

Looking inside the box: bacterial transistor arrays.

Molecular Microbiology, 69: 5-9

[citeXplore] [DOI] [Wiley]

2007

Laibe C., Le Novère N. (2007)

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

BMC Systems Biology, 1: 58

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

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. (2007)

SBML Models and MathSBML

Introduction to Systems Biology, Humana Press, USA, ISBN-10: 1588297063, ISBN-13: 978-1588297068

Le Novère N, Courtot M, Laibe C (2007)

Adding semantics in kinetics models of biochemical pathways.

Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations, available at http://www.beilstein-institut.de/index.php?id=196

[PDF]

Hucka M, Finney A, Hoops S, Keating S, & Le Novère N (2007)

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Nature Precedings (this is Level 2 Version 3)

[DOI] [SBML website]

Le Novère N. (2007)

The long journey to a Systems Biology of neuronal function

BMC Systems Biology, 1: 28

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

Rodriguez N, Donizelli M, Le Novère N (2007)

SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML).

BMC Bioinformatics, 8:79

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

2006

Fernandez E, Schiappa R, Girault JA, Le Novère N (2006)

DARPP-32 is a robust integrator of dopamine and glutamate signals.

PLoS Computational Biology, 2(12): e176.

[citeXplore] [DOI] [PLoS] [Pubmed Central]

Hucka M, Finney A & Le Novère N (2006)

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

(This is Level 2 Version 2)

[PDF]

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. (2006)

Novel pharmacological targets for the treatment of Parkinson's disease

Nature Reviews Drug Discovery, 5: 845-854.

[citeXplore] [DOI]

Le Novère N. (2006)

Model storage, exchange and integration

BMC Neuroscience, 7(Suppl 1):S11.

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

Tolle D., Le Novère N. (2006)

Particle-based Stochastic Simulation in Systems Biology

Current Bioinformatics, 1: 315-320.

[DOI] [PDF]

Schilstra M.J., Li L., Matthews J., Finney A., Hucka M., Le Novère N. (2006)

CellML2SBML: Conversion of CellML into SBML

Bioinformatics, 18: 1018-1020.

[citeXplore] [DOI] [Bioinformatics]

Donizelli M., Djite M.A., Le Novère N. (2006)

LGICdb. A manually curated sequence database after the genomes

Nucleic Acids Res., 34: D267-D269.

[citeXplore] [DOI] [NAR] [Pubmed Central]

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. (2006)

BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems

Nucleic Acids Res., 34: D689-D691.

[citeXplore] [DOI] [NAR] [Pubmed Central]

2005

Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado-Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005)

Minimum Information Requested In the Annotation of biochemical Models (MIRIAM)

Nature Biotechnology, 23: 1509-1515.

[citeXplore] [DOI] [NPG]

Le Novère N., Tolle D. (2005)

Particle-based stochastic simulations

Proceedings of the 4^th Workshop on Computation of Biochemical Pathways and Genetic Networks, Logos, Berlin, pp. 41-45.

[PDF]

Le Novère N. (2005)

BioModels.net, tools and resources to support Computational Systems Biology

Proceedings of the 4^th Workshop on Computation of Biochemical Pathways and Genetic Networks, Logos, Berlin, pp. 69-74.

[PDF]

Taly A., Delarue M., Grutter T., Nilges M., Le Novère N., Corringer P.-J., Changeux J.-P. (2005)

Normal mode analysis suggest a quaternary twist model for the nicotinic receptor gating mechanism

Biophysical Journal, 88: 3954-3965.

[citeXplore] [DOI] [Pubmed Central]

2004

Le Novère N., Donizelli M. (2004)

The Molecular Pages of the Mesotelencephalic Dopamine Consortium (DopaNet)

BMC bioinformatics, 5:174.

[citeXplore] [DOI] [BioMedCentral] [Pubmed Central]

Sallette J., Bohler S., Benoit P., Soudant M., Pons S., Le Novère N., Changeux J.-P., Corringer P.-J. (2004)

An extracellular microdomain controls up-regulation of neuronal nicotinic acetylcholine receptors by nicotine

J. Biol. Chem., 279: 18767-18775.

[citeXplore] [DOI] [JBC]

Complete list of publications from N. Le Novère.