Nicolas Le Novère

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)
    Nicolas Le Novère
    Computational Neurobiology, EMBL EBI, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK
    BMC Bioinformatics 5:174. 2004
  2. pmc LGICdb: a manually curated sequence database after the genomes
    Marco Donizelli
    European Bioinformatics Institute, EMBL Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 34:D267-9. 2006
  3. pmc Controlled vocabularies and semantics in systems biology
    Melanie Courtot
    Terry Fox Laboratory, Vancouver, Canada
    Mol Syst Biol 7:543. 2011
  4. pmc The long journey to a Systems Biology of neuronal function
    Nicolas Le Novère
    BMC Syst Biol 1:28. 2007
  5. pmc Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
    Dagmar Waltemath
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, D 18051 Rostock, Germany
    BMC Syst Biol 5:198. 2011
  6. pmc Schizophrenic: forever young?
    Benedetta Frida Baldi
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Genome Med 2:32. 2010
  7. pmc Software that goes with the flow in systems biology
    Michael Hucka
    Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Biol 8:140. 2010
  8. ncbi request reprint The Systems Biology Graphical Notation
    Nicolas Le Novère
    EMBL European Bioinformatics Institute, Hinxton, UK
    Nat Biotechnol 27:735-41. 2009
  9. ncbi request reprint Neurological disease: are systems approaches the way forward?
    N Le Novère
    Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Pharmacopsychiatry 41:S28-31. 2008
  10. ncbi request reprint Minimum information requested in the annotation of biochemical models (MIRIAM)
    Nicolas Le Novère
    European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Nat Biotechnol 23:1509-15. 2005

Detail Information

Publications43

  1. pmc The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)
    Nicolas Le Novère
    Computational Neurobiology, EMBL EBI, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD UK
    BMC Bioinformatics 5:174. 2004
    ..The project should lead to large-scale models of molecular and cellular processes involved in neuronal signaling. A prerequisite is the proper storage of knowledge coming from the literature...
  2. pmc LGICdb: a manually curated sequence database after the genomes
    Marco Donizelli
    European Bioinformatics Institute, EMBL Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 34:D267-9. 2006
    ..ebi.ac.uk/compneur-srv/LGICdb/). Despite the vast improvement of general sequence resources, the LGICdb still provide sequences unavailable elsewhere...
  3. pmc Controlled vocabularies and semantics in systems biology
    Melanie Courtot
    Terry Fox Laboratory, Vancouver, Canada
    Mol Syst Biol 7:543. 2011
    ..It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments...
  4. pmc The long journey to a Systems Biology of neuronal function
    Nicolas Le Novère
    BMC Syst Biol 1:28. 2007
    ..A systems biology of brain functions and disorders can now be envisioned. As it did for the last half century, neuroscience can drive forward the field of systems biology...
  5. pmc Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
    Dagmar Waltemath
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, D 18051 Rostock, Germany
    BMC Syst Biol 5:198. 2011
    ..The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools...
  6. pmc Schizophrenic: forever young?
    Benedetta Frida Baldi
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Genome Med 2:32. 2010
    ..Combining the conclusion of that study with the prevalent hypotheses of schizophrenia, we suggest that the schizophrenic brain might resemble a juvenile brain...
  7. pmc Software that goes with the flow in systems biology
    Michael Hucka
    Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Biol 8:140. 2010
    ..Their work is a harbinger of the next generation of more powerful software for systems biologists...
  8. ncbi request reprint The Systems Biology Graphical Notation
    Nicolas Le Novère
    EMBL European Bioinformatics Institute, Hinxton, UK
    Nat Biotechnol 27:735-41. 2009
    ..We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling...
  9. ncbi request reprint Neurological disease: are systems approaches the way forward?
    N Le Novère
    Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Pharmacopsychiatry 41:S28-31. 2008
    ..Comprehension of the pathology of those diseases is therefore very likely to benefit from Systems approaches. This is also true of their symptomatology, affecting neurological systems at molecular, cellular, and microcircuit levels...
  10. ncbi request reprint Minimum information requested in the annotation of biochemical models (MIRIAM)
    Nicolas Le Novère
    European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Nat Biotechnol 23:1509-15. 2005
    ....
  11. doi request reprint DARPP-32: molecular integration of phosphorylation potential
    N Le Novère
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
    Cell Mol Life Sci 65:2125-7. 2008
  12. pmc BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    Nicolas Le Novère
    European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 34:D689-91. 2006
    ..This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource...
  13. pmc Model storage, exchange and integration
    Nicolas Le Novère
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    BMC Neurosci 7:S11. 2006
    ..We expect that those resources, together with the use of formal languages such as SBML, will support the fruitful exchange and reuse of quantitative models...
  14. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
    ..In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification...
  15. pmc Designing and encoding models for synthetic biology
    Lukas Endler
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    J R Soc Interface 6:S405-17. 2009
    ..Evaluation of simulation results and validation of the model close the systems biology 'loop'...
  16. pmc BioModels.net Web Services, a free and integrated toolkit for computational modelling software
    Chen Li
    Computational Neurobiology Group, at the European Bioinformatics Institute, Hinxton, UK
    Brief Bioinform 11:270-7. 2010
    ....
  17. pmc Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII
    Melanie I Stefan
    EMBL European Bioinformatics Institute, Hinxton, UK
    PLoS ONE 7:e29406. 2012
    ..One of the predictions of our study is that calmodulin binding in itself is not sufficient for CaMKII activation, although high-affinity binding of calmodulin is...
  18. pmc Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum
    Michele Mattioni
    European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
    PLoS ONE 8:e66811. 2013
    ....
  19. doi request reprint Using chemical kinetics to model biochemical pathways
    Nicolas Le Novère
    Babraham Institute, Cambridge, Cambridgeshire, UK
    Methods Mol Biol 1021:147-67. 2013
    ..Finally we present a method to apply this type of approach to model any regulatory network...
  20. pmc Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII
    Lu Li
    EMBL European Bioinformatics Institute, Hinxton, United Kingdom
    PLoS ONE 7:e43810. 2012
    ..Finally, the extent of activation of CaMKII signals with high calcium frequency is further controlled by other factors, including the availability of calmodulin, and by the potency of phosphatase inhibitors...
  21. doi request reprint BioModels Database: a repository of mathematical models of biological processes
    Vijayalakshmi Chelliah
    EMBL Outstation European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 1021:189-99. 2013
    ..BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months...
  22. pmc Ranked retrieval of Computational Biology models
    Ron Henkel
    Database and Information Systems, University of Rostock, Rostock, Germany
    BMC Bioinformatics 11:423. 2010
    ..Secondly, it is hard to grasp the nature of an unknown model listed in a search result set, and to judge how well it fits for the particular problem one has in mind...
  23. pmc Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters
    Melanie I Stefan
    Computational Neurobiology Group, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    BMC Syst Biol 3:68. 2009
    ..Instead, experimentalists widely use the Adair-Klotz approach in order to describe their experimental data...
  24. pmc Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transduction
    Stuart J Edelstein
    European Bioinformatics Institute, Hinxton, United Kingdom
    PLoS ONE 5:e8449. 2010
    ..Therefore, we propose a new index of cooperativity based on the comparison of the properties of oligomers and their equivalent monomers...
  25. pmc LibKiSAO: a Java library for Querying KiSAO
    Anna Zhukova
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
    BMC Res Notes 5:520. 2012
    ..To retrieve this information programmatically an application programming interface (API) for KiSAO is needed...
  26. ncbi request reprint Controlled annotations for systems biology
    Nick Juty
    The EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
    Methods Mol Biol 1021:227-45. 2013
    ..Throughout, the reader is provided with explicit examples of use and directed to supplementary information where necessary...
  27. doi request reprint Supporting SBML as a model exchange format in software applications
    Sarah M Keating
    EMBL Outstation European Bioinformatics Institute, Cambridge, UK
    Methods Mol Biol 1021:201-25. 2013
    ..Finally the chapter also provides a description of the SBML Toolbox which provides a means of facilitating the import and export of SBML from both MATLAB and Octave ( http://www.gnu.org/software/octave/) environments...
  28. pmc DARPP-32 is a robust integrator of dopamine and glutamate signals
    Eric Fernandez
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS Comput Biol 2:e176. 2006
    ..Progressive inclusion of additional components should lead to a realistic model of signalling networks underlying the function of striatal neurons...
  29. pmc Towards the collaborative curation of the registry underlying Identifiers.org
    Nick Juty
    Proteomics Services, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Database (Oxford) 2013:bat017. 2013
    ..We briefly describe the Registry, the current curation duties entailed, and our plans to extend and distribute this workload through collaborative and community efforts...
  30. pmc Software support for SBGN maps: SBGN-ML and LibSBGN
    Martijn P van Iersel
    EMBL European Bioinformatics Institute, Hinxton, UK
    Bioinformatics 28:2016-21. 2012
    ..With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner...
  31. pmc Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
    Nick Juty
    European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D580-6. 2012
    ..The flexibility of the identification scheme and resolving system allows its use in many different fields, where unambiguous and perennial identification of data entities are necessary...
  32. pmc Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes
    Dominic P Tolle
    Computational Neurobiology Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Syst Biol 4:24. 2010
    ..Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes...
  33. pmc SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML)
    Nicolas Rodriguez
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Bioinformatics 8:79. 2007
    ..Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file...
  34. pmc MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
    Camille Laibe
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Syst Biol 1:58. 2007
    ..In order to enable interoperability of this annotation, the community has to agree on a set of standard URIs, corresponding to recognised data types. MIRIAM Resources are being developed to support the use of those URIs...
  35. pmc MELTING, a flexible platform to predict the melting temperatures of nucleic acids
    Marine Dumousseau
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, UK
    BMC Bioinformatics 13:101. 2012
    ..The program can use either an approximative approach or a more accurate Nearest-Neighbor approach...
  36. pmc Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP
    Dominic P Tolle
    Computational Neurobiology Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Syst Biol 4:25. 2010
    ....
  37. pmc The EBI RDF platform: linked open data for the life sciences
    Simon Jupp
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland
    Bioinformatics 30:1338-9. 2014
    ..The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI...
  38. pmc An allosteric model of calmodulin explains differential activation of PP2B and CaMKII
    Melanie I Stefan
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom
    Proc Natl Acad Sci U S A 105:10768-73. 2008
    ....
  39. doi request reprint Path2Models: large-scale generation of computational models from biochemical pathway maps
    Finja Büchel
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Syst Biol 7:116. 2013
    ..However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data...
  40. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008
  41. pmc Qualitative translation of relations from BioPAX to SBML qual
    Finja Büchel
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 28:2648-53. 2012
    ..Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations...