Research Topics
Genomes and GenesSpecies | Nicolas Le NovèreSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Detail Information
Publications
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...
MELTING, a flexible platform to predict the melting temperatures of nucleic acidsMarine 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...- Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup LanguageDagmar 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... - 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... - Software that goes with the flow in systems biologyMichael 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... - The Systems Biology Graphical NotationNicolas 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... - 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... 
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....- DARPP-32: molecular integration of phosphorylation potentialN Le Novère
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
Cell Mol Life Sci 65:2125-7. 2008 - BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systemsNicolas 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... - Model storage, exchange and integrationNicolas 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... - BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic modelsChen 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... - BioModels.net Web Services, a free and integrated toolkit for computational modelling softwareChen Li
Computational Neurobiology Group, at the European Bioinformatics Institute, Hinxton, UK
Brief Bioinform 11:270-7. 2010.... - Designing and encoding models for synthetic biologyLukas 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'... - Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKIIMelanie 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... - Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKIILu 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... - Ranked retrieval of Computational Biology modelsRon 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... - Computing phenomenologic Adair-Klotz constants from microscopic MWC parametersMelanie 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... - Software support for SBGN maps: SBGN-ML and LibSBGNMartijn P van Iersel
EMBL European Bioinformatics Institute, Hinxton, UK
Bioinformatics 28:2016-21. 2012..Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. CONTACT: sbgn-libsbgn@lists.sourceforge.net... - Identifiers.org and MIRIAM Registry: community resources to provide persistent identificationNick 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... - Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexesDominic 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... - Ligand depletion in vivo modulates the dynamic range and cooperativity of signal transductionStuart 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... - MIRIAM Resources: tools to generate and resolve robust cross-references in Systems BiologyCamille 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... - 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... - Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTPDominic P Tolle
Computational Neurobiology Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
BMC Syst Biol 4:25. 2010.... - Towards the Collaborative Curation of the Registry underlying identifiers.orgNick 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... - An allosteric model of calmodulin explains differential activation of PP2B and CaMKIIMelanie 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.... - LibKiSAO: a Java library for Querying KiSAOAnna 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... - Qualitative translation of relations from BioPAX to SBML qualFinja 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...