Nicolas Gambardella

According to our database1, Nicolas Gambardella authored at least 74 papers between 1999 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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In proceedings 
Article 
PhD thesis 
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Homepages:

On csauthors.net:

Bibliography

2020
Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies.
PLoS Computational Biology, 2020

2019
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.
J. Integr. Bioinform., 2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.
J. Integr. Bioinform., 2019

Community-driven roadmap for integrated disease maps.
Briefings Bioinform., 2019

2018
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.
PLoS Computational Biology, 2018

BioModels: expanding horizons to include more modelling approaches and formats.
Nucleic Acids Res., 2018

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
J. Integr. Bioinform., 2018

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.
J. Integr. Bioinform., 2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
J. Integr. Bioinform., 2018

2017
SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks.
BMC Syst. Biol., 2017

A brief history of COMBINE.
Proceedings of the 2017 Winter Simulation Conference, 2017

2016
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.
J. Integr. Bioinform., 2016

The systems biology format converter.
BMC Bioinform., 2016

2015
Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions.
PLoS Computational Biology, 2015

BioModels: ten-year anniversary.
Nucleic Acids Res., 2015

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.
J. Integr. Bioinform., 2015

Specifications of Standards in Systems and Synthetic Biology.
J. Integr. Bioinform., 2015

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.
J. Integr. Bioinform., 2015

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 .
J. Integr. Bioinform., 2015

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
J. Integr. Bioinform., 2015

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.
J. Integr. Bioinform., 2015

COMBINE Archive Specification Version 1.
J. Integr. Bioinform., 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
J. Integr. Bioinform., 2015

SPARQL-enabled identifier conversion with Identifiers.org.
Bioinform., 2015

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Bioinform., 2015

2014
Simulation Experiment Description Markup Language (SED-ML).
Proceedings of the Encyclopedia of Computational Neuroscience, 2014

BioModels Database: a public repository for sharing models of biological processes.
Proceedings of the Encyclopedia of Computational Neuroscience, 2014

COMBINE archive: One File To Share Them All.
CoRR, 2014

BioModels linked dataset.
BMC Syst. Biol., 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
BMC Bioinform., 2014

The EBI RDF platform: linked open data for the life sciences.
Bioinform., 2014

2013
Cooperative Binding.
PLoS Computational Biology, 2013

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations.
Nucleic Acids Res., 2013

Structure, function, and behaviour of computational models in systems biology.
BMC Syst. Biol., 2013

The systems biology simulation core algorithm.
BMC Syst. Biol., 2013

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 2013

Towards the Collaborative Curation of the Registry underlying identifiers.org.
Database, 2013

2012
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.
Nucleic Acids Res., 2012

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.
Frontiers Neuroinformatics, 2012

MELTING, a flexible platform to predict the melting temperatures of nucleic acids.
BMC Bioinform., 2012

Software support for SBGN maps: SBGN-ML and LibSBGN.
Bioinform., 2012

Qualitative translation of relations from BioPAX to SBML qual.
Bioinform., 2012

Delivering 'Cool URIs' That Do Not Change.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Wanting what we don't want to want: Representing addiction in interoperable bio-ontologies.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Considerations of graph-based concepts to manage of computational biology models and associated simulations.
Proceedings of the 57. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie, 42. Jahrestagung der Gesellschaft für Informatik, Was bewegt uns in der/die Zukunft?, 2012

2011
Minimum Information About a Simulation Experiment (MIASE).
PLoS Computational Biology, 2011

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.
BMC Syst. Biol., 2011

JSBML: a flexible Java library for working with SBML.
Bioinform., 2011

2010
Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP.
BMC Syst. Biol., 2010

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes.
BMC Syst. Biol., 2010

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
BMC Syst. Biol., 2010

Ranked retrieval of Computational Biology models.
BMC Bioinform., 2010

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
Briefings Bioinform., 2010

2009
Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters.
BMC Syst. Biol., 2009

Data Integration and Semantic Enrichment of Systems Biology Models and Simulations.
Proceedings of the Data Integration in the Life Sciences, 6th International Workshop, 2009

2008
Multiscale Modelling of Neuronal Signalling.
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

SED-ML - An XML Format for the Implementation of the MIASE Guidelines.
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

2007
Molecules for memory: modelling CaMKII.
BMC Syst. Biol., 2007

The long journey to a Systems Biology of neuronal function.
BMC Syst. Biol., 2007

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.
BMC Syst. Biol., 2007

SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML).
BMC Bioinform., 2007

2006
DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals.
PLoS Computational Biology, 2006

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Nucleic Acids Res., 2006

LGICdb: a manually curated sequence database after the genomes.
Nucleic Acids Res., 2006

CellML2SBML: conversion of CellML into SBML.
Bioinform., 2006

2004
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet).
BMC Bioinform., 2004

2003
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinform., 2003

2001
LGICdb: the ligand-gated ion channel database.
Nucleic Acids Res., 2001

STOCHSIM: modelling of stochastic biomolecular processes.
Bioinform., 2001

MELTING, computing the melting temperature of nucleic acid duplex.
Bioinform., 2001

1999
The Ligand Gated Ion Channel Database.
Nucleic Acids Res., 1999


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