List of works - Nicolas Le Novère

1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes

A brief history of COMBINE

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

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

scientific article

A single (−)-nicotine injection causes change with a time delay in the affinity of striatal D2 receptors for antagonist, but not for agonist, nor in the D2 receptor mRNA levels in the rat substantia nigra

scientific article published on 01 May 1995

ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling

scientific article published on 22 April 2020

Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain

scientific journal article

Acute and long-term changes in the mesolimbic dopamine pathway after systemic or local single nicotine injections

scientific article

An H-bond between two residues from different loops of the acetylcholine binding site contributes to the activation mechanism of nicotinic receptors ⬇️

scientific article published on May 1, 2003

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

scholarly article

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

scientific journal article

BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium

scientific article published on 13 December 2019

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

scientific article

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

scientific article

BioModels Database: a repository of mathematical models of biological processes

scientific article published on January 2013

BioModels Database: curation and annotation

BioModels linked dataset

scientific article

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

scientific article

BioModels: expanding horizons to include more modelling approaches and formats

scientific article published on 2 November 2017

BioModels: ten-year anniversary

scientific article

Brain nicotinic receptors: structure and regulation, role in learning and reinforcement

scholarly article by Jean-Pierre Changeux et al published May 1998 in Brain Research Reviews

Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP.

scientific article

COMBINE Archive Specification Version 1.

scientific article published on 4 September 2015

COMBINE and MIRIAM Registry

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

scientific article

COMBINE – What it is, what it could be

COMBINE – a vision

Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII

scientific article published in 2012

CellML2SBML: conversion of CellML into SBML.

scientific article published on 10 February 2006

Community-driven roadmap for integrated disease maps

scientific article published on 23 April 2018

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

scientific article published on 19 August 2008

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

scientific article

Conformational spread in a ring of proteins: a stochastic approach to allostery

scientific article

Control of neurulation by the nucleosome assembly protein-1-like 2.

scientific article published in August 2000

Controlled annotations for systems biology

scientific article published on January 2013

Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)

Cooperative binding

scientific article published in 2013

Cooperativity of Allosteric Receptors ⬇️

scientific article published on March 21, 2013

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Curation and annotation for BioModels Database, a resource of published quantitative kinetic models

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

scientific article

DARPP-32: molecular integration of phosphorylation potential.

scientific article published on July 2008

Delivering 'Cool URIs' That Do Not Change ⬇️

Designing and encoding models for synthetic biology

scientific article published on April 2009

Diversity and distribution of nicotinic acetylcholine receptors in the locus ceruleus neurons.

scientific article published on October 1999

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy

Enabling surface dependent diffusion in spatial simulations using Smoldyn

scientific article published on 8 December 2015

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

Experimentally based model of a complex between a snake toxin and the alpha 7 nicotinic receptor

scientific article

Finding our way through phenotypes

scientific article

Harmonizing semantic annotations for computational models in biology

Host lipidome analysis during rhinovirus replication in HBECs identifies potential therapeutic targets

scientific article published in 2018

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

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

scientific article

Identifiers.org/MIRIAM Registry annotation and cross-referencing framework

Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum

scientific article (publication date: 2013)

Involvement of alpha6 nicotinic receptor subunit in nicotine-elicited locomotion, demonstrated by in vivo antisense oligonucleotide infusion

scientific article

JSBML: a flexible Java library for working with SBML.

scientific article

JSBML: a flexible and entirely Java-based library for working with SBML

Kinetic Simulation Algorithm Ontology

scholarly article

LGICdb: a manually curated sequence database after the genomes

scientific article

LGICdb: the ligand-gated ion channel database

scientific article

LibKiSAO: a Java library for Querying KiSAO.

scientific article

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

scientific article

Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model ⬇️

scientific article published on 28 January 2015

Localization of [3H]nicotine, [3H]cytisine, [3H]epibatidine, and [125I]alpha-bungarotoxin binding sites in the brain of Macaca mulatta

scientific article published in June 2003

Localization of nAChR subunit mRNAs in the brain of Macaca mulatta

scientific article

Looking inside the box: bacterial transistor arrays

scientific article published on 12 May 2008

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

scientific article

MELTING, computing the melting temperature of nucleic acid duplex

scientific article published in December 2001

MIRIAM Resources: a robust annotation and cross referencing framework

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

scientific article

Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine

scientific article published on January 2016

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

scientific article published on November 2011

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

article by Dagmar Waltemath et al published 15 March 2014 in Standards in genomic sciences

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

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

scientific article

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Minimum information requested in the annotation of biochemical models (MIRIAM)

scientific article

Model storage, exchange and integration

scientific article

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism ⬇️

article

Models of the extracellular domain of the nicotinic receptors and of agonist- and Ca2+-binding sites

scientific article

Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions ⬇️

scientific article

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging

scientific article published on 06 February 2019

Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies

scientific article published on 12 February 2020

Neurological disease: are systems approaches the way forward?

scientific article published on September 2008

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON ⬇️

scientific article published on June 6, 2012

New Otx2 mRNA isoforms expressed in the mouse brain

scientific article published on February 2003

Nicotinic receptors at the amino acid level

scientific article

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

scientific article

Novel pharmacological targets for the treatment of Parkinson's disease

scientific article published on October 2006

PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K.

scientific article published on 17 October 2017

Particle-Based Stochastic Simulation in Systems Biology

Path2Models: large-scale generation of computational models from biochemical pathway maps

scientific article

Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop.

scientific article published on 12 October 2015

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

scientific article (publication date: 2015)

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Qualitative translation of relations from BioPAX to SBML qual

scientific article (publication date: 15 October 2012)

Quantitative and logic modelling of molecular and gene networks

scientific article

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

scientific article published on 15 February 2018

Ranked retrieval of Computational Biology models

scientific article

Rational understanding of nicotinic receptors drug binding

scientific article published on January 2004

Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition

scientific article

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

scientific article

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

scientific article published on 19 July 2011

SBML Level 3 Package Proposal: Annotation

SBML Level 3 package: Qualitative Models, Version 1, Release 1.

scientific article published in June 2015

SBML Models and MathSBML

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

scientific article

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

scientific article

SBOL Visual: A Graphical Language for Genetic Designs

scientific article published on 3 December 2015

SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks

scientific article

SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks

article published in 2017

SPARQL-enabled identifier conversion with Identifiers.org

scientific article

STOCHSIM: modelling of stochastic biomolecular processes

scientific article published in June 2001

Schizophrenic: forever young?

scientific article published on 18 May 2010

Significance of stroma in biology of oral squamous cell carcinoma.

scientific article published on 8 September 2017

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

scientific article published on 04 September 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

scientific article published in June 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). ⬇️

scientific article published on 19 March 2018

Software support for SBGN maps: SBGN-ML and LibSBGN.

scientific article

Software that goes with the flow in systems biology

scientific article

Some thoughts about the future of SBML

Specifications of Standards in Systems and Synthetic Biology

scientific article published on 04 September 2015

Specifications of Standards in Systems and Synthetic Biology

scientific article published in June 2015

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

scientific article published on 18 December 2016

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

scientific article published in September 2016

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

scientific article

Structure, function, and behaviour of computational models in systems biology

scientific article

Subunit composition of functional nicotinic receptors in dopaminergic neurons investigated with knock-out mice

scientific journal article

Supporting SBML as a model exchange format in software applications

scientific article

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations

scientific article

SysBioMed report: advancing systems biology for medical applications.

scientific article published on May 2009

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

scientific article published on 04 September 2015

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

scientific article

Systems Biology Graphical Notation: Entity Relationship language Level 1

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

scientific article published on 04 September 2015

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

scientific article

Systems Biology Graphical Notation: Process Description language Level 1

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

scientific article published on 04 September 2015

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

scientific article

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

scientific article

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

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

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

scientific article published on 2 June 2018

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The EBI RDF platform: linked open data for the life sciences

scientific article

The Ligand Gated Ion Channel Database

scientific article published on January 1999

The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)

scientific article

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

scientific article published on 04 September 2015

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

scientific article published on 20 June 2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

scientific article published on 9 March 2018

The diversity of subunit composition in nAChRs: evolutionary origins, physiologic and pharmacologic consequences

scientific article

The evolution of standards and data management practices in systems biology

scientific article

The health care and life sciences community profile for dataset descriptions

scientific article (publication date: 2016)

The health care and life sciences community profile for dataset descriptions

article published in 2016

The impact of mathematical modeling on the understanding of diabetes and related complications

scientific article published on 10 July 2013

The long journey to a Systems Biology of neuronal function

scientific article

The systems biology format converter

scientific article

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

scientific article (publication date: March 2003)

The systems biology simulation core algorithm

scientific article

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.

scientific article published on 13 September 2017

Towards the collaborative curation of the registry underlying Identifiers.org

scientific article (publication date: 2013)

Using chemical kinetics to model biochemical pathways

scientific article published in January 2013

WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series

scientific article published on 6 September 2017

List of works by Nicolas Le Novère

1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes

A brief history of COMBINE

A community-driven global reconstruction of human metabolism. ⬇️

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

A single (−)-nicotine injection causes change with a time delay in the affinity of striatal D2 receptors for antagonist, but not for agonist, nor in the D2 receptor mRNA levels in the rat substantia nigra

ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling

Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain

Acute and long-term changes in the mesolimbic dopamine pathway after systemic or local single nicotine injections

An H-bond between two residues from different loops of the acetylcholine binding site contributes to the activation mechanism of nicotinic receptors ⬇️

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

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

BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

BioModels Database: a repository of mathematical models of biological processes

BioModels Database: curation and annotation

BioModels linked dataset

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

BioModels: expanding horizons to include more modelling approaches and formats

BioModels: ten-year anniversary

Brain nicotinic receptors: structure and regulation, role in learning and reinforcement

Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP.

COMBINE Archive Specification Version 1.

COMBINE and MIRIAM Registry

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

COMBINE – What it is, what it could be

COMBINE – a vision

Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII

CellML2SBML: conversion of CellML into SBML.

Community-driven roadmap for integrated disease maps

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

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

Conformational spread in a ring of proteins: a stochastic approach to allostery

Control of neurulation by the nucleosome assembly protein-1-like 2.

Controlled annotations for systems biology

Controlled vocabularies and semantics in systems biology

Cooperative binding

Cooperativity of Allosteric Receptors ⬇️

Corrigendum: The BioPAX community standard for pathway data sharing

Curation and annotation for BioModels Database, a resource of published quantitative kinetic models

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

DARPP-32: molecular integration of phosphorylation potential.

Delivering 'Cool URIs' That Do Not Change ⬇️

Designing and encoding models for synthetic biology

Diversity and distribution of nicotinic acetylcholine receptors in the locus ceruleus neurons.

Do genome-scale models need exact solvers or clearer standards?

Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy

Enabling surface dependent diffusion in spatial simulations using Smoldyn

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

Erratum: The Systems Biology Graphical Notation

Experimentally based model of a complex between a snake toxin and the alpha 7 nicotinic receptor

Finding our way through phenotypes

Harmonizing semantic annotations for computational models in biology

Host lipidome analysis during rhinovirus replication in HBECs identifies potential therapeutic targets

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

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

Identifiers.org/MIRIAM Registry annotation and cross-referencing framework

Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum

Involvement of alpha6 nicotinic receptor subunit in nicotine-elicited locomotion, demonstrated by in vivo antisense oligonucleotide infusion

JSBML: a flexible Java library for working with SBML.

JSBML: a flexible and entirely Java-based library for working with SBML

JSBML: a flexible and entirely Java-based library for working with SBML

Kinetic Simulation Algorithm Ontology

LGICdb: a manually curated sequence database after the genomes

LGICdb: the ligand-gated ion channel database

LibKiSAO: a Java library for Querying KiSAO.

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

Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model ⬇️

Localization of [3H]nicotine, [3H]cytisine, [3H]epibatidine, and [125I]alpha-bungarotoxin binding sites in the brain of Macaca mulatta

Localization of nAChR subunit mRNAs in the brain of Macaca mulatta

Looking inside the box: bacterial transistor arrays

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

MELTING, computing the melting temperature of nucleic acid duplex

MIRIAM Resources: a robust annotation and cross referencing framework

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

Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine

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

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)