Aurélien Naldi

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Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2007, CMSB.

Logical modelling of regulatory networks with GINsim 2.3

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2009, Biosyst..

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

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2015, J. Integr. Bioinform..

BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks

Aurélien Naldi, A. Naldi, 2018, Front. Physiol..

Model checking to assess T-helper cell plasticity

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014 .

The combination of the functionalities of feedback circuits is determinant for the number and size of attractors of molecular networks

Aurélien Naldi, David A. Rosenblueth, Eugenio Azpeitia, 2016, bioRxiv.

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018, bioRxiv.

Logical modelling of gene regulatory networks with GINsim.

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2012, Methods in molecular biology.

bioLQM: a java library for the manipulation and conversion of Logical Qualitative Models of biological networks

Aurélien Naldi, A. Naldi, 2018, bioRxiv.

Reversed dynamics to uncover basins of attraction of asynchronous logical models

Aurélien Naldi, Claudine Chaouiya, Elisabeth Remy, 2017 .

Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Aurélien Naldi, Andrei Zinovyev, Laurence Calzone, 2018 .

Model Checking to Assess T-Helper Cell Plasticity

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

GOATOOLS: A Python library for Gene Ontology analyses

Patrick Flick, Fidel Ramírez, Aurélien Naldi, 2018, Scientific Reports.

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2009, CMSB.

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018 .

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control

Aurélien Naldi, Claudine Chaouiya, Pedro T. Monteiro, 2012, CMSB.

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2018, Front. Physiol..

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

Steffen Klamt, Aurélien Naldi, Denis Thieffry, 2013, BMC Systems Biology.

Reduction of logical models of regulatory networks yields insight into dynamical properties

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2010, 2010 IEEE International Conference on Control Applications.

Geometric analysis of pathways dynamics: Application to versatility of TGF-β receptors

Aurélien Naldi, Dima Grigoriev, Nathalie Théret, 2015, Biosyst..

Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells

Aurélien Naldi, Ovidiu Radulescu, Urszula Czerwinska, 2017, PLoS Comput. Biol..

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2006, ISMB.

Dynamically consistent reduction of logical regulatory graphs

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2011, Theor. Comput. Sci..

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

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2015, Journal of integrative bioinformatics.

Petri net representation of multi-valued logical regulatory graphs

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2010, Natural Computing.

Symbolic Dynamics of Biochemical Pathways as Finite States Machines

Aurélien Naldi, Dima Grigoriev, Andreas Weber, 2015, CMSB.

Cooperative development of logical modelling standards and tools with CoLoMoTo

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2014, bioRxiv.

MaBoSS 2.0: an environment for stochastic Boolean modeling

Aurélien Naldi, Emmanuel Barillot, Laurence Calzone, 2017, Bioinform..

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2010, PLoS Comput. Biol..

Erratum: The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks

Aurélien Naldi, Elena R. Alvarez-Buylla, Luis Mendoza, 2017, Scientific Reports.

The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks

Aurélien Naldi, Luis Mendoza, David A. Rosenblueth, 2017, Scientific Reports.

LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales

Aurélien Naldi, Clément Requilé, Ovidiu Radulescu, 2021, CMSB.

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2020, Briefings Bioinform..

On Circuit Functionality in Boolean Networks

Adrien Richard, Aurélien Naldi, Denis Thieffry, 2013, Bulletin of mathematical biology.

SBML Level 3: an extensible format for the exchange and reuse of biological models

Hiroaki Kitano, Aurélien Naldi, Denis Thieffry, 2020, Molecular systems biology.

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Aurélien Naldi, Denis Thieffry, Andrei Zinovyev, 2018, Front. Physiol..

Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation

Aurélien Naldi, Denis Thieffry, Céline Hernandez, 2019, PloS one.