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Centre National de la Recherche ScientifiqueORCID 0000-0002-6495-2655Unclaimed ORCID profile · follow to get notified of new preprints
13 papers
Recent·Most cited
Vincent Noël, Aurélien Naldi, Laurence Calzone…·Denis Thieffry
This tutorial demonstrates how to use the CoLoMoTo software suite to perform reproducible dynamical analyses of logical models of biological networks.
Vidisha Singh, Aurélien Naldi, Sylvain Soliman, Anna Niarakis
The paper develops a Boolean model of RA-FLS to predict drug synergies and identify therapeutic targets for rheumatoid arthritis.
Anna Niarakis, Marek Ostaszewski, Alexander Mazein…·the COVID-19 Disease Map Community
The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.
Gautier Stoll, Aurélien Naldi, Vincent Noël…·Laurence Calzone
UPMaBoSS simulates cell population dynamics by extending MaBoSS to model interactions and death/division, revealing TNF-induced resistance mechanisms.
Laura Cantini, Pooya Zakeri, Céline Hernandez…·Anaı̈s Baudot
This study benchmarks nine joint multi-omics dimensionality reduction methods using simulated and real cancer data, finding intNMF excels in clustering and MCIA shows consistent performance across contexts.
Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi…·Ovidiu Radulescu
LNetReduce simplifies linear dynamic networks by reducing them while preserving dynamics across all time scales.
Céline Hernandez, Morgane Thomas‐Chollier, Aurélien Naldi, Denis Thieffry
The paper introduces two computational methods for analyzing complex biological models and applies them to predict T cell responses to checkpoint inhibitors.
bioLQM is a Java library for manipulating and converting logical qualitative models of biological networks, enabling analysis, perturbation studies, and integration with existing tools.
Nicolas Levy, Aurélien Naldi, Céline Hernandez…·Loïc Paulevé
The paper demonstrates the use of the CoLoMoTo Interactive Notebook to analyze a Boolean model of tumor cell invasion, predicting mutations associated with metastasis.
Aurélien Naldi, Céline Hernandez, Nicolas Levy…·Loïc Paulevé
The paper introduces a framework for reproducible analysis of qualitative biological networks using an interactive notebook environment.
Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé…·Denis Thieffry
The paper introduces GINsim 3.0, a software tool for modeling and analyzing cellular regulatory networks using logical formalism, with a focus on the p53-Mdm2 network.
Aurélien Naldi, Pedro T Monteiro, Christoph Müssel…·Claudine Chaouiya
The paper outlines the logical modelling framework and achievements of the Consortium for Logical Models and Tools, emphasizing model reusability and interoperability.
Wassim Abou-Jaoudé, Pedro Monteiro, Aurélien Naldi…·Denis Thieffry
The paper uses symbolic model checking to analyze T-helper cell plasticity by examining attractor switches in a logical model of their differentiation network.