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

by Aurélien Naldi
Published 2018-11-01

Diversity and plasticity of Th cell types predicted from regulatory network modelling.

by Aurélien Naldi, Jorge Carneiro, Claudine Chaouiya, Denis Thieffry
Published 2010-09-01

Computational Verification of Large Logical Models—Application to the Prediction of T Cell Response to Checkpoint Inhibitors

by Céline Hernandez, Morgane Thomas-Chollier, Morgane Thomas-Chollier, Aurélien Naldi, Denis Thieffry
Published 2020-09-01

Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0

by Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé, Pedro T. Monteiro, Claudine Chaouiya, Denis Thieffry
Published 2018-06-01

Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer

by Laura Cantini, Pooya Zakeri, Celine Hernandez, Aurelien Naldi, Denis Thieffry, Elisabeth Remy, Anaïs Baudot
Published 2021-01-01

System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells.

by Leonore Wigger, Cristina Casals-Casas, Michaël Baruchet, Khanh B Trang, Sylvain Pradervand, Aurélien Naldi, Béatrice Desvergne
Published 2019-01-01

Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions

by Marion Buffard, Aurélien Naldi, Gilles Freiss, Marcel Deckert, Ovidiu Radulescu, Peter J. Coopman, Romain M. Larive
Published 2021-02-01

Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression

by Karla Fabiola Corral-Jara, Camille Chauvin, Wassim Abou-Jaoudé, Maximilien Grandclaudon, Aurélien Naldi, Vassili Soumelis, Denis Thieffry
Published 2021-04-01

Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals.

by Federica Gilardi, Eugenia Migliavacca, Aurélien Naldi, Michaël Baruchet, Donatella Canella, Gwendal Le Martelot, Nicolas Guex, Béatrice Desvergne, CycliX Consortium
Published 2014-03-01

Sex Dimorphism of Nonalcoholic Fatty Liver Disease (NAFLD) in <i>Pparg</i>-Null Mice

by Mariano Schiffrin, Carine Winkler, Laure Quignodon, Aurélien Naldi, Martin Trötzmüller, Harald Köfeler, Hugues Henry, Paolo Parini, Béatrice Desvergne, Federica Gilardi
Published 2021-09-01

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

by Aurélien Naldi, Romain M Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J Coopman, Ovidiu Radulescu
Published 2017-03-01

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

by José Antonio Sánchez-Villanueva, Otoniel Rodríguez-Jorge, Oscar Ramírez-Pliego, Gabriela Rosas Salgado, Wassim Abou-Jaoudé, Céline Hernandez, Aurélien Naldi, Denis Thieffry, María Angélica Santana
Published 2019-01-01

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

by Nicolas Levy, Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll, Gautier Stoll, Gautier Stoll, Gautier Stoll, Gautier Stoll, Denis Thieffry, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev, Laurence Calzone, Laurence Calzone, Laurence Calzone, Loïc Paulevé
Published 2018-07-01

Dynamical Boolean Modeling of Immunogenic Cell Death

by Andrea Checcoli, Jonathan G. Pol, Jonathan G. Pol, Aurelien Naldi, Vincent Noel, Vincent Noel, Vincent Noel, Emmanuel Barillot, Emmanuel Barillot, Emmanuel Barillot, Guido Kroemer, Guido Kroemer, Guido Kroemer, Guido Kroemer, Guido Kroemer, Denis Thieffry, Laurence Calzone, Laurence Calzone, Laurence Calzone, Gautier Stoll, Gautier Stoll
Published 2020-11-01

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

by Aurélien Naldi, Céline Hernandez, Nicolas Levy, Nicolas Levy, Gautier Stoll, Gautier Stoll, Gautier Stoll, Gautier Stoll, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev, Andrei Zinovyev, Laurence Calzone, Laurence Calzone, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé
Published 2018-06-01

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

by Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members
Published 2020-08-01