Aurélien Naldi

Publications

This page provides a list of my peer-reviewed scientific contributions published in international journals and conferences with full paper proceedings. The preprint section further provides a list of my latest work which did not yet go through peer-review. Some of these works have been presented in public seminars.

Online profiles: ResearcherID – ORCID – G scholar – DBLP – Pubmed

Article
Conference
Review
Preprint (no peer-review)

Preprints

Linear cuts in Boolean networks. A. Naldi, A. Richard, E. Tonello. (2022).

2021 - 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools. B. Shaikh, L. Smith, D. Vasilescu, G. Marupilla, M. Wilson, E. Agmon, H. Agnew, S. Andrews, A. Anwar, M. Beber, F. Bergmann, D. Brooks, L. Brusch, L. Calzone, K. Choi, J. Cooper, J. Detloff, B. Drawert, M. Dumontier, G. Ermentrout, J. Faeder, A. Freiburger, F. Fröhlich, A. Funahashi, A. Garny, J. Gennari, P. Gleeson, A. Goelzer, Z. Haiman, J. Hasenauer, J. Hellerstein, H. Hermjakob, S. Hoops, J. Ison, D. Jahn, H. Jakubowski, R. Jordan, M. Kalaš, M. König, W. Liebermeister, R. Sheriff, S. Mandal, R. McDougal, J. Medley, P. Mendes, R. Müller, C. Myers, A. Naldi, T. Nguyen, D. Nickerson, B. Olivier, D. Patoliya, L. Paulevé, L. Petzold, A. Priya, A. Rampadarath, J. Rohwer, A. Saglam, D. Singh, A. Sinha, J. Snoep, H. Sorby, R. Spangler, J. Starruß, P. Thomas, D. van Niekerk, D. Weindl, F. Zhang, A. Zhukova, A. Goldberg, J. Schaff, M. Blinov, H. Sauro, I. Moraru, J. Karr. Nucleic Acids Research (2022).
UPMaBoSS: a novel framework for dynamic cell population modeling. G. Stoll, A. Naldi, V. Noël, E. Viara, E. Barillot, G. Kroemer, D. Thieffry, L. Calzone. Frontiers in Molecular Biosciences (2022).

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms. M. Ostaszewski, A. Niarakis, A. Mazein, I. Kuperstein, R. Phair, A. Orta-Resendiz, V. Singh, S. Aghamiri, M. Acencio, E. Glaab, A. Ruepp, G. Fobo, C. Montrone, B. Brauner, G. Frishman, L. Gomez, J. Somers, M. Hoch, S. Gupta, J. Scheel, H. Borlinghaus, T. Czauderna, F. Schreiber, A. Montagud, M. de Leon, A. Funahashi, Y. Hiki, N. Hiroi, T. Yamada, A. Drager, A. Renz, M. Naveez, Z. Bocskei, F. Messina, D. Bornigen, L. Fergusson, M. Conti, M. Rameil, V. Nakonecnij, J. Vanhoefer, L. Schmiester, M. Wang, E. Ackerman, J. Shoemaker, J. Zucker, K. Oxford, J. Teuton, E. Kocakaya, G. Summak, K. Hanspers, M. Kutmon, S. Coort, L. Eijssen, F. Ehrhart, R. B., D. Slenter, M. Martens, R. Haw, B. Jassal, L. Matthews, M. Orlic-Milacic, A. Senff-Ribeiro, K. Rothfels, V. Shamovsky, R. Stephan, C. Sevilla, T. Varusai, J. Ravel, R. Fraser, V. Ortseifen, S. Marchesi, P. Gawron, E. Smula, L. Heirendt, V. Satagopam, G. Wu, A. Riutta, M. Golebiewski, S. Owen, C. Goble, X. Hu, R. Overall, D. Maier, A. Bauch, J. Bachman, B. Gyori, C. Vega, V. Groues, M. Vazquez, P. Porras, L. Licata, M. Iannuccelli, F. Sacco, D. Turei, A. Luna, O. Babur, S. Soliman, A. Valdeolivas, M. Esteban-Medina, M. Pena-Chilet, T. Helikar, B. Puniya, A. Nesterova, A. Yuryev, A. de Waard, D. Modos, A. Treveil, M. Olbei, B. Meulder, A. Naldi, A. Dugourd, V. Noel, L. Calzone, C. Sander, E. Demir, T. Korcsmaros, T. Freeman, F. Auge, J. Beckmann, J. Hasenauer, O. Wolkenhauer, E. Willighagen, A. Pico, C. Evelo, M. Gillespie, L. Stein, H. Hermjakob, P. D′Eustachio, J. Saez-Rodriguez, J. Dopazo, A. Valencia, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider. Molecular Systems Biology 17:e10387 (2021).
Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression. K. Corral-Jara, C. Chauvin, W. Abou-Jaoudé, M. Grandclaudon, A. Naldi, V. Soumelis, D. Thieffry. Molecular Biomedicine 2 (2021).
Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions. M. Buffard, A. Naldi, G. Freiss, M. Deckert, O. Radulescu, P. Coopman, R. Larive. Biomolecules 11:308 (2021).
Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer. L. Cantini, P. Zakeri, C. Hernandez, A. Naldi, D. Thieffry, E. Remy, A. Baudot. Nature Communications 12 (2021).
Sex Dimorphism of Nonalcoholic Fatty Liver Disease (NAFLD) in Pparg-Null Mice. M. Schiffrin, C. Winkler, L. Quignodon, A. Naldi, M. Trötzmüller, H. Köfeler, H. Henry, P. Parini, B. Desvergne, F. Gilardi. International Journal of Molecular Sciences 22:9969 (2021).
Logical modelling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions. K. Nuñez-Reza, A. Naldi, A. Sánchez-Jiménez, A. Leon-Apodaca, M. Santana, M. Thomas-Chollier, D. Thieffry, A. Medina-Rivera. Interface Focus 11:20200061 (2021).
LNetReduce: Tool for Reducing Linear Dynamic Networks with Separated Timescales. M. Buffard, A. Desoeuvres, A. Naldi, C. Requilé, A. Zinovyev, O. Radulescu. Computational Methods in Systems Biology :238--244 (2021).

2016 - 2020

Dynamical Boolean Modeling of Immunogenic Cell Death. A. Checcoli, J. Pol, A. Naldi, V. Noel, E. Barillot, G. Kroemer, D. Thieffry, L. Calzone, G. Stoll. Frontiers in Physiology 11 (2020).
Computational Verification of Large Logical Models — Application to the Prediction of T Cell Response to Checkpoint Inhibitors. C. Hernandez, M. Thomas-Chollier, A. Naldi, D. Thieffry. Frontiers in Physiology 11 (2020).
SBML Level 3: an extensible format for the exchange and reuse of biological models. S. Keating, D. Waltemath, M. König, F. Zhang, A. Dräger, C. Chaouiya, F. Bergmann, A. Finney, C. Gillespie, T. Helikar, S. Hoops, R. Malik-Sheriff, S. Moodie, I. Moraru, C. Myers, A. Naldi, B. Olivier, S. Sahle, J. Schaff, L. Smith, M. Swat, D. Thieffry, L. Watanabe, D. Wilkinson, M. Blinov, K. Begley, J. Faeder, H. Gómez, T. Hamm, Y. Inagaki, W. Liebermeister, A. Lister, D. Lucio, E. Mjolsness, C. Proctor, K. Raman, N. Rodriguez, C. Shaffer, B. Shapiro, J. Stelling, N. Swainston, N. Tanimura, J. Wagner, M. Meier-Schellersheim, H. Sauro, B. Palsson, H. Bolouri, H. Kitano, A. Funahashi, H. Hermjakob, J. Doyle, M. Hucka, . SBML Level 3 Community members. Mol. Syst. Biol. 16:e9110 (2020).
Automated inference of Boolean models from molecular interaction maps using CaSQ. S. Aghamiri, V. Singh, A. Naldi, T. Helikar, S. Soliman, A. Niarakis. Bioinformatics (2020).
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. A. Niarakis, M. Kuiper, M. Ostaszewski, R. Sheriff, C. Casals-Casas, D. Thieffry, T. Freeman, P. Thomas, V. Touré, V. Noël, G. Stoll, J. Saez-Rodriguez, A. Naldi, E. Oshurko, I. Xenarios, S. Soliman, C. Chaouiya, T. Helikar, L. Calzone. Briefings in Bioinformatics (2020).
PTPN13 induces cell junction stabilization and inhibits mammary tumor invasiveness. M. Hamyeh, F. Bernex, R. Larive, A. Naldi, S. Urbach, J. Simony-Lafontaine, C. Puech, W. Bakhache, J. Solassol, P. Coopman, W. Hendriks, G. Freiss. Theranostics 10:1016-1032 (2020).

Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation. J. Sánchez-Villanueva, O. Rodríguez-Jorge, O. Ramírez-Pliego, G. Rosas Salgado, W. Abou-Jaoudé, C. Hernandez, A. Naldi, D. Thieffry, M. Santana. PLoS ONE 14:e0226388 (2019).
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. L. Wigger, C. Casals-Casas, M. Baruchet, K. Trang, S. Pradervand, A. Naldi, B. Desvergne. PLOS ONE 14:e0220894 (2019).
Network Reconstruction and Significant Pathway Extraction Using Phosphoproteomic Data from Cancer Cells. M. Buffard, A. Naldi, O. Radulescu, P. Coopman, R. Larive, G. Freiss. Proteomics 19:e1800450 (2019).

BioLQM: a java toolkit for the manipulation and conversion of Logical Qualitative Models of biological networks. A. Naldi. Frontiers in Physiology 9:1605 (2018).
Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). N. Levy, A. Naldi, C. Hernandez, G. Stoll, D. Thieffry, A. Zinovyev, L. Calzone, L. Paulevé. Frontiers in Physiology 9:787 (2018).
Logical modelling and analysis of cellular regulatory networks with GINsim 3.0. A. Naldi, C. Hernandez, W. Abou-Jaoudé, P. Monteiro, C. Chaouiya, D. Thieffry. Frontiers in Physiology 9:646 (2018).
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. A. Naldi, C. Hernandez, N. Levy, G. Stoll, P. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulevé. Frontiers in Physiology 9:680 (2018).
GOATOOLS: A Python library for Gene Ontology analyses. D. Klopfenstein, L. Zhang, B. Pedersen, F. Ramirez, A. Warwick Vesztrocy, A. Naldi, C. Mungall, J. Yunes, O. Botvinnik, M. Weigel, W. Dampier, C. Dessimoz, P. Flick, H. Tang. Scientific Reports 8:10872 (2018).

Reconstruction and Signal Propagation Analysis of the Syk Signaling Network in Breast Cancer Cells. A. Naldi, R. Larive, U. Czerwinska, S. Urbach, P. Montcourrier, C. Roy, J. Solassol, G. Freiss, P. Coopman, O. Radulescu. PLoS Computational Biology 13:e1005432 (2017).
MaBoSS 2.0: an environment for stochastic Boolean modeling. G. Stoll, B. Caron, E. Viara, A. Dugourd, A. Naldi, G. Kroemer, A. Zinovyev, E. Barillot, L. Calzone. Bioinformatics 33:2226-8 (2017).
The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks. E. Azpeitia, S. Muñoz, D. González-Tokman, M. Martínez-Sánchez, N. Weinstein, A. Naldi, E. Álvarez-Buylla, D. Rosenblueth, L. Mendoza. Scientific Reports 7:42023 (2017).

Geometric analysis of pathways dynamics: application to versatility of TGF-beta receptors. S. Samal, A. Naldi, D. Grigoriev, A. Weber, N. Théret, O. Radulescu. Biosystems 149:3-14 (2016).

2011-2015

Symbolic Dynamics of Biochemical Pathways as Finite States Machines. O. Radulescu, S. Samal, A. Naldi, D. Grigoriev, A. Weber. Computational Methods in Systems Biology 9308:104-120 (2015).
Cooperative development of logical modelling standards and tools with CoLoMoTo. A. Naldi, P. Monteiro, C. Müssel, t. Consortium for Logical Models and Tools, H. Kestler, D. Thieffry, I. Xenarios, J. Saez-Rodriguez, T. Helikar, C. Chaouiya. Bioinformatics 31:1154-1159 (2015).
Model checking to assess T-helper cell plasticity. W. Abou-Jaoudé, P. Monteiro, A. Naldi, M. Grandclaudon, V. Soumelis, C. Chaouiya, D. Thieffry. Front Bioeng Biotechnol 2:86 (2015).

Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. F. Gilardi, E. Migliavacca, A. Naldi, M. Baruchet, D. Canella, G. Martelot, N. Guex, B. Desvergne. PLoS Genetics 10:e1004155 (2014).

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. C. Chaouiya, D. Bérenguier, S. Keating, A. Naldi, M. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P. Monteiro, A. Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Novère, J. Saez-Rodriguez, T. Helikar. BMC Systems Biology 7:135 (2013).
Dynamical modeling and analysis of large cellular regulatory networks. D. Bérenguier, C. Chaouiya, P. Monteiro, A. Naldi, E. Remy, D. Thieffry, L. Tichit. Chaos 23:025114 (2013).
On Circuit Functionality in Boolean Networks. J. Comet, M. Noual, A. Richard, J. Aracena, L. Calzone, J. Demongeot, M. Kaufman, A. Naldi, E. Snoussi, D. Thieffry. Bulletin of Mathematical Biology 75:906--919 (2013).

Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control. A. Naldi, P. Monteiro, C. Chaouiya. Computational Methods in Systems Biology :288--306 (2012).

Logical Modelling of Gene Regulatory Networks with GINsim. C. Chaouiya, A. Naldi, D. Thieffry. Bacterial Molecular Networks :463--479 (2011).
Petri net representation of multi-valued logical regulatory graphs. C. Chaouiya, A. Naldi, E. Remy, D. Thieffry. Natural Computing 10:727--750 (2011).
Dynamically consistent reduction of logical regulatory graphs. A. Naldi, E. Remy, D. Thieffry, C. Chaouiya. Theoretical Computer Science 412:2207--2218 (2011).

2006-2010

Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. A. Naldi, J. Carneiro, C. Chaouiya, D. Thieffry. PLoS Computational Biology 6:e1000912 (2010).
Reduction of logical models of regulatory networks yields insight into dynamical properties. C. Chaouiya, A. Naldi, E. Remy, D. Thieffry. 2010 IEEE International Conference on Control Applications (2010).

Logical modelling of regulatory networks with GINsim 2.3. A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry, C. Chaouiya. Biosystems 97:134--139 (2009).
Modular logical modelling of the budding yeast cell cycle. A. Fauré, A. Naldi, F. Lopez, C. Chaouiya, A. Ciliberto, D. Thieffry. Molecular BioSystems 5:1787 (2009).
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. A. Naldi, E. Remy, D. Thieffry, C. Chaouiya. Computational Methods in Systems Biology 5688:266--280 (2009).

Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. A. Naldi, D. Thieffry, C. Chaouiya. Computational Methods in Systems Biology :233--247 (2007).

GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks. A. Gonzalez, A. Naldi, L. Sánchez, D. Thieffry, C. Chaouiya. Biosystems 84:91--100 (2006).
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. A. Faure, A. Naldi, C. Chaouiya, D. Thieffry. Bioinformatics 22:e124--e131 (2006).