2021

[1] Jean Fabre-Monplaisir, Brigitte Mossé, and Elisabeth REMY. Isometries of the hypercube: a tool for boolean regulatory networks analysis  . Physica D: Nonlinear Phenomena, 2021. [ bib | http ]
[2] Léonard Hérault, Mathilde Poplineau, Adrien Mazuel, Nadine Platet, Élisabeth Remy, and Estelle Duprez. Single-cell rna-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells. BMC biology, 19(1):1--20, 2021. [ bib ]
[3] Laura Cantini, Pooya Zakeri, Celine Hernandez, Aurelien Naldi, Denis Thieffry, Elisabeth Remy, and Anaïs Baudot. Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer. Nature communications, 12(1):1--12, 2021. [ bib ]
[4] Léo Pio-Lopez, Alberto Valdeolivas, Laurent Tichit, Élisabeth Remy, and Anaïs Baudot. Multiverse: a multiplex and multiplex-heterogeneous network embedding approach. Scientific Reports, 11(8794), 2021. [ bib | http ]

2020

[1] Gianluca Selvaggio, Sara Canato, Archana Pawar, Pedro T Monteiro, Patrícia S Guerreiro, M Manuela Brás, Florence Janody, and Claudine Chaouiya. Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors. Cancer Res, 2020. [ bib | DOI ]
[2] Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S Malik Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C Freeman, Paul Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomáš Helikar, and Laurence Calzone. 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. Brief Bioinform, 2020. [ bib | DOI ]
[3] Pedro T Monteiro, Tiago Pedreira, Monica Galocha, Miguel C Teixeira, and Claudine Chaouiya. Assessing regulatory features of the current transcriptional network of saccharomyces cerevisiae. Scientific reports, 10(1):1--11, 2020. [ bib ]
[4] Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, et al. Sbml level 3: an extensible format for the exchange and reuse of biological models. Molecular systems biology, 16(8):e9110, 2020. [ bib ]
[5] Gianluca Selvaggio, Sara Canato, Archana Pawar, Pedro T Monteiro, Patrícia S Guerreiro, M Manuela Brás, Florence Janody, and Claudine Chaouiya. Hybrid epithelial--mesenchymal phenotypes are controlled by microenvironmental factors. Cancer research, 80(11):2407--2420, 2020. [ bib ]
[6] Damien Courtine, Jan Provaznik, Jerome Reboul, Guillaume Blanc, Vladimir Benes, and Jonathan J Ewbank. Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods. GigaScience, 9(9), 09 2020. giaa099. [ bib | DOI | arXiv | http ]
[7] Federico Battiston, Giulia Cencetti, Iacopo Iacopini, Vito Latora, Maxime Lucas, Alice Patania, Jean-Gabriel Young, and Giovanni Petri. Networks beyond pairwise interactions: Structure and dynamics. Physics Reports, 874:1--92, 2020. Networks beyond pairwise interactions: Structure and dynamics. [ bib | DOI | http ]
[8] Maxime Lucas, Giulia Cencetti, and Federico Battiston. Multiorder laplacian for synchronization in higher-order networks. Phys. Rev. Research, 2:033410, Sep 2020. [ bib | DOI | http ]
[9] Xing Zhang, Benjamin Harding, Dina Aggad, Damien Courtine, Jia-Xuan Chen, Nathalie Pujol, and Jonathan Ewbank. Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences. 11 2020. [ bib | DOI ]
[10] Vasundra Touré, Steven Vercruysse, Marcio Luis Acencio, Ruth C Lovering, Sandra Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi Del-Toro, Åsmund Flobak, et al. The minimum information about a molecular interaction causal statement (mi2cast). Bioinformatics. [ bib ]

2019

[1] Brigitte Mossé and Élisabeth Remy. A combinatorial exploration of boolean dynamics generated by isolated and chorded circuits. Acta Biotheoretica, July 2019. [ bib | DOI | http ]
[2] Sarvenaz Choobdar, Mehmet E. Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, David Lamparter, Junyuan Lin, Benjamin Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, Anaïs Baudot, Alain Guénoche, Laurent Tichit, Alberto Valdeolivas, Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, The DREAM Module Identification Challenge Consortium, and Daniel Marbach. Assessment of network module identification across complex diseases. Nature Methods, 16(9):843--852, 2019. [ bib | DOI | http ]
[3] Méline Wery, Olivier Dameron, Jacques Nicolas, Elisabeth Remy, and Anne Siegel. Formalizing and enriching phenotype signatures using boolean networks. Journal of Theoretical Biology, 467:66 -- 79, 2019. [ bib | DOI | http ]
[4] Vivek Keshri, Seydina M. Diene, Adrien Estienne, Justine Dardaillon, Olivier Chabrol, Laurent Tichit, Jean-Marc Rolain, Didier Raoult, and Pierre Pontarotti. An integrative database of β-lactamase enzymes: sequences, structures, functions and phylogenetic trees. Antimicrobial Agents and Chemotherapy, 2019. [ bib | DOI | arXiv | http ]
[5] Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Elisabeth Remy, and Anaïs Baudot. Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics, 35 3:497--505, 2019. [ bib ]
[6] Maria Katsogiannou, Jean-Baptiste Boyer, Alberto Valdeolivas, Elisabeth Remy, Laurence Calzone, Stéphane Audebert, Palma Rocchi, Luc Camoin, and Anaïs Baudot. Integrative proteomic and phosphoproteomic profiling of prostate cell lines. PLOS ONE, 14(11):1--25, 11 2019. [ bib | DOI | http ]
[7] Elisa. Tonello, Etienne. Farcot, and Claudine. Chaouiya. Local negative circuits and cyclic attractors in boolean networks with at most five components. SIAM Journal on Applied Dynamical Systems, 18(1):68--79, 2019. [ bib ]
[8] Pedro L. Varela, Pedro T. Monteiro, and Claudine Chaouiya. Impact of changing cell-cell communication network in models of epithelial pattern formation. IFAC-PapersOnLine, 52(26):38 -- 44, 2019. [ bib ]
[9] Leandro Correa, Denis Pallez, Laurent Tichit, Olivier Soriani, and Claude Pasquier. Population-based meta-heuristic for active modules identification. In Proceedings of the Tenth International Conference on Computational Systems-Biology and Bioinformatics, CSBio ’19, New York, NY, USA, 2019. Association for Computing Machinery. [ bib | DOI | http ]
[10] Michael Hucka, Frank T Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M Keating, Matthias König, Nicolas Le Novère, Chris J Myers, Brett G Olivier, Sven Sahle, James C Schaff, Rahuman Sheriff, Lucian P Smith, Dagmar Waltemath, Darren J Wilkinson, and Fengkai Zhang. The systems biology markup language (sbml): Language specification for level 3 version 2 core release 2. J Integr Bioinform, 16(2), Jun 2019. [ bib ]
[11] Maxime Lucas, Duccio Fanelli, and Aneta Stefanovska. Nonautonomous driving induces stability in network of identical oscillators. Physical Review E, 99, 01 2019. [ bib | DOI ]

2018

[1] Sarvenaz Choobdar, Mehmet E. Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, David Lamparter, Junyuan Lin, Benjamin Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, Daniel Marbach, Anaïs Baudot, Alain Guénoche, Laurent Tichit, Alberto Valdeolivas, The DREAM Module Identification Challenge Consortium, and Daniel Marbach. Open community challenge reveals molecular network modules with key roles in diseases. bioRxiv, 2018. [ bib | DOI | arXiv | http ]
[2] Martial Mermillod, Delphine Grynberg, Léo Pio-Lopez, Magdalena Rychlowska, Brice Beffara, Sylvain Harquel, Nicolas Vermeulen, Paula M. Niedenthal, Frédéric Dutheil, and Sylvie Droit-Volet. Evidence of rapid modulation by social information of subjective, physiological, and neural responses to emotional expressions. Frontiers in Behavioral Neuroscience, 11:231, 2018. [ bib | DOI | http ]
[3] PL Varela, CV Ramos, PT Monteiro, and C Chaouiya. Epilog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved, 1 approved with reservations]. F1000Research, 7(1145), 2018. [ bib | DOI ]
[4] Pedro L. Varela, Inês Lynce, Vasco Manquinho, Claudine Chaouiya, and Pedro T. Monteiro. Stable states of boolean regulatory networks composed over hexagonal grids. Electronic Notes in Theoretical Computer Science, 335:113 -- 130, 2018. 7th International Workshop on Static Analysis and Systems Biology (SASB 2016). [ bib | DOI | http ]
[5] Lucas Sánchez and Claudine Chaouiya. Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads. Journal of The Royal Society Interface, 15, 2018. [ bib | DOI ]
[6] Aurélien Naldi, Céline Hernandez, Wassim Abou-Jaoudé, Pedro T. Monteiro, Claudine Chaouiya, and Denis Thieffry. Logical modeling and analysis of cellular regulatory networks with ginsim 3.0. Frontiers in Physiology, 9:646, 2018. [ bib | DOI | http ]
[7] Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, and Loïc Paulevé. The colomoto interactive notebook: Accessible and reproducible computational analyses for qualitative biological networks. Frontiers in Physiology, 9:680, 2018. [ bib | DOI | http ]
[8] Nuno D. Mendes, Rui Henriques, Elisabeth Remy, Jorge Carneiro, Pedro T. Monteiro, and Claudine Chaouiya. Estimating Attractor Reachability in Asynchronous Logical Models. Frontiers in Physiology, 9:1161, sep 2018. [ bib | DOI | http ]
[9] Rostand Affogbolo, Claire Gauzente, Alain Guénoche, and Pascale Kuntz. Méta-analyse ordinale d'enquêtes d'opinion application aux usages de l'internet des objets en entreprise. Revue des Nouvelles Technologies de l'Information, Extraction et Gestion des Connaissances, RNTI-E-34:11--22, 2018. [ bib ]

2013--2017 (selection)

[1] Alain Guénoche. Analyse des Préférences et Tournois Pondérés. Journal of Interdisciplinary Methodologies and Issues in Sciences, Graphs and social systems, February 2017. [ bib | DOI | http ]
[2] Jon Sanchez-Valle, Hector Tejero, Kristina Ibanez, Jose Luis Portero, Martin Krallinger, Fatima Al-Shahrour, Rafael Tabares-Seisdedos, Anaïs Baudot, and Alfonso Valencia. A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer. Scientific Reports, 7(1):4474, 2017. [ bib | DOI | http ]
[3] G. Didier and L. Tichit. Designing optimal- and fast-on-average pattern matching algorithms. J. Discrete Algorithms, 42:45--60, 2017. [ bib | DOI | http ]
[4] Elisabeth Remy, Brigitte Mossé, and Denis Thieffry. Boolean Dynamics of Compound Regulatory circuits, pages 43--53. Springer International Publishing, Cham, 2016. [ bib | DOI | http ]
[5] Olivier Zugasti, Nishant Thakur, Jérôme Belougne, Barbara Squiban, C. Léopold Kurz, Julien Soulé, Shizue Omi, Laurent Tichit, Nathalie Pujol, and Jonathan J. Ewbank. A quantitative genome-wide rnai screen in c. elegans for antifungal innate immunity genes. BMC Biology, 14(1):35, Apr 2016. [ bib | DOI | http ]
[6] Rafael Tabarés-Seisdedos and Anaïs Baudot. Editorial: Direct and Inverse Comorbidities Between Complex Disorders. Frontiers in Physiology, 7(117), 2016. [ bib | DOI ]
[7] G. Didier, C. Brun, and A. Baudot. Identifying Communities from Multiplex Biological Networks. PeerJ, 3(e1525):1--9, 2015. [ bib | DOI ]
[8] S. Tripathi, A. Flobak, K. Chawla, A. Baudot, T. Bruland, L. Thommesen, M. Kuiper, and A. Lægreid. The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC Systems Biology, 9(1):40, 2015. [ bib | DOI | http ]
[9] A. Flobak, A. Baudot, E. Remy, L. Thommesen, D. Thieffry, M. Kuiper, and A. Lægreid. Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLOS Computational Biology, 11(8):e1004426, 2015. [ bib | DOI | http ]
[10] E. Remy, S. Rebouissou, C. Chaouiya, A. Zinovyev, F. Radvanyi, and L. Calzone. A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis. Cancer research, 75(19):4042--52, aug 2015. [ bib | DOI | http ]
[11] M. Katsogiannou, C. Andrieu, V. Baylot, A. Baudot, N.J. Dusetti, O. Gayet, P. Finetti, C. Garrido, D. Birnbaum, F. Bertucci, C. Brun, and P. Rocchi. The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets. Molecular & cellular proteomics : MCP, pages 3585--3601, oct 2014. [ bib | DOI | http ]
[12] Alain Guénoche. Single or Multiple Consensus for Linear Orders, pages 189--199. Springer New York, New York, NY, 2014. [ bib | DOI | http ]
[13] K. Ibáñez, C. Boullosa, R. Tabarés-Seisdedos, A. Baudot, and A. Valencia. Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses. PLoS Genetics, 10(2):e1004173, feb 2014. [ bib | DOI | http ]
[14] F. Montañana, R.A. Julien, P. Vaglio, L.R. Matthews, L. Tichit, and J.J. Ewbank. Icee an interface for c. elegans experiments. Worm, 3(3):e959420, 2014. PMID: 26430546. [ bib | DOI | arXiv | http ]
[15] A. Guénoche. Multi-clustering gives robustness to modules in network. British Journal of Mathematics and Computer Science, 4(16):2344--2351, 2014. [ bib | DOI ]
[16] C. Chaouiya and E. Remy. Logical modelling of regulatory networks, methods and applications. Bulletin of mathematical biology, 75(6):891--5, jun 2013. [ bib | DOI | http ]
[17] L. Spinelli, P. Gambette, C.E. Chapple, B. Robisson, A. Baudot, H. Garreta, L. Tichit, A. Guénoche, and C. Brun. Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters. BioSystems, 113(2):91--95, 2013. [ bib | DOI ]
[18] D. Bérenguier, C. Chaouiya, P.T. Monteiro, A. Naldi, E. Remy, D. Thieffry, and L. Tichit. Dynamical modeling and analysis of large cellular regulatory networks. Chaos (Woodbury, N.Y.), 23(2):025114, jun 2013. [ bib | DOI | http ]
[19] Alain Guénoche. Multiple consensus trees: a method to separate divergent genes. BMC Bioinformatics, 14(1):46, Feb 2013. [ bib | DOI | http ]