Publications 2013--present

[1] 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 ]
[2] 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 ]
[3] A. Valdeolivas, L. Tichit, C. Navarro, S. Perrin, G. Odelin, N. Levy, P. Cau, E. Remy, and A. Baudot. Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics, 35(3):497--505, 07 2018. [ bib | DOI | arXiv | http ]
[4] 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 ]
[5] 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 ]
[6] 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 ]
[7] 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 ]
[8] 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 ]
[9] 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 ]
[10] 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 ]
[11] 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 ]
[12] 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 ]
[13] 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 ]
[14] G. Didier and L. Tichit. Designing optimal- and fast-on-average pattern matching algorithms. J. Discrete Algorithms, 42:45--60, 2017. [ bib | DOI | http ]
[15] Elisabeth Remy, Brigitte Mossé, and Denis Thieffry. Boolean Dynamics of Compound Regulatory circuits, pages 43--53. Springer International Publishing, Cham, 2016. [ bib | DOI | http ]
[16] 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 ]
[17] Rafael Tabarés-Seisdedos and Anaïs Baudot. Editorial: Direct and Inverse Comorbidities Between Complex Disorders. Frontiers in Physiology, 7(117), 2016. [ bib | DOI ]
[18] G. Didier, C. Brun, and A. Baudot. Identifying Communities from Multiplex Biological Networks. PeerJ, 3(e1525):1--9, 2015. [ bib | DOI ]
[19] 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 ]
[20] 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 ]
[21] 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 ]
[22] 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 ]
[23] Alain Guénoche. Single or Multiple Consensus for Linear Orders, pages 189--199. Springer New York, New York, NY, 2014. [ bib | DOI | http ]
[24] 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 ]
[25] 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 ]
[26] A. Guénoche. Multi-clustering gives robustness to modules in network. British Journal of Mathematics and Computer Science, 4(16):2344--2351, 2014. [ bib | DOI ]
[27] 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 ]
[28] 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 ]
[29] 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 ]
[30] Alain Guénoche. Multiple consensus trees: a method to separate divergent genes. BMC Bioinformatics, 14(1):46, Feb 2013. [ bib | DOI | http ]

This file was generated by bibtex2html 1.98.