Enseignements

  • 2019-2023: Université Côte d'Azur
    • Bases de Données (60h, L2 Info - CM, TD, TP)
    • Systèmes d'Exploitation (48h, L2 Info - TD, TP)
    • Programmation Python (36h, L2 Info - TD, TP)
    • Programmation R (30h, L2 Bio & MIASHS - TP)
    • Programmation C (18h, L2 Info - TP)
    • Travaux d'Étude et de Recherche (M1 et M2 Info)
  • 2012-2018: Université d'Aix-Marseille
    • Programmation Structurée en langage Python (60h, M1 Bioinfo - CM, TP)
    • Programmation et Conception Orientée Objet en langage Java (60h, M2 Bioinfo - CM, TP)
    • Algorithmique et Structures de Données (24h, Prépa CAPES Maths option Info & L3 Statistiques - CM, TD)
    • Projet Algorithmique (60h, L2 Info - CM, TP)
    • Théorie et Algorithmique des Graphes (15h, M2 Bioinfo - CM, TD)
    • Ingénierie Logicielle (20h, M1 Bioinfo - CM, TP)
  • 2005-2012: Université de la Méditerranée
    • Algorithmique du Texte (15h, M2 Info - CM, TD)
    • Génie Logiciel (60h, M1 Info - CM, TD, TP)
    • Système Unix (60h, M2 Info - CM, TD, TP)
    • Langages XML (15h, M1 Info - CM, TP)
    • Programmation Web (15h, M1 Bioinfo - CM, TP)
    • Bases de Données (15h, M1 Bioinfo - CM, TP)
  • 2008-2011: Université Technique de Sofia, Bulgarie
    • Système Unix (20h, M1 Génie Info - CM, TP)

Thèmes de recherche

Mots-clés : algorithmique appliquée, réseaux multiplexes, réseaux temporels, partitionnement de réseaux, identification de communautés, méta-heuristiques, marches aléatoires, string matching

Publications

[1] Firas Hammami, Laurent Tichit, Béatrice Py, Frédéric Barras, Pierre Mandin, and Elisabeth Remy. Analysis of a logical regulatory network reveals how Fe-S cluster biogenesis is controlled in the face of stress. microLife, 03 2023. uqad003. [ DOI ]
[2] Maxime Lucas, Arthur Morris, Alex Townsend-Teague, Laurent Tichit, Bianca Habermann, and Alain Barrat. Inferring cell cycle phases from a partially temporal network of protein interactions. Cell Reports Methods, 3(2):100397, 2023. [ DOI ]
[3] 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 | DOI ]
[4] Michaël Pierrelée, Ana Reynders, Fabrice Lopez, Aziz Moqrich, Laurent Tichit, and Bianca H Habermann. Introducing the novel cytoscape app timenexus to analyze time-series data using temporal multilayer networks (tmlns). Scientific Reports, 11(1):1--17, 2021. [ bib | DOI ]
[5] Elva María Novoa-del Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, and Anaïs Baudot. A multi-objective genetic algorithm to find active modules in multiplex biological networks. PLOS Computational Biology, 17(8):1--24, 08 2021. [ bib | DOI ]
[6] Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Élisabeth Remy, and Anaïs Baudot. Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics, 35(3):497--505, Feb 2019. [ bib | DOI ]
[7] 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, 63(5), 2019. [ bib | DOI ]
[8] Leandro Corrêa, 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 ]
[9] 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, ..., Laurent Tichit, ..., Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, and Daniel Marbach. Assessment of network module identification across complex diseases. Nature Methods, 16(9):843--852, 2019. [ bib | DOI ]
[10] Alberto Valdeolivas, Élisabeth Remy, Laurent Tichit, Gaëlle Navarro, Odelin Claire, Sophie Perrin, Pierre Cau, Nicolas Levy, and Anaïs Baudot. Prediction of disease-associated genes by advanced random walk with restart on multiplex and heterogeneous biological networks. In JOBIM'17, 18th Open Days in Biology, Computer Science and Mathematics, volume 10, pages 38--43, 2017. [ bib ]
[11] Gilles Didier and Laurent Tichit. Designing optimal- and fast-on-average pattern matching algorithms. Journal of Discrete Algorithms, 42:45 -- 60, 2017. [ bib | DOI ]
[12] Olivier Zugasti, Nishant Thakur, Jérôme Belougne, Barbara Squiban, Leopold C. 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, pages 14--35, 2016. [ bib | DOI ]
[13] Nishant Thakur, Nathalie Pujol, Laurent Tichit, and Jonathan J. Ewbank. Clone Mapper: An online suite of tools for RNAi experiments in caenorhabditis elegans. G3: Genes|Genomes|Genetics, 2014. [ bib | DOI ]
[14] Frédéric Montañana-Sanchis, Renaud A. Julien, Philippe Vaglio, Lisa R. Matthews, Laurent Tichit, and Jonathan J. Ewbank. ICeE: an interface for C. elegans experiments. Worm, 3(3):e959420, 2014. PMID: 26430546. [ bib | DOI ]
[15] Lionel Spinelli, Philippe Gambette, Charles E. Chapple, Benoît Robisson, Anaïs Baudot, Henri Garreta, Laurent Tichit, Alain Guénoche, and Christine Brun. Clust&See: A Cytoscape plugin for the identification, visualization and manipulation of network clusters. Biosystems, 113(2):91 -- 95, 2013. [ bib | DOI ]
[16] Duncan Bérenguier, Claudine Chaouiya, Pedro T. Monteiro, Aurélien Naldi, Élisabeth Remy, Denis Thieffry, and Laurent Tichit. Dynamical modeling and analysis of large cellular regulatory networks. Chaos, 23(2), 2013. [ bib | DOI ]
[17] Claudine Chaouiya, Aurélien Naldi, Lionel Spinelli, Pedro T. Monteiro, Duncan Bérenguier, Luca Grieco, Abibatou Mbodj, Samuel Collombet, Anna Niarakis, Laurent Tichit, Élisabeth Remy, and Denis Thieffry. Logical modelling of cellular decision processes with GINsim. In JOBIM'12, 13th Open Days in Biology, Computer Science and Mathematics, 2012. [ bib ]
[18] Laurent Tichit, Philippe Gambette, and Alain Guénoche. Modclust: a cytoscape plugin for modularity-based clustering of networks. In MARAMI'11, Seconde conférence sur les Modèles et l'Analyse des Réseaux : Approches Mathématiques et Informatique, volume 2, 2011. [ bib ]
[19] Inga Engelmann, Aurélien Griffon, Laurent Tichit, Frédéric Montañana-Sanchis, Guilin Wang, Valerie Reinke, Robert H. Waterson, LaDeana W. Hillier, and Jonathan J. Ewbank. A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans. PLoS ONE, 2011. [ bib | DOI ]
[20] Alain Guénoche, Henri Garreta, and Laurent Tichit. About the largest subtree common to several X-trees. Mathematics and social sciences, 190(2):115--124, Sep 2010. [ bib | DOI ]
[21] Carl Herrmann, Sèverine Bérard, and Laurent Tichit. SimCT: a generic tool to visualize ontology-based relationships for biological objects. Bioinformatics (Oxford, England), 25(23):3197--3198, December 2009. [ bib | DOI ]
[22] Alain Guénoche, Henri Garreta, and Laurent Tichit. About the largest subtree common to several phylogenetic trees. In L. Sakalauskas, C. Skiadas, and E. K. Zavadskas, editors, Proceedings of the XIII International Conference "Applied Stochastic Models and Data Analysis" (ASMDA-2009), Vilnius, Lithuania, pages 6--10, July 2009. [ bib ]
[23] Nuria Gala, Véronique Rey, and Laurent Tichit. Dispersion sémantique dans des familles morpho-phonologiques : éléments théoriques et empiriques. In Actes de la 16ème conférence sur le Traitement Automatique des Langues Naturelles, 06 2009. [ bib ]
[24] Aïda Ouangraoua, Pascal Ferraro, Laurent Tichit, and Serge Dulucq. Local similarity between quotiented ordered trees. Journal of Discrete Algorithms, 5(1):23 -- 35, 2007. [ bib | DOI ]
[25] Sèverine Bérard, Laurent Tichit, and Carl Herrmann. Clusterinspector: a tool to visualize ontology-based relationships between biological entities. In JOBIM'05, 6th Open Days in Biology, Computer Science and Mathematics, 2005. [ bib ]
[26] Pascal Ferraro, Laurent Tichit, and Serge Dulucq. Local similarity between trees. In JOBIM'04, 5th Open Days in Biology, Computer Science and Mathematics, pages 1--12, 2004. [ bib ]
[27] Laurent Tichit. Algorithmique des structures biologiques : l'édition d'arborescences pour la comparaison de structures secondaires d'ARN. PhD thesis, Université Bordeaux I, September 2003. [ bib ]
[28] Serge Dulucq and Laurent Tichit. RNA secondary structure comparison: exact analysis of the Zhang–Shasha tree edit algorithm. Theoretical Computer Science, 306(1):471 -- 484, 2003. [ bib | DOI ]
[29] Serge Dulucq and Laurent Tichit. RNA secondary structure comparison: edition and alignment algorithms. In 4th colloquium GASCom’2001 Random Generation of Combinatorial Structures and Bijective Combinatorics, pages 53--58, Siena, Italy, November 2001. [ bib ]
[30] Serge Dulucq and Laurent Tichit. à propos de la comparaison de structures secondaires d'ARN. In JOBIM'01, 2nd Open Days in Biology, Computer Science and Mathematics, Toulouse, June 2001. [ bib ]