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PhD topic

Title: “Study of the dynamics of biological networks: learning models, time data integration and model checking analysis.“

Abstract: Over the last few decades, the emergence of a wide range of new technologies has produced a massive amount of biological data (genomics, proteomics...). Thus, a very large amount of time series data is now produced every day. The newly produced data can give us new ideas about the behaviour of biological systems. This leads to considerable developments in the field of bioinformatics that could benefit from these enormous data. This justifies the motivation to develop efficient methods for learning Biological Regulatory Networks (BRN) modelling a biological system from its time series data. Then, in order to understand the nature of system functions, we study, in this thesis, the dynamics of their BRN models. Indeed, we focus on developing original and scalable logical methods (implemented in Answer Set Programming) to deciphering the emerging complexity of dynamics of biological systems. The main contributions of this thesis are enumerated in the following. (i) Refining the dynamics of the BRN, modelling with the automata Network (AN) formalism, by integrating a temporal parameter (delay) in the local transitions of the automata. We call the extended formalism a Timed Automata Network (T-AN). This integration allows the parametrization of the transitions between each automata local states as well as between the network global states. (ii) Learning BRNs modelling biological systems from their time series data. (iii) Model checking of discrete dynamical properties of BRN (modelling with AN and T-AN) by dynamical formal analysis: attractors identification (minimal trap domains from which the network cannot escape) and reachability verification of an objective from a network global initial state.

Key words: Biological Regulatory Networks, Dynamical analysis, Learning models, Automata Networks, Inference and Revision of Delayed Biological Systems, Answer Set Programming.

Collaborations:

Maxime Folschette, Tony Ribeiro, Katsumi Inoue.

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2014-2017: Algorithmic, Programming, C++ language at ECN for 1st year students (bac+3). Practicals
2014-2017: Information systems, Databases, SQL at ECN for 1st year students (bac+3). Practicals
2016-2017: Logic programming, Answer Set Programming (ASP) at ECN for 2nd and 3rd year students (bac+4 and bac+5). Practicals