Histoires évolutives et autres comptes
Algorithmes et graphes pour la bioinformatique

Habilitation (H.D.R.)

Defended November 4, 2016 in Montpellier

Jury

Nadia El Mabrouk	Professeure, Université de Montréal, Canada	Rapportrice
Hélène Touzet	DR CNRS, Université de Lille	Rapportrice
Stéphane Vialette	DR CNRS, Université Paris-Est Marne-la-Vallée	Rapporteur
Alain Guénoche	DR CNRS, Université Marseille	Examinateur
Vincent Ranwez	Professeur, Montpellier SupAgro	Examinateur
Mireille Régnier	DR INRIA, École polytechnique	Examinatrice

Abstract

In this HDR, I present my research works that are in the topics of sequence alignment, comparative genomics and coevolution. The link between these themes is the reconstructiion of evolutionary histories. I outline four problems by following both the chronological order of these works and the increasing size of biological objects they involve:

• Tandem repeats alignment;
• Evolutionary scenarios between genomic markers (coded as permutations), under two different evolutionary models (inversions and DCJ);
• Reconstruction of ancestral genomes and improving extant genome assemblies (DeCo and ARt-DeCo);
• Multiple alignment of complete genomes of bacteriophages (mosaic genomes).

All these works rely on graph theory and string algorithms. We applied our solutions to biological data leading to various applications. Inferring evolutionary histories allowed us to align the sequences, to provide access to the structure of ancestral genomes or to improve genomes assemblies in databases.

The last part of the HDR is dedicated to the presentation of my research projects. They are in the fields of co-evolution and sequence alignment with applications to assembling genomes and annotation transfert

HDR: .pdf (in french only)- Slides : .pdf

	Severine.Berard{AT}umontpellier.fr	ISE-M, UMR 5554 CNRS/UM
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	Last modified 04/01/2022