Combinatorial Objects in Bio-Algorithmics: Related problems and complexities

Unénorme mercì a celles qui font fonctionner le LIGM et l'IGM, avec qui les pauses cafés sont bien plus plaisantes. Mercì a mes co-auteurs qui ont indéniablement tous contribuéà monépanouissement scienti-fique. Mercì a Florian Sikora et Paul Morel d'avoir accepter d'ˆ etre mes doctorants cobayes. Finalement, un grand merci aux membres de ma famille età mes amis. Toutparticulì erement ma m` ere que j'aime et que j'adore toujours. Introduction I defended my PhD the 17 th of November 2005. In the mean time (September 2005), I joined the Laboratoire d'Informatique Gaspard-Monge as an Assistant Professor for a one year period (as a result – at least partially – of an unformal discussion in a RER B with Maxime Crochemore). At that time, the bioinformatic research group was only composed of two Assistant Professors freshly elevated to the rank of Doctors (including myself) and three PhD students (directed by the INRIA Senior Researcher Marie-France Sagot from Lyon). Somehow, the group was leader-less since no Full Professor, nor even Associate ones were physically in the laboratory. Indeed, Maxime Crochemore (which was leading the research group) was Deputy Scientific Director of the Information and Communication Department of CNRS from 2004 to 2006 and thus was not often in the lab. In this context, my Assistant Professor period gave rise to both cutting the umbilical cord with my scientific mentors (Guillaume Fertin and Irena Rusu) and enhancing my collaborators set. To do so, I did not hesitated to migrate to Montréal, Quebec for a four weeks period just a couple of days after my PhD defense. This trip gave me the opportunity to meet some of my nowadays collaborators (Mathieu Blanchette, Nadia El-Mabrouk, Annie Chateau and Cédric Chauve) and work on new aspects and problems in the field of comparative genomics which led to two inproceedings and a journal paper. Back in France, I was contacted by one of my PhD reviewer – namelyHéì ene Touzet – that had nice intuitions on the links between two problems I faced during my PhD: LAPCS and EDIT (see Chapter 1 for more details). We ended up with a nice unifying framework called ALIGN bringing together most of the comparison models for arc-annotated sequences. Working without a PhD director supervision with this researchers undeniably contributed to my scientific bloom. In September 2006, simultaneously to my access to a permanent position as Associate Professor at the LIGM, both …