Photo by S Brouillet TM
Atelier de BioInformatique
Atelier de BioInformatique
Interests in Biology
- Theoretical Biology, Molecular Evolution, Bioinformatics.
- Fitness landscapes
I am working with several colleagues (including S Brouillet, L Ferretti, D Weinreich and F Tajima) on properties of fitness landscapes. We are trying to characterize the models that fits the best experimental fitness landscapes. We also have developped a tool to explore visually fitness landscapes, that is accessible from the Magellan webpage.
- Coalescent Theory
I have developped tests for neutrality related to the famous Tajima's D. In an attempt to correct for sequencing errors, I built new tests that exclude singletons. I also have also develop a unifying framework that encompasses all neutrality tests based on the frequency spectrum and makes easy the creation of new ones. To compute these new tests (and the previous ones), please visit the online neutrality tests. More work is currently being with L Ferretti done on method to simulate coalescent trees with mutations and on the SFS decomposition. Furthermore, with my close colleague A Lambert and with M Lapierre, we are working on the roots of the standard neutral model and other related models.
- Species Delineation
I worked on a method that delineate species from a genetic dataset (aligned sequences) and propose partitions into a priori species. The method was develop in collaboration with N Puilandre (MNHN), A Lambert (UPMC, UFR Maths) and S Brouillet (ABI). The Automatic Barcod Gap Discovery method (ABGD) can be used from here. We are working on ASAP, a new (better) version of the method.
- HIV infection
I analyze HIV populations to decipher their evolution during the infection. This project is a collaboration with J Wakeley and Coffin lab. People from the latter lab sample blood from infected patients at different time points after the infection. We developed tools to analyze serial in addressing two major questions. (1) When can we a asses that populations from two time points look different? To adress this question, we used a non-parametric test for panmixia. We set up a online version of the test. (2) Can we characterize and quantify the effects of drug treatment?
- Coding SSRs
I have worked with E. Loire and then M. Lapierre on the coding SSRs, that are located on coding sequences. Using a phylogenetic and more recently polymorphisms, we have been estimating their selective cost.
- Generic repeats
I worked on the duplication process, especially on "generic" DNA repeats (repeats that are not mobile elements, microsatellites, etc...). Considering these repeats as vestiges of genome dynamics, we use them to explore the forces that are involved in genome evolution. We thus proposed a model for the intrinsic dynamics of these generic repeats based on a continuous genesis of tandem repeats which can be spaced away by further rearrangements. Repseek is a simple and handy software that allow any user to detect non-strict repeats in a large sequence or shared by two large sequences. We are working with M Carpentier on an extension that handles repeat families.
- Redundancy, Function and Rate of evolution
I have worked with C. Castillo-Davis and D. Hartl on the coupling between regulatory and protein evolution. We developed a measure of cis-regulatory evolution (dSM - divergence in Shared Motifs) and used it to analyze the rate of protein and cis-regulatory evolution in orthologs and in duplicates in the C. elegans/C. briggsae genomes. The software to compute dSM can be downloaded from the wakeleylab website. I also worked with JF Rual on the impact of duplicates on RNAi.
Database and web-engeneering
I worked (04/05-08/05) for Modul-Bio, a biotech company, to built-up the first version of the ViralORFeome database, a db dedicated to the description of all interactions between viral proteins and non-viral ones.
- You can retrieve my scientific publications from PubMed or from Google scholar
- PhD thesis: Etude de la dynamique des génomes : les répétitions intrachromosomiques
- HDR : Evolution moléculaire : des données aux modèles, et vice-versa
- Elementary computer science (Licence ~ Bachelor)
- Elementary mathematics (Licence ~ Bachelor)
- Some aspects of Bioinformatics (Master)
- Population genetics (Master). French readers interested in an introductory text in coalescent theory could cast a glance coalescence.pdf.
Where and when
- 2010-now : maître de conférences (UPMC).
- 2009-2010: delegation CNRS (sabbatical at Kyoto Univ).
- 2005-2009: maître de conférences (UPMC).
- 2005 : bioinformatics engineering (Modul-Bio, Marseille).
- 2002-2005: postdoc with John Wakeley (Harvard University).
- 1999-2002: PhD with Eric Coissac & Pierre Netter (UPMC ; IJM).
Some other interests
I spent some of my freetime to organize games (i.e. live action role-playing games) in an association named les pèlerins de Métamorphée.
Players of Talisman are welcome to visit and download a enhanced Dragon Cult expansion.
Interested players of Arkham Horror may try few of my variants and heralds that sits on photobucket
Bandes dessinées (Graphic Novels)
I am setting up to website dedicated to Rork, a hit in graphic novels from Andreas. Even though the novel has been translated in english, the web page is only in french.