Photo by S Brouillet TM
UMR7138 (Systematique, Adaptation, Evolution),Interests in Biology
Atelier de BioInformatique and
KeywordsSome other interests
- Theoretical Biology, Molecular Evolution, Bioinformatics.
- 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. In each sample, they sequence a region of 1.3 kb for about 20 individual virus. We developed tools to analyze these sequences 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?
- 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 develop more recently 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.
- 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.
- Generic DNA Rerepepeatss
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. We detect and analyze repeats in the genomes of (1) S. cerevisiae, (2) five other eucaryote genomes, (3) 53 bacterial genomes. If you want more, you can download a PhD Abstract/Résumé de Thèse (en francais). If you really want more, and you can read french, please download my whole PhD (8.2 Mo). We also investigated the relationship between repeats and chromosomal stability in bacterial chromsomes and show that repeats are not randomnly distributed in chromosomes but shaped by selection for chromosomal stability.
We have developped recently a simple and handy software that allow any user to detect non-strict repeats in a large sequence or shared by two large sequences. The latest version of repseek can be downloaded from the repseek webpage.
- Redundancy, Function and Rate of evolution
I 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. More recently, I worked with JF Rual on the relative impact of funtion and redundancy on the rate of gene evolution. We extracted the relationships between function (GO terms and RNAi phenotypes), redundancy (stable or unstable duplicates families) and/or rate of gene evolution (protein and cis-regulatory evolution between C. elegans and C. briggsae).
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
- 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).
I spent some of my freetime to organize games (i.e. live action role-playing games) in an association named les pèlerins de Métamorphée.
I developped an expansion for the amazing boardgame Talisman. Interested players are welcome to visit and download a enhanced Dragon Cult expansion.
I spent some time expanding the even more amazing board game Arkham Horror (a mixture of Talisman-like with Cthulhu Mythos). Interested players may try few of my heralds that sits on photobucket
Bandes dessinées (Graphic Novels)
I like to read "bédés" (belgium/french graphic novel) and set a small webpage with freely available short stories. French readers may would have a look.
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.