France PhD Studentship Universite Pierre et Marie Curie Paris

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May 20, 2008

A 3-year PhD studentship is available at Universite Pierre et Marie
Curie (Paris, France) to study lateral gene transfers and genomic
evolution, mostly through bioinformatics approaches. The project will be
supervised by Dr Philippe LOPEZ (bioinformatics, phylogenomics) and Dr
Eric BAPTESTE (evolutionary biology, philosophy of sciences), within UMR
7138 ‘Systematique, Adaptation, Evolution’.

This project will involve bioinformatic analyses, genomic and
metagenomic studies, phylogenetics and of course lots of fun discoveries
(see below for a short summary). A full description of the proposal can
be found at

http://pbg-05.snv.jussieu.fr/phd/phd_lopez_bapteste.pdf

The position is open to EU citizens. The ideal applicant should have an
MSc in Evolutionary Biology or Mathematics or Bioinformatics, and should
show a great interest in evolution. The position will start anytime from
October to December 2008. Requests for further information and
applications (a CV, cover letter and names of 2 academic referees)
should be made to Philippe LOPEZ (philippe.lopez@upmc.fr) or Eric
BAPTESTE (eric.bapteste@snv.jussieu.fr). The deadline for applications
is June 1st, 2008.

Universite Pierre et Marie Curie is located in the historical center of
Paris, by the Seine river and in front of the Jardin des Plantes, and is
the largest french university (ranked 1st in France, 6th in Europe and
39th worldwide). Scientific environments is stimulating, since the host
unit has strong connections with a wide variety of biologists: deep sea
oceanographers, transposons specialists, experts from Museum National
d’Histoire Naturelle and so on.

Thank you for your attention, we’re looking forward to hearing from you,

Philippe Lopez
Eric Bapteste

Short summary of the proposal:

Over the last years, our views of the evolution of microbial genomes
changed radically. It is now admitted that these genomes are affected by
evolutionary processes conjugating both vertical inheritance and lateral
gene transfer, via phages, plasmids and integrons. Genomes recombine,
become larger or smaller by gene losses and gains, according to rules
that still largely remain to be determined. This PhD aims at studying
the evolution of microbial genomes fluidity via genomics and
metagenomics approaches to understand how the genetic material flows
within Life’s three domains. This ambitious project relies first on the
unprecedented accumulation of molecular data from organisms in pure
culture (the genomic data) and from the sequencing of whole microbial
communities in their environment (the metagenomic data). Second, it
exploits the latest developments in bioinformatics : phylogenetic
methods of tree and network reconstruction, and possibly in silico
modeling of microbial genomes evolution.
This PhD addresses three major questions:
- Does the nature of the mobile genetic material change over time and
across lineages?
- How does the environment influence genomic fluidity?
- Are in situ and in silico data supporting similar conclusions?