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Friday, 05 April 2013 15:32

We are looking for a PhD candidate,

starting on October 2018.


The 'Adaptation, Integration, Recticulation, Evolution' team at Sorbonne
Universite, Paris, France is searching for the right candidate for
either the following PhD topic : Networks approaches to characterize
novel microbial lineages and divergent defense/communication mechanisms
from metagenomes of extreme environments. OR the following PhD topic :
Networks approaches to characterize divergent microbial lineages and
novel genes encoding primary metabolisms from metagenomes of extreme
There are good chances (circa 40%) that one of these grants will be
funded, but the candidate will have to pass an audition in late
May/early June to ensure this.
There will be in fact two separate auditions since each project (one
focusing on communication mechanisms/ the other focusing on primary
metabolisms) has been preselected in a separate instance.

Supervisors for this project will be Philippe Lopez and Eric Bapteste,
and the first project will also be co-supervised by Yanyan Li (Museum
National d'Histoire Naturelle, Paris, France). If interested, please
send a mail to 
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A brief summary of the first project can be found below :

Our knowledge on the evolution of important gene families has so far
largely relied on the comparative analysis of sequences from cultured
microbial organisms, which represent a minor fraction of Life on Earth.
However, the growing amount of molecular data from environmental samples
or single cells is now providing important additional data to test
whether genetic diversity in environmental sequences is significantly
larger than genetic diversity in the gene families of cultured
organisms. This project aims at finding very divergent homologs of
proteins of interest (see below) in environmental data.

The Lopez/Bapteste lab owns unique metagenomic datasets from
under-explored extreme environments (Dallol, Lake Tirez, Lost Hammer),
as well as the corresponding samples collected and stored. This lab also
masters sequence similarity network methods, that allow to analyze
metagenomic and genomic data and to investigate highly divergent gene
forms and relationships of distant homology. These graphs allow for
mathematical analyses of genetic diversity over dozens of millions of
sequences, providing a powerful framework to address the evolution of
divergent genes and genomes.

The Li/Bourguet-Kondracki lab is specialized in the functional studies
of molecular mechanisms involved in the microbial communication, defense
and adaptation to the environment, using multi-disciplinary approaches
(biochemistry, microbiology). This team will provide expertise in
guiding the selection of genes involved in microbial communication and
defense to study and will provide experimental validation of
newly-identified gene families identified by bioinformatics.

This project, at the interface of bioinformatics, evolutionary
microbiology/ecology and biochemistry will mine publicly available and
original environmental datasets to:

- identify new forms of microbial defense and communications genes,
e.g.  those involved in quorum sensing, two-component systems as well as
antibiotic production and resistance genes.

- identify new lineages hosting these genes, with a particular focus on
microbes belonging to still undetected deep-branching microbial lineages 

- sequence these new lineages through design of original primers and
single cell genomic studies.  

Last Updated on Friday, 13 April 2018 11:12