Associated Team SIMBIOSI
The
Associated Teams programme of the INRIA is
intended to promote and develop the international collaborations of
the INRIA with high-level research teams throughout the world,
in line with the international strategy of the institute.
As one of international scientific policy tools of the INRIA, the Associate
Teams programme provides valuable incentive to upgrade relationships
with targeted institutions, and promotes the presence of the institute
in the scientific environment of other countries.
The Associated Team SIMBIOSI is funded starting from Jan. 1st
2009. It has a three partners, the Dipartimento di Informatica e Sistemistica,
Università di Roma "La Sapienza"; the Free University and CWI,
Amsterdam;
and the
BAMBOO team at the INRIA. The groups are headed,
respectively, by Alberto Marchetti-Spaccamela, Leen Stougie and
Marie-France Sagot.
SIMBIOSI's main purpose
The huge variety in the types of close and long-term relations observed between
different species, the so-called symbiotic relations that involve a
symbiont and its host, is mirrored
by a huge variety of genomic and biochemical landscapes inside the
symbiont world, and at the interface between symbionts and hosts. The
purpose of this project is to combinatorially explore those landscapes
at the molecular
level, that is at the level of the genome and of two of the main types of
biochemical networks that may be reconstructed from the sequenced
genomes of symbionts and hosts. Such networks are the metabolic
and protein-protein interaction (PPI) networks. The final objective is
to try to relate the contours of the landscapes to the modus operandi of the
symbiotic relation, thereby offering a hope of better understanding the
latter, in particular its evolution.
The symbiosis issue is vast and complex. The SIMBIOSI Associate Team will focus
first on two questions concerning the evolution of symbionts,
one at the genome level, namely the studies of rearrangements, and one
at the biochemical network level and interface between genome
and network. The evolution of symbionts may be largely dependent on
the evolution of their hosts. In a third part of the project, we
therefore address the question of the evolution of the
intimate relations themselves by studying the co-cladogenesis
(co-speciation) of hosts and symbionts, and more generally their
co-evolution, that is the mutual evolutionary influence they exert on
each other.
Graph (tree) combinatorics and algorithmics underlie each of these
problems, as well as issues related to random graph enumeration under
certain models to improve confidence in the evolution and co-evolution
scenarii inferred.
SIMBIOSI's future
A proposal to continue this association in the
form of an INRIA International Partnership has been
submitted. Information on this proposition may be found on the
web page in construction for this Partnership, called
AMICI. This Partnership would extend the association to
two other partners who were actively involved with SIMBIOSI:
the University of Florence partner headed by
Pierluigi Crescenzi,
and the University of Pisa partner headed by
Nadia Pisanti.