Graph Decompositions for Phylogenetic Network Reconstruction
(En français)
My PhD topic
Phylogenetic networks
are models more expressive than phylogenetic trees
to represent species or gene evolution, as they can show exchanges of genetic material
through
lateral gene transfer,
recombination or
hybridization.
Lots of combinatorial approaches have been designed to reconstruct them from data extracted from a
set of contradictory gene trees. My thesis will describe some reconstruction methods from triplets, quartets
and clusters, based on graph decompositions, which rely on an underlying tree structure.
I will present some limits of these combinatorial methods (complexity explosion,
restrictions on the network model, ambiguity in the data) and show how to handle them.
A more detailed version of my subject in French
Who is who in Phylogenetic Networks
I'm currently compiling a bibliography
on
phylogenetic networks.
This work is still in progress (I still have a lot of articles to tag
with keywords, and keyword definitions missing) but you can already access
Who's Who in Phylogenetic Networks
,
a bibliographic database with more than 300 references by more than 300 authors,
tagged with a total of more than 100 keywords.
Publications
About phylogenetic networks:
- 2011 :
Philippe Gambette and
Katharina Huber,
Encodings of Phylogenetic Networks of Bounded Level,
manuscript submitted to JMB, under revision.
- 2011 : Philippe Gambette, Vincent Berry
and Christophe Paul,
Quartets and unrooted phylogenetic networks,
manuscript submitted to JBCB.
- 2010 : Philippe Gambette,
Méthodes combinatoires de reconstruction de réseaux phylogénétiques
(Combinatorial methods for phylogenetic network reconstruction),
PhD Thesis. Jury:
Vincent Berry et Christophe Paul (directors), Guillaume Fertin et Vincent Moulton
(reviewers), Alain Guénoche, Violaine Prince et Éric Tannier (examinators).
- 2009:
Philippe Gambette,
Reconstruction combinatoire des réseaux phylogénétiques,
Journées de la Société Française de Systématique,
Biosystema, à paraître
(matériel supplémentaire).
- 2009:
Daniel Huson,
Regula Rupp,
Vincent Berry,
Philippe Gambette
and Christophe Paul,
Computing Galled Networks from Real Data,
ISMB/ECCB'09
(Proceedings of the 17th Annual Conference on Intelligent Systems for Molecular Biology
& 8th European Conference on Computational Biology),
Bioinformatics 25(12), p. i85-i93,
[DOI].
- 2009:
Philippe Gambette,
Vincent Berry
and Christophe Paul,
The Structure of Level-k Phylogenetic Networks,
CPM'09
(Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching),
LNCS 5577, p. 289-300,
[DOI].
- 2008:
Philippe Gambette
and Daniel H. Huson,
Improved
Layout of Phylogenetic Networks,
TCBB
(IEEE/ACM Transactions on Computational Biology and Bioinformatics),
5(3), p. 472-479,
[DOI].
I've worked on other topics, here is my
complete publication list.