Postdoctoral Opportunity University of Paris

June 10, 2008

We propose a postdoctoral opportunity in the group of Dr. Ch. Froidevaux
at the University of Paris-Sud on the following theme: Towards a language
to query phylogenetic data

Please send a motivation letter, a resume, and the name of
collaborators/advisors able to recommend your application by June 10th,
2008 to Christine Froidevaux (chris@lri.fr) and Sarah Cohen-Boulakia
(cohen@lri.fr)

More information is available below and
at http://www.lri.fr/~cohen/phylo.html

* Advisors Sarah Cohen-Boulakia (Assistant Professor), Christine
Froidevaux (Professor)
* Collaborators Bernard Labedan, Olivier Lespinet (Institut de Genetique
et de Microbiologie, Universite Paris-Sud, Orsay, France) Val Tannen
(University of Pennsylvania, USA)
* Location Bioinformatics group at LRI (Laboratoire de Recherche en
Informatique), Universite Paris-Sud, Orsay, France

* Topic Understanding the relationships between different species may
have consequences both at practical level (e.g., history of a pathogen
agent involved in a disease), and at fundamental level (e.g.,
construction of the tree of life: finding the history of all
organisms). The study of evolution requires various and numerous
pieces of data such as morphological characteristics of a set of
specimens or, more importantly, genomic and proteomic sequences of a
group of species, functional and structural annotations. For several
years now, there has been an avalanche of data available. Combining
and integrating masses of phylogenomics data is of parmount importance
for better understanding evolution.

* Background More specifically, this subject is part of two projects,
pPOD and Microbiogenomics.

** On the one hand, pPOD is an international project, in which
data are collected throughout the world by research groups having
distinct interests (specialized on different groups of species). Data
collected by those various groups are available in a variety of formats
(relational, tabulated files, and so on.).

** On the other hand, partners of the the French project “ANR masses de
donnees” Microbiogenomics study evolution by building phylogenetic trees
based on families of proteins, part of their data is currently stored in
flat-files format (trees) and within a relational warehouse (sequences,
annotations).

In both projects, phylogenetists need to ask complex questions involving
all the data, both produced and consumed by the various steps of the
generation and analysis of phylogenetic trees, including the trees
themselves or families of trees. Examples of queries include: What are
the differences between those two trees? If I modify the alignment by
adding gaps, what would be the impact on the final generated tree?” or

“Among the available trees, what are the subtrees whose proteins are all
involved in a given metabolic pathway? Which are the protein modules
appearing in trees in which a given group of species is monophyletic?”

* Work The aim of this work is to enable various phylogenetists to make
use of all these data in a unified way, in the context of a relational
database. One of the main challenges lies in that the relational model
does not fit with hierarchical (tree-based) data.

As a first step, queries frequently asked by major pPOD and
Microbiogenomics partners should be identified. Queries may be
increasingly complex and can be expressed using different kinds of
language (relational algebra, SQL and so on). In particular, queries
may involve families of trees, comparison and clustering algorithms,
and topological features of the trees.

A classification of queries should then be proposed.

The third step would consist in exploring the limitations of current
relational standards (latest versions of SQL) to represent
phylogenetic data and express queries. This study should provide the
building blocks for a more expressive high-level query language.

More information on the pPOD project: http://phylodata.seas.upenn.edu
More information on the Microbiogenomics project: http://microbiogenomics.u-psud.fr
More information on the Bioinformatics group at LRI: http://www.lri.fr/bioinfo

Sarah Cohen-Boulakia and Christine Froidevaux

Sarah Cohen Boulakia

Tags: opportunity, phylogenetic, Postdoctoral, University of Paris

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