Computational Molecular Biology and Phylogenetics

Type de poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce

<p>Swiss Institute of Bioinformatics</p>
Lausanne, Geneve

Nicolas Salamin
Email du/des contacts

*Job description*
The two PhD positions are part of a collaborative project, funded by the Swiss 
National Science Foundation, between the groups of Nicolas Salamin 
(Computational Biology and Phylogenetics, Department of Ecology and Evolution) 
and Marc Robinson-Rechavi (Bioinformatics, Department of Ecology and 
Evolution) at the University of Lausanne, and the group of Bastien Chopard 
(Computer Science Department) at the University of Geneva; all three groups 
are members of the Swiss Institute of Bioinformatics.

The overall aim of the project is to develop and improve the algorithms used 
to estimate the selective pressure acting on DNA sequences by combining 
biological realism and computational efficiency. More specifically, the project 
is divided in two parts:
 - The first one aims at proposing novel algorithms to enable efficient 
parallelisation of the likelihood calculations of codon models. The goal is to 
develop a true high-performance computer approach to the optimisation of 
maximum likelihood to study molecular evolution within a phylogenetic context.
 - The second one aims at developing a Bayesian approach to estimate positive 
selection. The goal is to propose novel approaches to facilitate the 
identification of specific sites and lineages under different types of selective 

Both parts of the project will be enhanced by using high performance computing 
facilities (e.g.~IBM Blue Gene/Q) available within the CADMOS center.

*Profile requirements*
We are looking for autonomous and ambitious students with enthusiasm for 
inter-disciplinary work. The students will need to interact productively with 
evolutionary biologists, genome biologists and computer scientists, and read 
the corresponding range of scientific literature. Candidates must have 
completed their Master's degree or equivalent in a relevant field.

The requirements for each part of the project include a strong mathematical or 
statistical and computer science background and deep interest in theoretical 
aspects of evolutionary biology and bioinformatics. Previous experience with 
evolutionary biology and/or parallel computing is a plus but not a 

The successful candidates will be part of the Department of Ecology and 
Evolution of the University of Lausanne, the Department of Computer Science of 
the University of Geneva, as well as the Swiss Institute of Bioinformatics. 
Our research groups offer a supportive and stimulating environment, with access 
to excellent computer and academic facilities.

*Contact details*
To apply, please send by email
 - a letter describing your research motivation and experience
 - a detailed CV
 - contact details of three referees

Nicolas Salamin (