LIRMM – UMR 5506 & Univ Montpellier 2 is looking for an enthusiastic and motivated post-doctoral fellow with a background in computer science and algorithms to investigate theoretically, as well as to conceive and develop novel algorithms for analysing sequence data coming from High Throughput Sequencing technologies.
With their huge throughput and scope of applications, Next Generation Sequencing (NGS) technologies are turning biology into a data driven science. Many questions related to genome organisation and funtion can now be asked as computational questions and require large scale analysis on large volumes of sequence data. A key to scalability of used methods is to design sophisticated algorithms for processing this data and inferring biological knowledge. The IBC is a multidisciplinary institute with five collaborating axis of research, one of which is devoted to approaches for analysing sequencing data.
Overall topic: Practical algorithms and indexing data structures for NGS processing
For example, the following topics are of interest:
– Designing methods for comparing sequences to a collection of similar genomes. Genomes from individual or populations from the same species usually differ by a limited number of positions. Hence, a succint representation of several of these genomes in a compact form in memory encode some reference and the differences from other genomes with respect to the reference one.
– Novel approaches for large scale sequence assembly. Current genome assembly methods have strong limitations and are hindered by a varying level of sequencing depth. To solve these limitations it is promising to develop approaches able to exploit variable size of overlaps between the input sequences, without loosing the effectiveness of de Bruijn graph based solutions.
The position is available as soon as possible. The prospective candidate should send a CV and the name and e-mail contacts for 3 references to rivals@lirmm.fr. The official application will be made on the IBC website: http://www.ibc-montpellier.fr/
** Background and requirements
– Background keywords: computer science, text algorithms, combinatorial algorithms, indexing techniques, data compression
– Required: advanced knowledge in algorithmics, software development in C/C++
– Required: interested in life sciences, eager to work in a team and to collaborate with scientists from other disciplines
– Knowledge of French is not required
– Desired: strong publication record, good communication skills in English.
– Appreciated: experience in High Performance Computing or in genomics analyses
– Offered: good working environment, dynamic team, research budget, access to meso-computing server, opportunities of local and international collaborations with highly qualified life scientists, fantastic region and nice living quality.
** Practical issues
– Duration: 24 months
– Salary: depend on experience, according official salary grid
– Social security and Health insurance are included
– Employer: Université de Montpellier, France
– Institute: Institut de Biologie Computationnelle
– Location: Montpellier, south of France
– contact: E. Rivals, rivals@lirmm.fr
– The official application will be made on the IBC website: http://www.ibc-montpellier.fr/open-positions