Γραφείο Διασύνδεσης & Σταδιοδρομίας

Researchers of the BONSAI team design bioinformatics algorithms and methods with a special interest for biological problems such as the investigation of (i) high throughput sequence processing, (ii) structural RNA, (iii) non ribosomal peptides and their synthetases, and (iv) genomic rearrangements.
Researchers in the BONSAI team have successfully proposed methods in high-throughput sequence methods [Chikhi et al. 2014] and in genomic rearrangements [Darracq et al., 2011, Perrin et al. 2014] (see also our web server bioinfo.lifl.fr). We are looking forward a motivated applicant who will design and implement original algorithms, that will be tested on both simulated and real datasets. The applicant will benefit from the experience of the team and its collaborations. For more information, please visit the team website: www.lifl.fr/bonsai

Description

During the last decade, DNA sequencing has been drastically improved through several new technologies. High-throughput instruments produce a huge number (from millions to billions) of short DNA segments, called reads, very quickly and at a moderate cost. Sequenced reads are much shorter than chromosomes. Algorithms are thus needed to infer the actual genome from the reads.
In this proposal we focus on the analysis of assembly graphs from third-generation sequencing data. We propose the following three research directions. Firstly, via a re-mapping of the reads to the assembly graph, one is in a position to extract meaningful biological information from the graph, e.g. whether contigs were broken down due to lack of coverage or due to a genomic repetition, and furthermore annotate the assembly graph. Secondly, the integration of reference sequences could help in disentangle the assembly graph, in a similar fashion to reference-assisted contigs scaffolding [Kima, J. et al. 2014]. Thirdly, techniques can be developed to properly assemble a population of genomes being sequenced at the same time.

Nr of positions available : 1

Research Fields

Computer science

Career Stage

Early stage researcher or 0-4 yrs (Post graduate)

Research Profiles

First Stage Researcher (R1)

Benefits

• Possibility of French courses
• Help for housing
• Financial support from Inria to catering and transportation expenses
• Scientific Resident card and help for visa
• Catering service
• Monthly salary after taxes: around 1580 € the 1st two years and 1660 € the 3rd year (social security included).