4 year PhD scholarship
Flexible bioinformatics pipelines for the integration of genotype-to-phenotype experiments
Where: Genetics department & Groningen Bioinformatics Center, University Medical Center Groningen, Netherlands
Apply: To m.a.swertz@rug.nl before November 6st, 2009
Start: Before December 31st, 2009
Summary:
Most (disease) phenotypes have a complex inheritance. Integrated analyses of (i) high-throughput sequencing, genotype, transcript, protein, metabolic and phenotypic/clinical profiling data, (ii) use of model organisms such as mouse and worm, and (iii) integration of background information from literature and public database show much potential to unravel these genome-to-phenotype trajectories.
This exciting project will (i) define minimal parameters, models, algorithms and tools for the efficient generation of (ii) flexible “cyber infrastructures” to pipeline far greater volumes of experimental, functional and network data on human and mouse than can be achieved using manual analysis (iii) to pinpoint genes and molecular networks underlying complex phenotypes at significantly increased accuracy and reduced effort. You will build on novel "model-driven strategies" to generate the necessary software efficiently (Swertz, Nature Reviews Genetics, 2007), minimal models and ontologies for integrated representation of all these types of data (e.g. http://www.xgap.org, http://www.ebi.ac.uk/EFO), and a suite of open source software for the integration of data and tools (e.g. http://www.molgenis.org).
The ideal candidate has an MSc in bioinformatics, computer science, molecular biology, computational biology, artificial intelligence or a related field, proven interest in biology and bioinformatics, a strong programming background and excellent English communication skills. This bursary grant is guaranteed for 4 years at approximate € 1500 euro/month with an evaluation after one year.
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