Bioinformatician (1,0 fte)

As a bioinformatician in the Division of Clinical Infectiology (KLIF) of the Department of Infectious Diseases & Immunology, your main job is applied bioinformatics. You work in a research team with molecular microbiologists and veterinarians with focus on the genomics of selected pathogens (in particular Campylobacter and Staphylococci) and on the analysis of complex microbiota (nose and gut) in relation to colonization and environmental cues (e.g. antimicrobial usage). Genomic approaches are considered to be applied in our routine diagnostic microbiology in close collaboration with the University Medical Center Utrecht.

Your main task as bioinformatician will be to set up and implement existing tools and pipelines for analysis of high-throughput scale next-generation sequencing (NGS) of bacterial genomes with focus on bacterial environmental adaptation and dissemination of antibiotic resistance among bacterial populations. The NGS-based analysis includes phylogenetic reconstructions, estimations of mutation rates, detection of gene gain / loss and single nucleotide positions, gene annotation and the identification of mobile genetic elements, such as drug-resistant plasmids. Metagenomic and metatransciptomic analysis of the microbiota during colonization and environmental pressure requires computational analysis of sequence data to characterize ecological communities and identify the flow of resistance genes. You will assist in the design of sequencing experiments catered to the research projects, and in the development of new tools for mining, analyzing and visualizing sequence data. You will advise the team on the use of bioinformatics in running projects, and will be given the possibility to explore and develop own research ideas

The position will be linked to the ‘Evolutionary Genomics and Integrative Bioinformatics’ group of Theoretical Biology & Bioinformatics. The Division has a close collaboration with the bioinformaticians of the department of Medical Microbiology of the UMC Utrecht.

• A PhD in microbiology with a proven strong affinity for bioinformatics and hands-on programming experience. Alternatively, you hold a PhD in bioinformatics or computer science with proven experience in solving microbiological questions.
• Experience with Linux command line and programming languages such as Python, Perl, C, or Java are required.
• Experience with Next-Generation Sequencing data, preferably in the context of microbial genomics is recommended.
• Experience with large-scale data management or data visualization is recommended.
• You are a dedicated and flexible team player with excellent communicative skills to work with scientists from different domains.

We offer a position of 1.0 fte initially for a period of two years with possibilities for extension and potentially a permanent position. The gross salary depends on qualifications and experience and ranges between € 3.259,- and € 5.070 per month for a full time employment of 38 hours per week. The salary is supplemented with an annual holiday pay of 8% and an end-of-year bonus of 8.3% per year. Additionally, we offer a pension scheme, a collective health insurance and flexible employment conditions. Conditions are based on the Collective Labor Agreement of the Dutch Universities.

Utrecht University has great ambitions for its teaching quality and study success rates. This also applies to its clear research profiles which are centred around four themes: Sustainability, Life Sciences, Youth & Identity, and Institutions. Utrecht University plays a prominent role in our society and contributes to finding the answers to topical and future societal issues and is the only Dutch university and in fact the only university in continental Europe in the Times Higher Education Ranking of the Top 50 Social Sciences Universities 2012/2013.

The Faculty of Veterinary Medicine of Utrecht University (FVM-UU) is the only Veterinary School in the Netherlands and belongs to the international top in education, research and patient care. FVM-UU is one of the few European veterinary schools accredited by the American and Canadian Veterinary Medical Associations.

The faculty employs approximately 800 veterinarians, scientists and support staff and counts 1,500 students. Detailed information about the FVM-UU and Utrecht University is available via the website www.uu.nl

For more information about this position, please contact Dr Birgitta Duim: b.duim@uu.nl, telephone: +31 30 253 3603 or Prof Dr Jaap Wagenaar: j.wagenaar@uu.nl, telephone:+31 30 253 4376.

Please do NOT send your application to these addresses.

Please send your application accompanied by a letter of motivation, a curriculum vitae and the names of at least two persons to be contacted for professional reference. You can apply via http://www.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?PortalID=4063&VacatureID=671919