[BBC] Bioinformatician, Division of Clinical Infectiology, Faculty of Veterinary Medicine of Utrecht University

[Berend Snel]

Bioinformatician (1,0 fte)
*Functie*

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.


*Profiel*

   - 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.


*Aanbod*

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
<http://www.uu.nl/en/informationfor/jobseekers/working-for-utrecht-university/terms-of-employment/pages/default.aspx>.
Conditions are based on the Collective Labor Agreement of the Dutch
Universities.

*Over de organisatie*

Utrecht University <http://www.uu.nl/En/Pages/default.aspx> 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
<http://www.uu.nl/faculty/veterinarymedicine/en/Pages/default.aspx>
(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

*Aanvullende informatie*

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

Please do *NOT *send your application to these addresses.

*Solliciteren*

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

     *Reageren uiterlijk*  13/07/2014
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