In this PhD position at the Netherlands Centre for One Health (NCOH), you will be working in the challenging multi-disciplinary field of bioinformatics, metagenomics and evolutionary microbiology. Your objective will be to develop novel computational methods for reconstructing dissemination networks of mobile genes (including antimicrobial resistance genes) from metagenomic data from the microbial community of food-producing animals, the farming and wider environment, and the human population. You will be writing scientific software in accordance with best practices in reproducible open research, analyzing data, presenting your results, and writing scientific publications. In doing so, you will be working with high-throughput sequencing data in a high-performance computing environment, and collaborating with other researchers involved in the ‘Complex Systems’ NCOH research theme.

As the successful candidate for this PhD project, you must have general experience in bioinformatics and an affinity for microbiology, and hold a university degree in bioinformatics, medical biology or biology. Familiarity with at least one scripting language (Python, R), and the UNIX operating systems is required, as is fluency in both spoken and written English. You must also possess excellent communication and presentation skills. Important qualities include enthusiasm, an inquisitive mindset, self-reliance and flexibility, as well as the ability to work together in teams.

Fixed-term contract: for 4 years.

The maximum salary for this position (100%) is € 3.020,00 gross per month based on full-time employment (work week 36 hours).

University Medical Centre Utrecht

With over 1,100 beds and more than 11,000 employees, the University Medical Center Utrecht is one of the largest academic health care centers in the Netherlands. Our aim is to improve. Our patients’ health, but also our students and employees. Whether you are a doctor or a business economist, a researcher or a SAP-specialist: working with us means having a job that matters, access to the best facilities and the opportunity to grow as a professional and contribute towards innovative health care.

Scientific research at the UMC Utrecht is rooted in the world around us. We listen to people; the wishes and needs of patients come first. Together with our national and international partners, we invest in innovation and research in order to ensure that our care remains of the highest quality. Focus is pivotal in this, which is why we have concentrated our research in six programs:

• Brain
• Infection & Immunity
• Circulatory Health
• Personalized Cancer Care
• RM & Stem Cells
• Child Health

http://www.werkenbijumcutrecht.nl/

The department

The position is based in the research groups run by Dr. Anita Schürch and Prof. Rob Willems at the Department of Medical Microbiology of the University Medical Center Utrecht (UMCU). The Department of Medical Microbiology is responsible for infectious disease diagnostics (bacteriology, virology, serology, mycology and parasitology), clinical microbiological consultancy, and infection prevention at the University Medical Center Utrecht. The department also plays an important role in teaching and training medical doctors, PhD candidates and undergraduate students, and performs research in a variety of fields including comparative and functional genomics to identify and characterize genes that contribute to the success of antibiotic-resistant opportunistic pathogens that frequently colonize and infect hospitalized patients.