PhD candidate Population Genomics and Epidemiology
- Regio Utrecht
- Vaste aanstelling
- Niet nader bepaald
In this PhD project on the population genomics and epidemiology of Gram-negative bacteria, you will be analyzing high-throughput sequencing data from bacteria collected during the R-GNOSIS ICU study, focusing on the population genomics of E. coli and potential plasmid or other transmission between isolates and patients. The R-GNOSIS ICU study was a clinical trial comparing three infection prevention strategies, two of which used antibiotics, for a period of standard care in intensive care unit patients. The currently available data was used to answer several research questions relating to the transmission of antibiotic resistant E. coli, between both patients and isolates, and at the level of species, chromosomal genes and plasmids, under the different treatment conditions investigated in the trial. In this position, your tasks will be to apply epidemiological methods and bioinformatics tools in a UNIX operating system, present your research, and write scientific publications. You will receive the opportunity to participate in a PhD program run by the Graduate School of Life Sciences at Utrecht University, which includes courses in Computational Life Sciences, Epidemiology and Infection & Immunity, as well as in research skills.
The position is based in the research group run by Prof. Rob Willems at the Department of Medical Microbiology of the University Medical Center Utrecht (UMCU) and will be carried out under the supervision of Dr. Nienke Plantinga (epidemiology) and Dr. Anita Schürch (bioinformatics). 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 HIV, virus-host interactions, bacterial infections and immunity, infectious disease epidemiology, and comparative and functional genomics. The latter theme aims to identify and characterize genes that contribute to the success of antibiotic-resistant opportunistic pathogens that frequently colonize and infect hospitalized patients; the current position falls within this theme.
As the successful candidate for this PhD project, you must have a strong affinity for epidemiology or bioinformatics (or both), and hold a university degree in epidemiology, bioinformatics, medical biology or biology. You should have extensive experience with at least one scripting language (R, Python), and a statistical background. Experience with UNIX operating systems is a plus. You must be fluent in English (both spoken and written) and possess excellent communication and presentation skills, as well as a strong team spirit. You bring with you a high degree of curiosity and enthusiasm, and are more than capable of working and thinking independently.
The maximum salary for this position (100%) is € 3.020,00 gross per month based on full-time employment (work week 36 hours). This job is based on a temporary position for 3 years.
In addition, we offer an annual benefit of 8.3%, holiday allowance, travel expenses and career opportunities. The terms of employment are in accordance with the Cao University Medical Centers (UMC).
Acquisition based on this jobopening is not appreciated.