PhD scholarship in Infectious Diseases and Whole Genome Sequencing

DTU Food
Monday 12 Mar 18

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Apply no later than 26 March 2018
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The National Food Institute (DTU Food) seeks a qualified candidate for a vacant PhD position to work in the area of using studying clinical and ecological relevant phenotypes combined with whole genome sequencing of pathogenic bacteria.

The PhD student will be affiliated with the Research Group for Genomic Epidemiology, which studies medically relevant and foodborne microorganisms using whole genome and whole community sequencing for surveillance and outbreak detection. The research group is EU and WHO reference laboratory for antimicrobial resistance and genomics, and combines expertise in conventional and molecular microbiology with bioinformatics and epidemiology. The GenEpi group is, together with several partners worldwide, developing a global real-time system for surveillance and diagnostics of infectious diseases and antimicrobial resistance (,, and being able to predict relevant phenotypes, such as antimicrobial resistance, persistence, virulence and survival based on sequencing information is one of the key activities.

Responsibilities and tasks
The ideal candidate combined a background in classical microbiology with experience in whole genome sequencing and bioinformatics. Preferably, the candidate has experience with laboratory characterisation of bacteria, including antimicrobial susceptibility testing, as well as DNA-sequencing and the bioinformatics analyses. The preferred candidate is ambitious, has a strong drive for obtaining high-quality results and is interested in working in an international research environment. The candidate should be able to work independently and be able to plan and carry out complex tasks while also becoming well integrated into a large and dynamic research group.

Specifically, the PhD project aims at investigating whether it based on whole genome sequencing information is possible to predict relevant phenotypes, such as antimicrobial resistance and persistence or survival in the environment. The focus will be on human clinical isolates from hospitals as well as Listeria monocytogenes survival in the environment.

The day-to-day work will be performed in close collaboration with other researchers in the Research Group for Genomic Epidemiology.

Candidates should have a master's degree in engineering or a similar degree with an academic level equivalent to the master's degree in engineering.

Approval and Enrolment
The scholarships for the PhD degree are subject to academic approval, and the candidates will be enrolled in one of the general degree programmes of DTU. For information about the general requirements for enrolment and the general planning of the scholarship studies, please see the DTU PhD Guide.

The assessment of the applicants will be made by Senior Scientist Rene S. Hendriksen, and Professor Frank Aarestrup.

In the assessment of the applicants, special emphasis will be put on:
  • Experience with laboratory work
  • Experience with NGS sequencing and analyses
  • Ability to work in an interdisciplinary and international research environment
The candidates should have a strong interest for health surveillance, and combining microbiology, bioinformatics, epidemiology and genomics.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and an academic freedom tempered by responsibility.

Salary and appointment terms
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed with the relevant union. The period of employment is 3 years.

The PhD student is expected to spend 3-6 months at a collaborating institution in another country.

Further information
Further information may be obtained from Senior Scientist Rene S. Hendriksen, +45 3588 6288 or Professor Frank M. Aarestrup, +45 3588 6281.

You can read more about the National Food Institute on

Please submit your online application no later than 26 March 2018.

Applications must be submitted as one pdf file containing all materials to be given consideration. To apply, please open the link "Apply online," fill in the online application form, and attach all your materials in English in one pdf file. The file must include:

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Grade transcripts and BSc/MSc diploma
  • Excel sheet with translation of grades to the Danish grading system (see guidelines and excel spreadsheet here)

Candidates may apply prior to obtaining their master's degree, but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 5,800 advance science and technology to create innovative solutions that meet the demands of society; and our 11,000 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government, and public agencies.
25 MARCH 2018