Researcher in Epidemiology and Machine Learning

DTU Fødevareinstituttet
mandag 08 apr 19

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Frist 29. april 2019
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The National Food Institute (DTU Food) seeks a candidate for a researcher in epidemiology and machine learning, within the area of combining next generation sequencing data (whole genome and metagenomics) with unstructured and high-dimensional explanatory data for studying local and global evolution, virulence, microbial risk assessment or source attribution and transmission of antimicrobial resistance and different, mainly foodborne, bacterial species.


The researcher will be affiliated with the Research Group for Genomic Epidemiology, which has the primary task of conducting targeted research with the aim of predicting and preventing infectious diseases in humans and animals, and supporting global detection, surveillance and control. The group provides advisory service to the Danish Food Authorities on detection of foodborne outbreaks. The research group is an EU reference laboratory for antimicrobial resistance. The research combines expertise in conventional and molecular microbiology with epidemiology and bioinformatics

The position as researcher is a permanent entry-level position.

The Research Group for Genomic Epidemiology provides advisory service on the use of whole genome sequencing for pathogen detection and characterisation including sharing of data and outbreak detection to the Danish Food Authorities, EU, WHO and FAO.

The group is also, engaged in several projects and partner collaborations globally, where we aim to understand the emergence and transmission of AMR, burden of foodborne diseases and socio-economic factors associated therewith.


An important objective is advance the groups competences in use of advanced mathematical methodologies (i.e. machine learning) for determining associations between for example prevalence of AMR and diseases or presence of virulence factors and relations to epidemiological data.

The researcher’s main responsibility will be to use epidemiological and machine learning methodologies to analyse and interpret sequencing and other epidemiological data from various, mainly bacterial isolates or metagenomes, assist in global capacity building projects and provide assistance, including development of training for sharing and analysing such data.

Responsibilities and tasks
  • Your main responsibility will be to develop and use novel methodologies for analysing and interpreting biological data in combination with multiple explanatory variables.
  • You will accomplish this by performing research into the use of machine learning methods for identifying and predicting emergence, transmission and survival of bacterial isolates and single genes based on available epidemiological or phenotypic data and setting up relevant analytic pipelines.
  • You will communicate research results by presenting data at project meetings and international conferences, and write reports and manuscripts for publication.
  • You will engage in the general advisory service carried out by the research group, including continuous advice to the Danish Veterinary and Food Administration and international organizations.
  • You will assist in training, capacity building and development of online teaching tools, including eLearning.

The ideal candidate:

  • Holds a PhD degree within the fields of microbiology, epidemiology or related disciplines.
  • Has documented experience with analysing NGS data in combination with epidemiological data using advanced mathematical modelling such as machine learning.
  • Preferably, has experience with foodborne diseases and advisory service, as well as capacity building though courses and eLearning.
  • Has experience from capacity building in low and middle income countries.
  • Is able to work independently and able to plan and carry out complex tasks, while also having the ability to engage constructively and positively in a large, international and cross-disciplinary research group.
  • Has good English communication skills, oral and written.
  • Is ambitious and has a strong drive for obtaining high-quality results

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 academic freedom tempered by responsibility.

Salary and terms of employment

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 position as researcher is a permanent entry-level position. After a maximum of 4 years, a researcher can be promoted to a senior researcher position after assessment. More information can be found here: Career paths at DTU.

Further information

Further information may be obtained from Professor Frank M. Aarestrup,, +45 3588 6281.

You can read more about the Genomic Epidemiology Research Group at

Application procedure

Please submit your online application no later than 29 April 2019 (local time).


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:

  • Application (cover letter)
  • CV
  • Views regarding teaching and research, based on the “Assessment” bullets
  • Documentation of previous teaching and research based on the “Assessment” bullets
  • List of publications
  • H-index, and ORCID (see e.g.
  • Diploma (MSc/PhD)

 Applications and enclosures received after the deadline will not be considered.


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


DTU Food (The National Food Institute, Technical University of Denmark) works within six technical focus areas: Biotechnology, nutrition, food quality, food safety, food technology and environment & human health. Activities cover a wide range of food products throughout the entire food chain from farm to table, comprising both research activities and research-based consulting and teaching. 

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 6,000 advance science and technology to create innovative solutions that meet the demands of society, and our 11,200 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.