PhD Position in Developing a Federated Metadata Repository for Clinical Data

The Department of Mathematics and Computer Science at the University of Southern Denmark for the Computational Biology group chaired by Associate Professor Richard Röttger and Novo Nordisk jointly invite applications for a PhD position for the creation of a federated metadata repository for sensitive clinical data to be filled as soon as possible.

A large roadblock of medical research is the difficult access to sensitive data which therefore hinders the training of complex and powerful machine learning concepts. This issue is amplified when considering rare diseases with low incidence numbers per hospital. In order to enable the identification of suitable patients for clinical studies amenable to machine learning, a privacy-preserving metadata repository is required. Here, the actual patient data remains at the site of storage, but virtual cohorts can be identified according to clinical phenotypes, symptoms, or diagnoses. Crucially, the data must remain at the site of storage and must not leave the site, not even in anonymized form.

Therefore, the main task of the successful candidate will be the development and establishment of such a system, including user-friendly front-end and the required back-end. The central idea should be the storage and organization of pre-computed aggregate statistics of the connected and the support of on-the-fly queries to the storage sites to answer new queries to the metadata repository. The envisioned system should be developed following industry best practices in terms of code flexibility, reusability, and deployment in containerized form.

The position itself is part of the European IMI project Screen4Care. In this project, 35 international partners from private and public sectors are working together to shorten the path to treatment of rare disease patients. The envisioned metadata repository will for the backbone of the project be to enable all partners to share data (without actually physically sharing data) and conduct advanced computational analyses.

The successful candidate will be jointly supervised by the University of Southern Denmark and Novo Nordisk. The candidate will gather research as well as industrial experience through the close collaboration between SDU and Novo Nordisk. The candidate will spend time at both facilities and ensure that the ongoing research maximizes utility and impact due to its clinical and practical relevance. We also provide the candidate with direct access to state-of-the-art computing facilities optimized for deep learning and distributed computing.

We are seeking outstanding candidates with strong analytical and problem solving skills, who are strong in written and oral communication (in English), and have documented experience in the development of complex compute systems. The applicant should have provable skills in the state-of-the-art web-development frameworks, virtualization techniques as well as database technologies. Expertise in clinical data science and machine learning, as well as computer security and data privacy are welcome.

Place of work:
Computational Biology Group (Associate Professor Richard Röttger, [email protected]), Department of Mathematics and Computer Science, located at the main campus of the University of Southern Denmark, Odense, Denmark.

Novo Nordisk is a leading global healthcare company, founded in 1923 and headquartered in Denmark. Our purpose is to drive change to defeat diabetes and other serious chronic diseases such as obesity and rare blood and endocrine disorders. We do so by pioneering scientific breakthroughs, expanding access to our medicines, and working to prevent and ultimately cure disease. Novo Nordisk employs about 45,800 people in 80 countries and markets its products in around 170 countries.


Application, salary etc.
Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

The successful applicant will be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application must be made in the form of a Declaration of Interest and must include the following documents:
• A research proposal/description of your approach to the above project (max one page excluding references)
• A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form")
• Detailed CV, including personal contact information
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Further information for international applicants about entering and working in Denmark.