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PhD fellowship in Deep Learning for Precisions Psychiatry at Novo Nordisk Foundation Center for Protein Research



A PhD position is available in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research (CPR – The Center has been established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. The Center comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms.

The Programme for Disease Systems Biology (DSB) consists of three research groups covering many systems level aspects of biology and medicine, including large scale analysis of human variation data and integration of molecular-level and healthcare data.
The Human Proteome Variation group ( is part of DSB and led by Simon Rasmussen focus on proteome and genome variation, coding variation and deep learning for integration of genomics, proteomics and clinical data.

Responsibilities and tasks
The PhD will work in a multidisciplinary project team. The candidate will be working as part of the Precision Psychiatry Initiative (PRECISE) funded by the Lundbeck Foundation with close collaborations with Psychiatric Centre Copenhagen. The project aims at developing accurate predictive models from biomedical data to improve clinical decision-making and patient treatment response. A unique aspect of the project is the interplay between big data on a national level and detailed person-level data that will be combined to identify markers predicting cross-diagnostic disease clusters, disease trajectories, treatment response and adverse events in mental disorders.

The candidate will focus on developing deep learning frameworks for integration of diverse biomedical data such as multi-omics, clinical, electronic health record, wearable and registry data. Initially, the models will be based on deep learning such as variational autoencoders that will be used for unsupervised and supervised modeling as well as patient stratification. Furthermore, the models will be used to integrate multiple molecular level datasets and therefore also used to investigate potential molecular mechanisms important for disease progression.

Principal supervisor is Associate Professor Simon Rasmussen, Novo Nordisk Foundation Center for Protein Research; e-mail:, Direct Phone: +45 3533 2159.
Co-supervisor is Head of Research, Senior Researcher Michael Eriksen Benros, Mental Health Centre Copenhagen, Copenhagen University Hospital.

Start date: 1 September 2019.
Duration: 3 years.

Job description
Your key tasks are:

  • Carry through an independent research project under supervision.
  • Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points.
  • Participate in active research environments including a stay at another research team.
  • Obtain experience with teaching or other types of dissemination related to your PhD project.
  • Teach and disseminate your knowledge.
  • Write a PhD thesis on the grounds of your project.

Key criteria for the assessment of applicants
You hold a master or equivalent in computational biology, bioinformatics, data analysis or related discipline of biomedical research. You have preferably experience using machine learning and deep learning models. Programming experience in R and python is required as well as having worked with big data. Research experience within mental health diseases is a plus.

Furthermore, the successful candidate will have experience within some of the following areas:

  • Bioinformatics and systems biology at the molecular level.
  • Experience with registry data.
  • Project management of interdisciplinary research projects within translational bioinformatics.
  • Experience with data structures, databases and data architectures.
  • Knowledge of biomedical resources and infrastructures.

Place of employment
The employment is at CPR (, University of Copenhagen, located in central Copenhagen. The research environment at CPR is ambitious and international, with approx. 30 different nationalities currently represented. The Center comprises modern laboratories, supercomputer resources and state-of-the-art facilities within protein science. Seminars with high-profile international speakers and regular internal research seminars are organized at the Center. The selected candidate should expect some travel activity.

For more information on working and living in Denmark visit (International Staff Mobility) and

Terms of employment
The employment as PhD fellow is full time and for 3 years.

It is conditioned upon the applicant's successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree. Salary, pension and terms of employment are in accordance with the agree¬ment between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary begins at DKK 27,135/approx. EUR 3.642 (April 2019 level) plus pension.

For specific information about the PhD fellowship, please contact the above principal supervisor.
General information about PhD study at the Faculty of Health and Medical Sciences is available at the Graduate School’s website:

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:

  1. Motivated letter of application (max. one page).
  2. CV incl. education, experience, language skills and other skills relevant for the position.
  3. Master of Science diploma and transcript of records. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor will do.
  4. Publication list (if possible).
Deadline for applications: 17 June 2019, 23:59 p.m. CET.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

The Faculty of Health and Medical Sciences comprises approximately 7800 students, 1550 PhD students and 4400 employees. The Faculty advances the field of health sciences through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions benefitting patients and the community. The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.