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PhD in computational disease systems biology
University of Copenhagen
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking
universities, the University of Copenhagen promotes research and teaching of the highest international standard.
Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate
their talent in an ambitious and informal environment. An effective organisation - with good working conditions
and a collaborative work culture - creates the ideal framework for a successful academic career.
PhD in computational disease systems biology
A number of PhD positions are available in the Translational Disease Systems Biology group at The Novo Nordisk Foundation
Center for Protein Research (CPR - www.cpr.ku.dk). The Center was 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 two research groups
covering many systems level aspects of biology and medicine, including the integration of molecular-level data and healthcare
data, for example laboratory test data and biomedical texts.
The Translational Disease Systems Biology group (www.cpr.ku.dk/research/disease-systems-biology/brunak/) part of DSB and led
by Søren Brunak, focuses on establishing early competitive advantages in disease-relevant computational analyses across the
general areas of bioinformatics, chemoinformatics, systems biology and medical informatics.
The PhDs will work in a multidisciplinary project team. One candidate will work in the EU-ToxRisk consortium, a H2020-funded
pan-European research consortium, aiming at delivering strategies to enable reliable animal-free hazard and risk assessment of
chemicals. One goal of the EU-ToxRisk consortium is to integrate advancements in system biology and computational modeling to
define the complex chains of events that link chemical exposure to toxic outcome. Another candidate will work on data-driven
models of temporal disease development using a combination of molecular data and data from the healthcare sector, where the
latter has the form of clinical, registry data or complete electronic patient records. These models will in part be descriptive
and show how different diseases and diagnosis follow each other over long periods and in part predictive in the sense that
longitudinal patterns of illnesses, medication and procedures will indicate future events. The models may be augmented by
molecular level biomarker data from genomics or proteomics further increasing the predictive power. Prior knowledge of
disease classification schemes and standard vocabularies is an advantage.
The candidates will focus on data analysis using computational systems biology methods. The candidates will utilize data
integration, statistical genetics and pathway-based methods to identify novel biomarkers associated to toxicology.
The candidates hold a master degree or equivalent in biology, genetics, statistics, computational biology, bioinformatics or a
related discipline of biomedical research. Preferably, the candidates have experience in statistical genetics, genomics, computational
chemistry and knowledge of R. Programming experience is an advantage as is having worked with big data. Research experience in chemical
toxicology is a plus. Furthermore, the successful candidates have experience within some of the following areas:
Bioinformatics and systems biology at the molecular level
Experience with toxicology
Medicine, pharmacology or genomics
Project management of interdisciplinary research projects within translational bioinformatics
Experience with data structures, databases, and data architectures
Knowledge of biomedical resources and infrastructures
Competences within statistics and/or machine learning techniques
Broad understanding of Healthcare data from national registries and electronic patient records from hospitals
Prior research experience with healthcare terminologies, schemes and ontologies, e.g. ICD9, ICD10, ATC, and SNOMED CT
Experience with CDISC
The translational disease systems biology group is highly multidisciplinary and collaborates with many other research groups
nationally and internationally. Strong networking and team player skills are therefore preferred.
Place of employment and work
The employment is at CPR (www.cpr.ku.dk), 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. The Center organizes seminars with
high-profile international speakers and regular internal research seminars. The selected candidate should expect some travel activity.
Salary and terms of employment
The duration of the positions is three years. It is conditioned upon the candidates´ successful enrollment in the PhD programme.
This requires submission and acceptance of an application for the specific project formulated by the candidate. The PhD study must
be completed in accordance with The Ministerial Order on the PhD programme (2013) and the University’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 around
26,000 DKK (ca. 3.450 EUR) plus 17% pension.
The Danish Ministry of Finance and the Danish Confederation of Professional Associations (AC) have agreed on a protocol that makes
it possible for all international researchers employed by the University to achieve a pension exemption, where the pension will
be paid as salary. For more information about the different pension schemes:
Your application should include the following documents:
1. Motivated letter of application
2. Curriculum vitae, incl. education and experience, publications (if any), language skills and other skills relevant for the position
3. A certified/signed copy of Master of Science certificate. 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. Names and contact details for two referees
Deadline for application: October 31th 2017
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice
of the Appointments Committee. All applicants are then immediately notified whether their application has been passed for assessment
by an expert assessment committee. Selected applicants are notified of the composition of the committee and each applicant has the
opportunity to comment on the part of the assessment that relates to the applicant him/herself.
Assessment: The selected applications will be assessed according to the Ministry Order on the Appointment of Academic Staff at
Universities 2012 and the University of Copenhagen’s guidelines 2013. The Assessment Committee 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