Postdoc position on biomedical text mining at the Novo Nordisk Foundation Center for Protein Research
A postdoc position is available jointly between the Cellular Network Biology and the Translational Disease Systems Biology groups at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). The Center was established in 2007 at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. It comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms. The Disease Systems Biology program consists of three research groups covering many systems level aspects of biology and medicine, including the integration of molecular-level data and healthcare data, including biomedical texts.
Responsibilities and tasks
The Cellular Network Biology group (www.cpr.ku.dk/research/disease-systems-biology/jensen/) is led by Lars Juhl Jensen, a leading expert on literature mining and network-based biomedical data integration. The Translational Disease Systems Biology group (www.cpr.ku.dk/research/disease-systems-biology/brunak/) is led by Søren Brunak, a pioneer in the biomedical sciences focusing on new computational strategies for analysis of patient-level data.
To address the challenging task of extracting information on lifestyle from text, we have developed a prototype lifestyle-factor ontology. You will train state-of-the-art deep learning-based language models to identify lifestyle descriptors, such as diet, from one of the large biomedical text collections comprising millions of full-text articles. Subsequently you will use it in combination with existing pretrained models and vocabularies to resolve cases of ambiguity, extract associations between diseases and lifestyle factors, and construct an open publicly available knowledge graph from the results.
In collaboration with other members of the groups, you will also use cross-lingual representation learning to identify lifestyle factors in text from Danish electronic health records. Furthermore, you will use the literature-based knowledge graph to interpret patient-level data on the progression from healthy to sick from electronic health records and registry data.
Projected start date: Second quarter of 2021.
Candidates for the postdoctoral positions must hold a PhD degree in bioinformatics (or equivalent) within a relevant discipline and have strong programming experience. The successful candidates will have strong qualifications or experience within several of the following areas:
- Text mining
- Bioinformatics / computational biology
- Machine learning
- Statistical data mining
- Biomedical ontologies
- Programming in Python
Both research groups are highly multidisciplinary and international. Members are expected to collaborate both within the group, within the center, nationally, and internationally; strong networking and team player skills are therefore valued.
Place of employment and work
The employment is at CPR (www.cpr.ku.dk), Faculty of Health and Medical Sciences, 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 www.ism.ku.dk (International staff mobility) and www.workingconditions.ku.dk.
Salary, pension and terms of employment will be in accordance with the agreement between the Ministry of Finance and The Academics Central organization. Currently, the monthly salary is around 34,650 DKK / approx. 4,640 € (April 2020-level) plus 17.1 % in pension contribution. Depending on qualifications, a supplement may be negotiated.
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: https://ism.ku.dk/onarrival/pension/
Duration: 2 years with possibility for extension
Your application should be submitted electronically to:
Only applications sent through this link will be accepted.
Your application should include the following documents:
1. Motivated letter of application
2. Curriculum vitae, incl. education and experience
3. Copy of diplomas/degree certificate(s)
4. List of publications
Deadline for application: March 15th, 2021
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. You can read about the recruitment process at http://employment.ku.dk
For further information about the position or the process, please contact CPR: firstname.lastname@example.org
CPR and the University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of personal background.
Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.