PhD fellowship on biomedical text mining at the Novo Nordisk Foundation Center for Protein Research

A PhD fellowship is available jointly between the Cellular Network Biology group and the Translational Disease Systems Biology groups at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk).

Before entering the fellowship, the successful candidate will be have an initial employment as Research assistant for 1 year scheduled to start second quarter of 2020.

About CPR
CPR 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. 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.

Our groups and research
The Cellular Network Biology group (www.cpr.ku.dk/research/disease-systems-biology/jensen/) led by Professor Lars Juhl Jensen has strong expertise in text mining of the biomedical literature, whereas the Translational Disease Systems Biology group (www.cpr.ku.dk/research/disease-systems-biology/brunak/) led by Professor Søren Brunak focuses on analysis of many diverse types of patient-level data.

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.

The PhD project
The PhD fellow will develop advanced text-mining methods and apply them to a 20+ million full-text articles to identify life-style descriptors in text and associate them with diseases. In collaboration with other members of the groups, the PhD fellow will subsequently use the resulting knowledge graph to interpret patient-level data on the progression from healthy to sick from electronic health records and registry data.

Principal supervisor is Prof. Lars Juhl Jensen, Novo Nordisk Foundation Center for Protein Research, e-mail: lars.juhl.jensen@cpr.ku.dk.

Start date: Second quarter of 2020.
Duration:   1 year as Research assistant + 3 years as a PhD fellow.

Qualifications and key criteria for the assessment of applicants
Candidates for the fellowship must hold an MSc degree (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.

Other important criteria are:

  • The grade point average achieved.
  • Professional qualifications relevant to the PhD project.
  • Previous publications, relevant work experience, other professional activities.
  • Curious mind-set with a strong interest in biomedical text mining.
  • Good oral and written communication skills in English.

Job description and tasks
During the first year as Research assistant, the candidate will have to formulate a PhD project and apply for enrolment as PhD fellow.

  • During the enrolment and employment as PhD fellow your tasks will be:
  • 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.

Place of employment
The place of employment is at CPR, Faculty of Health and Medical Sciences, University of Copenhagen, located in central Copenhagen. CPR offers creative and stimulating working conditions in dynamic and international research environment. Our research facilities include 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.

Terms of employment
You will be employed as Research assistant for 1 year followed by 3 years as PhD fellow.

The transfer to PhD employment after the first year is conditioned upon satisfying performance and 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 first year as Research assistant.

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 agree­ment 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 27,362/approx. EUR 3,648 (October 2019-level) plus an employer paid pension contribution of 17.1 %.

For international researchers, it is possible to achieve a pension exemption (http://ism.ku.dk/onarrival/pension/). Foreign candidates may also find information on working and living in Denmark on www.ism.ku.dk (UCPH’s International Staff Mobility).

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/.

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).

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.

Application deadline: 1 March 2020, 23.59 p.m. CET.

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 notified whether their application has been passed for assessment by an unbiased assessor. The assessment is according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

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 http://employment.ku.dk/faculty/recruitment-process/.

The Faculty of Health and Medical Sciences comprises approximately 7500 students, 1500 PhD students and 3200 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.

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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.

Deadline: 1 March 2020
Unit: Faculty of Health and Medical Sciences
Campus: Novo Nordisk Foundation Center for Protein Research

Phone:
Read the job description and apply online

Post expires on Sunday March 1st, 2020