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PhD position in pancreatic cancer bioinformatics

Department of Biology
Faculty of Science
University of Copenhagen

Department of Biology, Faculty of Science at University of Copenhagen is offering
1 PhD scholarships in Marie Sklodowska-Curie Actions Innovative Training Networks on
pH and Ion Transport in Pancreatic Cancer (pHIoniC) from October 2019

Scientific environment
This pHIonic training network is financed by the European Commission Horizon 2020. The project is a collaboration between 10 academic and 3 industrial partners from 7 European countries. The consortium brings together highly synergistic expertise in the field of ion transport and cancer research.

Our focus is on pancreatic ductal adenocarcinoma (PDAC), which is rising in incidence and is so far incurable. The programme’s central idea is that the unique pancreatic microenvironment contributes to disease development and progression. The programme has a strong grounding in the physiology of acid/base transport in the exocrine pancreas and it develops new concepts and tools in the cancer field and beyond. Jointly, pHioniC will map pH landscape in normal and diseased pancreas, characterize the impact of the acidic microenvironment on PDAC development, and apply drug/nanocarrier/antibody designs for targeting of tumors. For further details of the network, please visit

pHioniC will provide training and collaborative network and structured PhD programme. The training will cover the fields of ion transport, oncology, imaging, bioinformatics and antibody technology, extensive transferable skills and personalized training elements.

The specific PhD project will be within Prof Sandelin’s group at the Bioinformatics Centre at University of Copenhagen. The group is a world leader in medical transcriptomics and gene regulation biology. Examples of our work include promoter-based classification of inflammatory bowel disease (Nat Commun. 2018 9(1):1661), enhancer transcription (Science 2015 347(6225):1010-4) and the creation of enhancer atlases across human cell types (Nature. 2014 507(7493):455-461)

Project description: Relation and causality between pH homeostasis and driver mutation generation in PDAC development
We hypothesize that acidic conditions synergize with PDAC mutations to drive PDAC development. An outstanding question is the causality between the two: are PDAC driver mutations more easily generated in an acidic environment, or is their ability to drive PDAC development increased due to the acidity. The experiments will be based on exposing organoid cultures that carry one, two or none of the typical PDAC driver mutations to acid conditions, and then assess changes in RNA response (RNA-seq) and generation of new mutations. This is a collaboration with another PhD in the training network, who will also assess cell phenotypes in parallel.

Principal supervisor is Prof. Albin Sandelin, Section for Computational and RNA Biology,, Phone: +45 353-21285

Who are we looking for?
Marie Curie Training Networks offer a unique opportunity to get cutting-edge training in a multidisciplinary environment with a focus on academic and personal development of the PhD fellows. The supervisors in the network each provide specific competences and as part of the network you develop your skills and carry out research both independently and as part of a network of 15 PhD fellows. The consortium ensures exchange of ideas through network-wide training events, summer schools and intersectoral secondments. As a PhD fellow in the pHIoniC network, you need to have good social skills, be innovative and goal-oriented and be willing to conduct the planned secondments.

Formal requirements
Applicants should hold, or be close to completing, an MSc in Bioinformatics or related fields. In particular, we require that candidates can program in a script language (e.g. Python) and R, and have experience in analysing high-throughput sequencing data in R and unix systems. Knowledge of statistics, cancer biology and genetics are considered great advantages. Excellent command of spoken and written English is required. As criteria for the assessment of your qualifications, emphasis will also be laid on previous publications (if any) and relevant work experience.

Job conditions
The PhD student will be appointed under a 3-year employment contract with a competitive salary and mobility allowance at the host institution. The fellow is expected to start on 1. October 2019. The PhD student will be enrolled in the PhD program of the Faculty of Science, University of Copenhagen, with the specific intent that it results in a PhD degree and scientific publications.

Job description
The position is available for a 3-year period. Your key tasks as a PhD student at SCIENCE/pHIoniC network are.

  • To manage and carry through your research project
  • Attend PhD courses both within and outside the pHIoniC network
  • Write scientific articles and your PhD thesis
  • Participate in international congresses and pHIoniC network meetings
  • Stay at the research institutions abroad for the secondments
  • Teach and disseminate your research

EU eligibility criteria for candidates
  • The applicant may be of any nationality but in order to be eligible for the positions the following criteria applies to all applicants:
  • The applicant shall at the time of recruitment be eligible as an Early Stage Researcher (ESR) by being in the first four years of his/her research career (after finishing of Masters degree) and not have been awarded a doctoral degree.
  • The applicant must not have resided or carried out his/her main activity in the country of the host institute for more than 12 months in the 3 years immediately prior to the recruitment.

Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.
Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.
The starting salary is currently at a minimum DKK 312.879 including annual supplement (+ pension up to DKK 43.219). Negotiation for salary supplement is possible.

Application procedure
The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include
Cover Letter, detailing your motivation and background for applying for the specific PhD project (max. 2 pages)
CV (max. 2 pages) including a list of publications (if any)
Summary of last degree thesis (1 page)
Diploma and transcripts of records (BSc and MSc)
Two references and full contact details (name, address, telephone & email) of professional referees

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

The deadline for applications is 15 June 2019, 23:59 GMT +1.

Applications received after the deadline for applications will not be considered.
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.

The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science. You can read more about the recruitment process at General information about PhD programmes at SCIENCE is available at

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