PhD position in Bioinformatics and Oncology

    Vrije Universiteit Amsterdam (VU)
    First Stage Researcher (R1)
    17/12/2019 11:18 - Europe/Brussels
    Netherlands › Amsterdam

We are looking for a PhD student in the field of translational bioinformatics. The project aims to detect chromosomal breakpoints with impact on colorectal cancer. Colorectal cancer (CRC) is caused by genomic alterations such as point mutations, DNA copy number aberrations and structural variants, the latter comprising deletions, insertions, inversions, and intra- and inter- chromosomal translocations, all of which involve chromosomal breaks. The impact of recurrent chromosomal breaks in CRC has been poorly characterized (van den Broek et al, 2015). This project will use advanced bioinformatics analyses and machine learning techniques to characterize recurrent breakpoint genes in more detail, in order to improve molecular DNA-based classification and thereby stratification of CRC patients for early diagnosis, prognosis and therapy prediction.

The computational challenge is to detect relevant breakpoints while filtering the experimental and biological background signal. The aim of this project is to use advanced machine learning techniques to characterize recurrent breakpoint genes in more detail, in order to detect those events with a direct impact on the tumor. By learning over multiple molecular and clinical data sources, we hope to improve molecular DNA-based classification and thereby stratification of CRC patients for early diagnosis, prognosis and therapy prediction. Our long-term goal is to implement detection of SVs with diagnostic, prognostic and/or predictive value into clinical care to improve disease management of CRC patients.

This is a collaborative project lead by Remond Fijneman (NKI, Translational Gastrointestinal Oncology group; head Gerrit Meijer) and Sanne Abeln (VU University, dept. of Computer Sciences, bioinformatics section; head, Jaap Heringa).

Your duties

  • Analyzing large omics data sets
  • Applying machine learning methods to heterogeneous datasets
  • Developing methods to detect high resolution breakpoints
  • Perform complex statistical analysis
  • Communicate your work with both biomedical researchers and computer scientists
  • Teaching computer practicals to MSc students (<5% fte)


A challenging position in a socially involved organization. The salary will be in accordance with university regulations for academic personnel and amounts €2,325 (PhD) per month during the first year and increases to €2,972 (PhD) per month during the fourth year, based on a full-time employment. The job profile: is based on the university job ranking system and is vacant for at least 1 FTE.

The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 4 years.
Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:

  • a maximum of 41 days of annual leave based on full-time employment
  • 8% holiday allowance and 8.3% end-of-year bonus
  • solid pension scheme (ABP)
  • a wide range of sports facilities which staff may use at a modest charge

Additional comments

Are you interested in this position? Please apply via the application button and upload your:

  • curriculum vitae (CV)
    • highlighting research experience
    • including two references we may contact
  • cover letter (CL)
    • including a motivation for this PhD position
    • explaining ho you fulfil the requirements for this position
  • BSc and MSc academic transcripts
    • containing all your grades at university level

The application deadline is 31 January 2020. The job interviews are planned for the middle of February, when possible please take them into account when applying for the position.

Applications received by e-mail will not be processed.

Vacancy questions
If you have any questions regarding this vacancy, you may contact:

Name: Caroline Waij
E-mail: informatica.secretariaat.few@vu.nl

No agencies

Web site for additional job details

Offer Requirements

Specific Requirements

  • An MSc degree in Bioinformatics, computational biology or an MSc degree in the Life Sciences, with a specialization in Bioinformatics
  • A strong interest in biomedical research and oncology
  • Able to write bioinformatics workflows using Python and R
  • Good communication and academic writing skills

Map Information

Job Work Location Personal Assistance locations
Work location(s)
1 position(s) available at
Vrije Universiteit Amsterdam (VU)
1081 HV
De Boelelaan 1105

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EURAXESS offer ID: 419765
Posting organisation offer ID: 284109


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