PhD student Translational Bioinformatics
Solliciteer

PhD student Translational Bioinformatics

Jouw functie

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).

Jouw profiel

We seek an ambitious PhD student to proactively tackle the project’s research questions.
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 translational oncology
  • Able to write bioinformatics workflows using Python and R
  • Good communication and academic writing skills

Jouw ontwikkelingsmogelijkheden en arbeidsvoorwaarden

You will join dynamic international research teams both at the Netherlands Cancer Institute and the VU, and will collaborate with scientists with expertise in different disciplines. Your temporary employment will initially be for a period of 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 4 years. The gross salary per month is € 2.798,- to € 3.446 according to the standard PhD scales. The terms of employment will be in accordance with the CAO Ziekenhuizen (Collective Labour Agreement for Hospitals).

For additional information, please visit the VU website:
https://workingat.vu.nl/ad/phd-position-in-bioinformatics-and-oncology/umau0y

Contact informatie

To apply, please also use the VU website:
https://workingat.vu.nl/ad/phd-position-in-bioinformatics-and-oncology/umau0y