PhD Student ‘Genomics based Prediction Models’ (36 hours)
Epidemiology and Biostatistics, VU University medical center, Amsterdam
How can we find better diagnostics markers for early stages of cancer?
The project
How can we find better diagnostic markers for early stages of cancer? How can we better predict which therapy is best for which patient? We aim to develop a novel methodological and computational framework that improves the selection of predictive biomarkers from cancer genomics data.
Your job
Your job is to adapt known prediction methods (e.g. penalized regression, random forest, spike-and-slab models) to allow for the inclusion of (big) ‘co-data’: auxiliary information on the genomic variables (e.g. genes). Examples are p-values from related external studies or data from cancer cell lines. This should lead to ‘weighted learners’.
The challenge is to determine those weights in an automatic and objective way. Collaborators in oncology will support us with data and biomedical know-how. You will apply our approach to several tumor types for the purpose of i) Cancer diagnostics based on body fluids and specimens, in particular for oral and cervical (pre)cancer; ii) Prediction of therapy response, in particular response to chemotherapy in neo-adjuvant breast cancer and metastatic colorectal cancer. You will finalize the research with a PhD thesis.
Job requirements
We are looking for a PhD student with the following experience and background:
- You hold an MSc in Statistics, Mathematics, Bioinformatics or a closely related discipline;
- You have a strong background in quantitative modeling enabling the development of new computational and/or statistical methods;
- You have programming skills, preferably in R;
- You are able to explain complex ideas to biologists/non-specialists;
- Knowledge of any of the areas involved in the project (such as penalized regression models, supervised machine learning) are an advantage;
- You have good communication skills, you are self-disciplined and can work in a multi-disciplinary environment.
Terms of employment
Salary scale OiO: EUR 2.224 gross/month which increases yearly to EUR 2.874 gross/month in the fourth year. In addition to an excellent basic salary we offer among secondary terms of employment an end-of-year bonus of 8.3% and a holiday allowance of 8%. For more information on our terms of employment see: https://www.werkenbijvumc.nl/arbeidsvoorwaarden/
For Dutch nationals, a VOG (Verklaring Omtrent Gedrag) is mandatory.
Additional information
See www.bigstatistics.nl for more information on the group. The project is granted by the The Netherlands Organisation for Health Research and Development (ZONMW-TOP). It is a collaboration with the Netherlands Cancer Institute & Delft University of Technology (prof. dr. Lodewyk Wessels).
Interested?
For any questions regarding the project, you can contact prof. dr. ir. Mark van de Wiel at telephonenumber +31(0)20 – 444 5405. For more information about the application procedure, please contact mr. Wessel Haytink at telephonenumber +31(0)20 – 444 5635.
You can apply online with reference number D6.2017.00024WH via the following link: http://bit.ly/PhDGenomics
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