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  3. PhD candidate in Computational Proteomics and Applied Machine Learning

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PhD candidate in Computational Proteomics and Applied Machine Learning

The Tissue Proteomics group of the Van't Hoff Institute for Molecular Sciences (HIMS) is looking for a PhD candidate in Computational Proteomics and Applied …

4 maanden geleden


Spui, Amsterdam, Noord-Holland
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
38 uur
€ 2325 - € 2972 per maand


The Tissue Proteomics group of the Van't Hoff Institute for Molecular Sciences (HIMS) is looking for a PhD candidate in Computational Proteomics and Applied Machine Learning in Kidney Transplantation.

Renal transplantation is the preferred treatment for end-stage kidney disease worldwide, which unfortunately requires life-long medication to suppress the development of rejection. These medicaments have serious side-effects and in some patients they are less effective at treating rejection than anticipated. The cornerstone of current transplant diagnostics is biopsy. Biopsies taken from the transplant are analyzed by a pathologist, who is a medical specialist trained at pattern recognition. Over the past years, new methods to aid pathologists at better performing these difficult classification tasks have been emerging, of which the most important is the use of machine learning algorithms for pattern recognition. Machine learning algorithms are interesting tools to integrate various data sources (modalities), which include clinical data, patterns derived from deep neural network analysis of digitized biopsies and molecular data, including data from tissue proteome and transcriptome analysis. Such multimodal integrated algorithms will form the solid basis for personalized treatmentadjustment, outcome prediction and clinical patient management.

The DEEPGRAFT project is a multidisciplinary collaboration between the Van ‘t Hoff Institute for Molecular Sciences (HIMS), the Amsterdam UMC, the UMC Utrecht and the UvA Informatics Institute, subsidized by the Dutch Kidney Foundation. The projecte combines expertise from domains of clinical medicine, immunology, artificial intelligence and systems biology to demonstrate that integrated data analysis can be used to predict kidney transplant outcomes. You will be working in a multidisciplinary environment to perform both “wet-lab” and “dry-lab” experiments. Responsibilities include the development and application of novel high-throughput proteomics assays on kidney biopsy material (including SWATH-MS) and the application of state-of-the-art statistics and machine learning applications. The goal is to create a multimodal multitasking algorithm that can be applied in the clinical setting. The project has a high analytical and computational character and due to the multidisciplinary approach, an experimental and flexible yet structured mindset is a necessity.


What do we require of you?

  • A master’s or equivalent degree in a relevant field (Life Sciences, Systems Biology, Computational Biology, Artificial Intelligence);
  • working knowledge on relevant programming languages (Python, R, Bash, etc.);
  • affinity with translational research, analytical validation and complex systems modelling;
  • ability to work both independently and as a team member;
  • good communication skills in English.

Experience with mass spectrometry and proteomics is preferred.

If you have not finished your master’s studies yet, you can still apply. In exceptional cases the starting date of your PhD can be extended until after you obtain your MSc degree, but must start in 2019.

Applicants with an MD or those who would like to pursue an MD/PhD, if the mathematical and programming background is sufficiently developed, are encouraged to apply.


The desired start date of the project is as soon as possible, but excellence prevails over starting date.

The full-time appointment will be on a temporary basis for a maximum period of four years (18 months plus a further 30 months after a positive evaluation) and should lead to a dissertation (PhD thesis). An educational plan will be drafted that includes attendance of courses and (international) meetings. Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2,325 in the first year to €2,972 in the final year, according to the Dutch salary scales for PhD candidates. This is excl. 8% holiday allowance and 8,3% end of year bonus. The Collective Labour Agreement of Dutch Universities is applicable.

Additional information

For further information, e.g. suitability of your background studies, please contact:


You may apply using this link. Please upload the following information in a single PDF file (not zipped):

  • cover letter/letter of motivation (at most 1 page), why did you choose to apply for this position;
  • CV, including list of publications and academic transcripts and/or diplomas;
  • the names and contact details (email and telephone numbers) of two academic references.

We will recruit until the position is filled. The selection process commences immediately, but will close when a suitable candidate has been found, even if this prior to the final date of the application window.