PhD candidate in Computational Proteomics and Applied Machine Learning

Updated: 3 months ago
Deadline: 01 Mar 2019

Faculty of Science – Van 't Hoff Institute for Molecular Sciences
Publication date
22 January 2019
Level of education
Master's degree
Salary indication
€2,325 to €2,972 gross per month
Closing date
1 March 2019
38 hours per week
Vacancy number

The Van't Hoff Institute for Molecular Sciences (HIMS) is one of eight institutes of the University of Amsterdam’s Faculty of Science. HIMS performs internationally recognized chemistry and molecular research, curiosity driven as well as application driven. This is done in close cooperation with the chemical, flavour & food, medical and high-tech industries. Research is organised into four themes: Sustainable Chemistry, Analytical Chemistry, Computational Chemistry and Molecular Photonics.

The Tissue Proteomics group is a collaborative effort between the HIMS and the Amsterdam UMC, location AMC of the University of Amsterdam. The group has a special interest in translational research on the use of novel reproducible and quantitative proteomics methods on tissues and body fluids to diagnose various diseases and predict their prognosis. The overall goal is to implement these techniques into the routine clinical pipeline.

Project description

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.

Further information

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



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.

Job application

The UvA is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. We value a spirit of enquiry and endurance, provide the space to keep asking questions and cherish a diverse atmosphere of curiosity and creativity.

You may apply using the link below. 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. #LI-DNP

No agencies please

Published by  University of Amsterdam

View or Apply

Similar Positions