EU-LIFE

Building and promoting Excellence in Life Sciences in Europe
Building and promoting Excellence in Life Sciences in Europe

PhD/Postdoc Computational Biology - Mining a genomics compendium to identify therapeutic targets

Description

Your function within the department

Project description
Human cells perform highly complex tasks and are equipped with the required machinery and decision-making processes that largely remain poorly understood. Although human genes play a central role, no wiring diagram exists depicting their function. This project will link the function of all human genes to a compendium of cellular processes. This will suggest new entry points to manipulate cellular processes and therapeutic strategies to rebalance disease.

Public-private, multi-disciplinary collaboration. 

This consortium will draw upon:

  1. Phenosaurus, a large collection (~130) of haploid screens generated in collaboration with Scenic Biotech BV employing the Cell-seq technology developed by the Brummelkamp laboratory; 
  2. The screening, cell and molecular biology expertise of the Brummelkamp laboratory and the computational know-how of the Wessels laboratory. With the Cell-seq technology proven to be highly effective, the opportunity exists now to cover diverse cellular functions and to use advanced computational network inference approaches to deduce the underlying genetic control mechanisms. 

The successful candidate will be employed in the Wessels and Brummelkamp groups at the Netherlands Cancer Institute, and will regularly liaise with Scenic Biotech to generate sufficient cohesion and momentum.

Consortium Partners:
Wessels Laboratory, The Netherlands Cancer Institute (NKI), Amsterdam.
Brummelkamp Laboratory, The Netherlands Cancer Institute (NKI), Amsterdam.
Scenic Biotech BV, Amsterdam, The Netherlands

Your profile

We are seeking a highly motivated PhD candidate with:

  • A degree in bioinformatics, computer science or a related discipline
  •  Experience in statistics, machine learning and/or pattern recognition 
  • Proficiency in bioinformatics programming languages (e.g. R, Python)
  • Good cross-disciplinary collaborative and communication skills 
  • Experience in analysing high-throughput molecular data is a plus
  • Experience in cancer biology and clinical applications is a plus

Your career opportunities and terms of employment

Approximately 550 people work in the research laboratories. Research discussions, lectures and seminars in English and a large number of Dutch and non-Dutch postdocs, students and staff members contribute to the stimulating and international atmosphere of the Institute. We offer an inspiring and interactive research environment, state-of-the-art facilities, training, a competitive salary (including possibilities for tax-reduction for expats) and housing facilities in the vicinity of the Institute. The Institute is located close to the city centre of Amsterdam and the international Schiphol airport.

The appointment will initially be for 1 year with the intension to extend.

PHD-Position:
For the PHD-position the gross salary per month will range from € 2.665,- to € 3.282, according to the standard PhD scales.

Post-doc position:
For the Post-doc position the gross salary per month ranges from € 3.490,- to € 3.917 according to the postdoc scales and depends on previous experience. The terms of employment will be in accordance with the CAO Ziekenhuizen (Collective Labour Agreement for Hospitals).

Interested?

Please send your resume and letter of interest to recruitment@nki.nl or preferable upload it via our apply button. Please include the names and contact information of at least two references.

The closing date for this vacancy is on the 1st of October 2019

Relevant Literature

  1. van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell. 2019 May 30;177(6):1375-1383.
  2. Aben N, Westerhuis JA, Song Y, Kiers HAL, Michaut M, Smilde AK, Wessels LFA. iTOP: inferring the topology of omics data. Bioinformatics. 2018 Sep 1;34(17):i988-i996. 
  3. Brockmann, M., Blomen, V.A., Nieuwenhuis, J., Stickel, E., Raaben, M., Bleijerveld, O.B., Altelaar, A.F.M., Jae, L.T. 1 and Brummelkamp, T.R1. (2017) Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. Nature 546, 307-311.
  4. Nieuwenhuis, J., Adamopoulos, A., Bleijerveld, O.B., Mazouzi, A., Stickel, E., Celie, P., Altelaar, M., Knipscheer, P., Perrakis, A., Blomen, V.A., and Brummelkamp, T.R. (2017) Vasohibins encode tubulin detyrosinating activity. Science 6369, 1453-1456.
  5. Mezzadra, R. 1, Sun, C. 1, Jae, L.T. 1, Gomez-Eerland, R., de Vries, E., Wu, W., Logtenberg, M.E.W., Slagter, M., Rozeman, E.A., Hofland, I., Broek,s A., Horlings, H.M., Wessels, L.F.A., Blank, C.U., Xiao, Y., Heck A.J.R., Borst, J., Brummelkamp, T.R. and Schumacher, T.N.M. (2017) Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Nature 549, 106-110.

How to apply

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