PhD-student: Single-cell dynamics in intestinal organoids

Date posted March 29, 2021
Type PhD positions

Organoids are miniature organs that display the striking ability to grow and self-organize from single adult stem cells. Recently developed techniques are now making organoids an exciting system for quantitative (biophysics) studies. You will use advanced 3D fluorescence time-lapse microscopy (confocal and light-sheet), machine-learning enabled tracking of individual cells, statistical data analysis methods, and organoid growth technology, to follow all cellular lineages in time and space over multiple generations and to hence elucidate how organoids form and function.

Specifically, this project focusses on a class of rare cell types (enteroendocrine, Tuft, and microfolds cells). These cell types are poorly understood, yet are thought to play crucial roles in hormone production and immune defense, and hence are implicated in conditions including allergies, obesity, depression, and auto-immune diseases. You will study the yet-unknown dynamics of these cell types: their shape changes, movement, spatial organization, differentiation from other lineages, and notably, their interaction with bacteria and immune cells. These data will give unprecedented insight into these remarkable cell types and their functions.

About the group

This project will take place jointly in the Tans and van Zon labs at AMOLF Amsterdam. It is part of a larger program together with the Snippert lab at the University Medical Center Utrecht (UMCU), the Van Rheenen lab at the Netherlands Cancer Institute (NKI) and the Clevers lab at the Hubrecht institute, the ten Wolde lab at AMOLF, and the Simons lab in Cambridge, and hence brings together a range of cutting-edge approaches in organoid technology, genetic engineering, in-vitro and in-vivo microscopy, single-cell sequencing, data analysis, and mathematical modelling.

About the group


We are looking for an outstanding experimental physicist, chemist, or biologist with skills in handling complex data and an interest in fundamental questions about development, and a strong drive to excel in a competitive international environment. You will need to meet the requirements for an MSc-degree, to ensure eligibility for a Dutch PhD examination. Prior experience with quantitative (light-sheet) microscopy, organoid/tissue culture or quantitative analysis of single-cell behavior is not required, but is considered a plus.

Terms of employment

The position is intended as full-time (40 hours / week, 12 months / year) appointment in the service of the Netherlands Foundation of Scientific Research Institutes (NWO-I) for the duration of four years, with a starting salary of gross € 2,441 per month and a range of employment benefits. After successful completion of the PhD research a PhD degree will be granted at Delft University of Technology. Several courses are offered, specially developed for PhD-students. AMOLF assists any new PhD-student with housing and visa applications and compensates their transport costs and furnishing expenses.

Contact info

Prof.dr. Jeroen van Zon
Group leader Quantitative Developmental Biology
Phone: +31 (0)20-754 7100

Prof.dr. ir. Sander Tans
Group leader Biophysics
Phone: +31 (0)20-754 7100

You can respond to this vacancy online via the button below.
Please annex your:
–  Resume;
–  Motivation on why you want to join the group (max. 1 page).

It is important to us to know why you want to join our team. This means that we will only consider your application if it entails your motivation letter.
Applications will be evaluated on a rolling basis and as soon as an excellent match is made, the position will be filled.

Online screening may be part of the selection.

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