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PhD in (AMOLF), Tans lab Single-cell dynamics in intestinal organoids

Research / Job description
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 functions.

This project will take place jointly in the Tans and van Zon labs. 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.

Required qualifications
We are looking for an outstanding experimental physicist, chemist, or biologist with programming skills to handle complex data and an interest in fundamental questions about development, and a strong drive to excel in a competitive international environment. 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.

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