PhD Candidate in Developmental Signaling in Gastruloids

PhD Candidate in Developmental Signaling in Gastruloids

Published Deadline Location
16 Feb 19 Mar Amsterdam

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Job description

Are you fascinated by embryonic development and excited by the idea of imaging the dynamic activity of developmental signaling pathways in a state-of-the-art 3D in vitro model for early embryogenesis? Then this may be the job for you!

We are looking for a PhD candidate to study how individual pluripotent cells decide their future fate in response to developmental signals using gastruloids as a model system. The position is supported by a recently awarded NWO-ENW-XL consortium grant and will therefore be a highly collaborative effort between the University of Amsterdam, Radboud Universiteit, the Netherlands Cancer Institute and the Hubrecht Institute.

You will be embedded in the Developmental, Stem Cell and Cancer Biology group (led by dr. Renée van Amerongen), which is part of the Swammerdam Institute for Life Sciences in the Faculty of Science at the University of Amsterdam. Research in our group aims to understand how complex tissues are built and maintained. We study this at multiple different levels - "from man or mouse to molecule" - using a variety of experimental approaches and with a specific focus on WNT and BMP/NODAL signaling. See our website for more details.

What are you going to do?

The early mammalian embryo, or epiblast, is composed of pluripotent cells that can generate all specialized cell types of the body. Local gradients of instructive signaling cues determine which developmental trajectory the different cells will take. At the same time, the epiblast cell population is highly heterogeneous with cell-to-cell variation at the transcriptomic and epigenomic level. The goal of our NWO-XL consortium is to unravel how a system that is composed of intrinsically stochastic cells can show robust and deterministic fate decisions.

Your main focus will be on studying the interplay between BMP, WNT and NODAL signaling using live cell imaging in a 3D model of early embryonic development ("gastruloids"). At the start of your PhD, a part-time technician will provide experimental support with setting up the gastruloid cultures from mouse embryonic stem cells (mESCs). As part of our larger consortium network, you will also get the opportunity to incorporate experimental single-cell -omics approaches and computational modeling in collaboration with PhD students and experts throughout the Netherlands (Amsterdam, Utrecht and Nijmegen).

During your PhD research, you will apply a variety of techniques, including (but not limited to) DNA cloning and testing of reporter constructs for BMP, NODAL and WNT signaling, 2D mESC culture and targeting using CRISPR/Cas9, 3D gastruloid culture, live-cell confocal microscopy, FACS sorting, and manipulation of gastruloids using a combination of classical developmental biology and state-of-the-art (epi)genome perturbation approaches.

Tasks and responsibilities
  • complete a PhD thesis within the official appointment duration of four years;
  • use different molecular and cell biology based experimental approaches to visualize and manipulate individual cell behavior
in 3D gastruloids;
  • develop and apply quantitative image analysis pipelines (including cell segmentation and tracking with state-of-the art
deep-learning based methods);
  • perform your experiments in a systematic and well controlled manner and keep accurate records by properly documenting
and organizing your work;
  • discuss your work in our lab and consortium meetings, incorporate feedback and give input to others;
  • assist in teaching and supervise BSc/MSc students during their research internship;
  • participate in the Faculty of Science PhD training programme.
You will get the opportunity to
  • build a network as part of our consortium collaborations;
  • present your work at (inter)national meetings in talks or posters;
  • continuously hone your academic, professional and personal skills.


University of Amsterdam (UvA)


You are passionate about science and have a particular interest in developmental and stem cell biology with affinity for, and preferably knowledge of, developmental signaling pathways. You like a challenge and are motivated to work in an interdisciplinary environment. You are well organized, enabling you to meet deadlines. Finally, you are a team player and a nice colleague with good communication and problem-solving skills.

Your experience and profile
You have/are:
  • a recent MSc degree in the biomedical sciences (or a related area in molecular, cell and/or tissue biology);
  • proficient in mammalian tissue culture;
  • demonstrated hands-on experience with one or more of the following techniques: DNA cloning, CRISPR/Cas mediated
(epi)genome editing, 3D cell culture, live-cell imaging, FACS analysis;
  • affinity with confocal microscopy, image analysis, gene regulation and chromatin biology;
  • a high intrinsic motivation and aptitude for fundamental research (reflected by your CV);
  • fluent in English, both written and spoken.
It will work to your advantage if, in addition, you have experience with one or more of the following: embryonic stem cell culture, some proficiency with image analysis (e.g. FIJI, CellPose), bioinformatics analyses and/or computational biology (e.g. R, Python, Matlab).

Conditions of employment

A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is May/June 2023 or September 2023. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

Within the NWO-ENW-XL consortium, you will work closely with researchers from the Radboud Institute for Molecular Life Sciences (Hendrik Marks group), Hubrecht Institute (Jop Kind group) and Dutch Cancer Institute (Tineke Lenstra group). Your appointment will be at the University of Amsterdam, where you will be supervised by experts in developmental signaling, early embryonic development and quantitative image analysis.

Your salary will range between €2,541 in the first year to €3,247 gross per month in the last year of employment, on the basis of a full working week of 38 hours. This sum does not include the 8% holiday allowance and the 8.3% year-end allowance. A favorable tax agreement, the 30% ruling, may apply to non-Dutch applicants. The Collective Labour Agreement for Dutch Universities (CAO NU) is applicable.

Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:
  • 232 holiday hours per year (based on fulltime);
  • multiple courses to follow from our Teaching and Learning Centre;
  • a complete educational program for PhD students;
  • a pension at ABP for which UvA pays two third part of the contribution;
  • the possibility to follow courses to learn Dutch;
  • help with housing for a studio or small apartment when you're moving from abroad.
Are you curious to read more about our extensive package of secondary employment benefits, take a look here.


Faculty of Science

The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.

The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

The Swammerdam Institute for Life Sciences is one of eight institutes in the Faculty of Science (FNWI). SILS is a multidisciplinary research institute with a systems biology approach to the life sciences. The institute brings together approximately 240 researchers in 18 research groups.

Want to know more about our organisation? Read more about working at the University of Amsterdam.


  • PhD
  • Natural sciences
  • max. 38 hours per week
  • max. €2541 per month
  • University graduate
  • 11238


University of Amsterdam (UvA)

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Science Park 904, 1098XH, Amsterdam

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