PhD Position in Deep Learning on Single-Cell Sequencing Data

Do you enjoy using computational approaches to study biological problems? Are you interested in developing and applying deep learning methodology to investigate cells at the molecular level? We invite enthusiastic and dedicated candidates to join our cutting-edge research team as a PhD student to work on developing novel methodology for the analysis of single-cell sequencing data using deep learning based approaches.

Come work at the largest university of Amsterdam!
Single-cell omics data offer unprecedented opportunities for method development towards opening up new ways of understanding cell biology. Much of this involves the use of deep learning. Currently these methods are typically applied without taking existing prior knowledge into account. However, taking such biological knowledge into account might help improve predictive performance and/or interpretability. Examples of available knowledge include protein structures, gene regulatory interactions, or cell hierarchies and developmental stages. Another important direction is the integration of multiple different types of data using unsupervised learning of embeddings that can be used for downstream clustering and classification tasks. This is relevant for various modalities within single-cell sequencing, but also for integrating single-cell sequencing data with various other types of data.

What are you going to do?
You will be part of the Biosystems Data Analysis group (BDA) of the Swammerdam Institute for Life Sciences (SILS). BDA works on the development of methodology for data mining, machine learning/deep learning, data fusion, and modelling and application of these methods to answer biological questions, in close collaboration with domain experts. Within SILS, various experimental groups have started or will soon start to use single-cell sequencing data, and we will closely collaborate with researchers in these groups.

You will work on the following research objectives:

1) Develop methodology to integrate existing biological knowledge in single-cell sequencing analysis e.g. towards cell-cell communication analysis or trajectory analysis.

2) Develop methodology for unsupervised learning of embeddings to integrate single-cell sequencing data with other data modalities.

3) In collaboration with researchers in SILS, apply the methodology to address specific biological questions of interest e.g. in plant science, immunology or neuroscience.

Tasks and responsibilities
You will:

• develop computational approaches;
• make use of available single-cell sequencing data and data newly obtained by our collaborators, as input for training machine learning models;
• collaborate with both experimental researchers as well as with computational researchers (other PhD students working at UvA);
• be an active member of the research group and take responsibility for shared tasks; incorporate feedback and give input to others;
• take a leading role in writing manuscripts and complete a PhD thesis within the official appointment duration of four years;
• participate in the Faculty of Science PhD training program;
• assist in teaching and supervise Bachelor and Master theses.

Your profile
You are passionate about science and have a particular interest in deep learning applications in biology. You enjoy close collaboration with domain experts. You have a creative mind and look forward to work at the cutting-edge of computational technology. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of computational researchers and experimental researchers.

You have/are

• an MSc in Data Science, Artificial Intelligence, Computational Science, Bioinformatics, or similar;
• interested in using machine learning/deep learning on single-cell sequencing data;
• able to communicate with non-experts on computational issues;
• professional command of English.

Our offer
We offer 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 as soon as possible. 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. Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2.872 in the first year to €3.670 (scale P) in the last year. This does not include 8% holiday allowance and 8,3% year-end allowance. The UFO profile PhD candidate applicable The Collective Labour Agreement of Universities of the Netherlands 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 contract)
• 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.

Where you will work
The Swammerdam Institute for Life Sciences (SILS) is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdam's Faculty of Science (FNWI). With around 240 employees, SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical, biotech, chemical, flavor, food & agricultural, and high-tech industries, and revolves around 4 main themes, Cell & Systems biology, Neurosciences, Microbiology and Green Life Sciences.

If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. We accept applications until and including 31 December 2024. Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation;
• the names and email addresses of two references who can provide letters of recommendation.

A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). Only complete applications received within the response period via the link below will be considered. The interviews will be held early January 2025.

Do you have any questions or do you require additional information? Please contact:

• prof. dr. Aalt-Jan van Dijk
• Email: a.d.j.vandijk@uva.nl
• T: +31 20 525 5519

The UvA is an equal-opportunity employer. We prioritise diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity. If you encounter Error GBB451, reach out to our HR Department directly. They will gladly help you continue your application. No agencies please.

38 hours per week

Science Park 904