> Markdown version of [/jobs/ext/3042058-job-offer](https://www.wearedevelopers.com/jobs/ext/3042058-job-offer). Every page supports `.md` or `Accept: text/markdown`. Links point to the HTML versions so they work for humans too. Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Job offer - **Company:** Universiteit van Amsterdam - **Location:** Amsterdam, Netherlands - **Salary:** €3,204.0 - **Contract:** Temporary contract - **Skills:** Artificial Intelligence, Data Analysis, Bioinformatics, Computer Simulation, Python (Programming Language), Machine Learning, High Performance Computing, Deep Learning, Information Technology - **Published:** September 24, 2026 - **Apply:** https://www.academictransfer.com/en/jobs/364169/phd-candidate-in-explainable-machine-learning-for-studying-biology-at-single-cell-resolution/apply/ ## About the Role Are you a MSc graduate with background in data science, computer science, biostatistics, bioinformatics or a related field? Do you have a solid foundation in machine learning? Are you passionate about biology and interested in building new machine learning and AI to accelerate biological discoveries? Then this position is for you!, We are looking for a motivated PhD candidate to develop novel methodology for the analysis of single-cell (multi)-omics data by incorporating existing biological knowledge into machine learning models. You will join a collaborative and internationally-oriented team working at the interface of computer science, mathematics, and biology in the Biosystems Data Analysis group at the Swammerdam Institute for Life Sciences at the University of Amsterdam., * hold a MSc in Bioinformatics, Artificial Intelligence, Data Science, Biostatistics or a closely related discipline; * have demonstrable experience with training machine and deep learning models, preferably using Python; * have a basic understanding of biology and/or are interested in using computational methods to understand biology; * are fluent in English, written and spoken. Experience with single-cell transcriptomics data analysis and working with high-performance computing systems are considered a plus. ## Description Interpretable machine learning is a growing research area, with important applications in the biological sciences, such as understanding how different genes regulate each other within biological pathways. However, the current common practice is first to build complicated, "black-box" models and try to understand what they learned afterwards. This has the disadvantage that a) interpretation is still not always possible and b) it is inefficient as the model must re-discover patterns that are already well-known from scratch every time it is trained. Recent technological advances have allowed us to study DNA and RNA not only in a "bulk" tissue, but also at a single-cell resolution, giving us unprecedented insights into how organisms form, how diseases develop, and how cells communicate with each other inside a tissue. In this project, you will build interpretable-by-design machine learning models for biological data that offer biological insights in a direct way. Such models will be applicable to a variety of single-cell datasets and experiments in different fields of biology. Tasks and responsibilities: * complete a PhD thesis within the official appointment duration (four years); * develop novel algorithms for analyzing single-cell (multi)-omics data and design and perform in silico experiments to test them; * be an active and responsible member of the research group and collaborate closely with fellow group members; * discuss work with group members and at departmental meetings, and incorporate feedback; * take a leading role in writing manuscripts for publication in peer-reviewed journals and conferences; * participate in the PhD training programme of the University of Amsterdam; * assist with teaching and supervision of Bachelor's and Master's students. You will have the opportunity to: * work at the interface of machine learning and biology; * collaborate closely with biologists from a variety of disciplines including immunology and cancer biology; * present results at national and international scientific conferences; * expand academic, professional and personal skills; * use high-end compute infrastructure via the national ICT cooperative (SURF) What we ask of you You are passionate about research and want to develop into an independent scientist. You have a background in machine learning and artificial intelligence and like to build novel methods for the analysis of biological data. You are methodical, curious and able to take initiative, while also valuing close collaboration in an interdisciplinary and international research environment., 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). 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., 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. 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