Postdoctoral position in Bayesian inference for cell biology applications

Are you interested in working with Bayesian inference for cell biology applications, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a postdoctoral research position at Uppsala University.

Uppsala University has a long tradition of successful research – among its alumni are 16 Nobel Prize laureates, including, most recently, Svante Pääbo. The University is unique when it comes to combining IT with wider research, from life sciences to the humanities, and this collaboration is currently facilitated by AI4Research and the Centre for Interdisciplinary Mathematics.

The Department of Information Technology holds a leading position in both research and education at all levels. We are currently Uppsala University's third largest department, have around 350 employees, including 120 teachers and 120 PhD students. Approximately 5,000 undergraduate students take one or more courses at the department each year. You can find more information about us on the Department of Information Technology website.

At the Division of Systems and Control, we develop both theory and concrete tools to design systems that learn, reason, and act in the real world based on a seamless combination of data, mathematical models, and algorithms. Our research integrates expertise from machine learning, optimization, control theory, and applied mathematics, spanning diverse application domains such as medicine, energy systems, biomedical systems, neuroscience, and safety and security.

The Division of Systems and Control enjoys a wide network of strong international collaborators all around the world, for example at the University of Cambridge, University of Oxford, Imperial College, University of Sydney, University of Newcastle and Aalto University. We strive for all PhD students to get a solid international experience during their PhD.

The position is a part of the Beijer Laboratory for Artificial Intelligence Research, funded by Kjell and Märta Beijer Foundation. The Beijer Laboratory for Artificial Intelligence Research was established in 2023 at Uppsala University with an ambition to grow activities within the subject of AI, focusing on applications in the life sciences and questions related to societal development.

The selected candidate will work in the Department of Information Technology, Division of Systems and Control. The selected candidate will work closely with Assistant Professors Sara Hamis (Department of Information Technology, Division of Systems and Control) and Måns Magnusson (Department of Statistics).

Duties
Technological advances in molecular staining and cell imaging have resulted in a multitude of spatio-temporal cell imaging data. These data hold rich information about how cells act and interact. In this research project, we are developing mathematical and probabilistic models that quantify cell actions and cell-to-cell interactions from dynamic point patterns (where points represent cell coordinates) that are extracted from imaging data.

The postdoctoral researcher’s main task will be to develop Bayesian inference methods and computational pipelines designed to estimate mathematical models from dynamic point pattern data. Model inference will mainly be done using a probabilistic programming framework, such as Stan.

Moreover, the postdoctoral researcher will

• collaborate with a multidisciplinary team of experts in mathematics, statistics, machine learning and pre-clinical cancer research,
• lead the writing of scientific manuscripts and present their work at international conferences, 
• have the opportunity to teach (up to 20%),
• have the opportunity to supervise students.

The postdoctoral researcher will join the Artificial Intelligence and Mathematics for Oncology (AIMOn) group.

Requirements
PhD degree in Applied Mathematics, Statistics, Machine Learning, Biophysics, or a related subject or a foreign degree equivalent to a PhD degree in one of the aforementioned subjects. The degree needs to be obtained by the time of the decision of employment. Those who have obtained a PhD degree three years prior to the application deadline are primarily considered for the employment. The starting point of the three-year frame period is the application deadline. Due to special circumstances, the degree may have been obtained earlier. The three-year period can be extended due to circumstances such as sick leave, parental leave, duties in labour unions, etc.

Applicants should be team players with excellent communication skills. Mathematical problem solving and programming skills are required. No previous knowledge of cancer biology is required but applicants should have a genuine interest in using mathematical, probabilistic and computational methods to better understand cancer.

Additional qualifications
Research experience in one or more of the following subjects is meriting (without order of importance):

1. Bayesian inference/ probabilistic modeling.
2. Computational statistics.
3. Markov chain Monte Carlo methods such as Hamiltonian Monte Carlo.
4. Programming in Python, R, Mathematica.
5. Programming in Stan or similar probabilistic programming frameworks.
6. Fourier analysis.
7. Mathematical biology.
8. Mathematical modelling.

About the employment
The employment is a temporary position of 2 years according to central collective agreement. Full time position. Starting date August 1st 2024 or as agreed. Placement: Uppsala

For further information about the position, please contact: Assistant Professor Sara Hamis, (+46) 18-471 1061, sara.hamis@it.uu.se. 

Please submit your application by 29 April 2024, UFV-PA 2024/856.

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