Universiteit van Amsterdam

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PhD student position in formal methods for biology, Kungens Lyngby (Denmark)

Deadline: Friday 29 November 2019

The section for Formal Methods of DTU Compute offers a 3-years PhD position starting in late 2019 or early 2020. The position is funded by the Independent Research Fund of Denmark through the project 'REDUCTO: A novel approach for the reduction of Boolean networks'. The PI of the project is the Associate Professor Andrea Vandin in collaboration with Luca Cardelli (University of Oxford, UK), Claudine Chaouiya (I2M, Aix Marseille Univ, CNRS, Centrale Marseille, Marseille, France & Instituto Gulbenkian de Ciência, Portugal), and Lars Keld Nielsen (Novo Nordisk Foundation Center for Biosustainability, Denmark). Funds are allocated for research visits to the project collaborators. The PhD student will be co-supervised by Andrea Vandin and the Head of Section Alberto Lluch Lafuente.

Project Description

Boolean networks (BN) are a graph-based well-established method to model biological systems. In order to accurately model systems, we often face models too complex to be interpreted or analyzed. Several reduction techniques exist to mitigate this problem. Our crucial hypothesis is that novel approaches to the reduction of BNs are needed, and that those can be developed by using a theoretical computer science approach. The project aims at developing novel mathematically-grounded techniques and tools to reduce and simplify complex BNs. The starting point will be recent work of the PI, presented e.g. in:

- Maximal aggregation of polynomial dynamical systems, L Cardelli, M Tribastone, M Tschaikowski, A Vandin, Proceedings of the National Academy of Sciences 114 (38), 10029-10034, https://doi.org/10.1073/pnas.1702697114
- Symbolic computation of differential equivalences, L Cardelli, M Tribastone, M Tschaikowski, A Vandin, Proceedings of POPL 2016, https://doi.org/10.1145/2837614.2837649

Tool support will be based on the tool ERODE, maintained by the PI.

Requirements

Candidates must have (or be close to complete) a master degree in computer science and engineering, applied mathematics, or similar academic qualifications. Preference will be given to candidates with documented experience in formal methods, while interest in biological topics will be positively considered. Good command of the English language is essential.

We offer

We offer an interesting and challenging job in an international environment. DTU is a leading technical university in northern Europe which benchmarks with the best universities in the world. Salary is competitive (roughly in the order of 2400 EUR net per month). This is a 3 years full-time position.

 

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