Are you interested in a comprehensive, interactive and international research programme? Do you want your research to cover the broader aspects and interface between biology, bioinformatics, statistics, systems biology, predictive microbiology and artificial intelligence? Then, please apply for this PhD fellowship at Vrije Universiteit Amsterdam (VU).
Location: AMSTERDAM
FTE: 1.0
In this project, we will develop tools and methods to integrate dynamic multi-level omics data with genome-scale mechanistic models in the context of microbial communities. With partners in the E-MUSE Network (KUL, UNIBO, USZ, CHRH) we will explore: (1) The use of machine-learning approaches for feature selection, for example SVM, Random forest, Ensemble techniques, etc., for model development and prioritization. (2) Conversely the use of the mechanistic models and Individual-based Model as prior knowledge to constrain the search space in data-driven approaches. We will integrate the data into dynamic constraint-based ecosystem models, and apply the tools and methods to the biological study cases, i.e. the cheese ripening case and the growth physiology of associated microbial species.
Expected results:
We expect to deliver tools (open source software) and methods (algorithms, modelling strategies) to use multi-omics data to generate insight in the relevant interactions inside and between microorganisms in complex dynamic ecosystems. We will provide insight in the usefulness of combining machine-learning and mechanistic modelling approaches. Finally, we will provide, in collaboration with the network partners, specific models and predictions that will lead to a better understanding of the biological use cases.
Planned secondment(s):
In total, 2 months will be spent at the Agencia estatal consejo superior de investigaciones cientificas in Spain (dynamic optimisation technologies), 2 months at the Katholieke Universiteit Leuven in Belgium (modelling aspects) and 3 months at the Institut national de recherche pour l’agriculture, l’alimentation et l’environnement in France and at the Chr. Hansen A/S in Denmark (biological data)
Enrolment in Doctoral degree: Vrije Universiteit Amsterdam (VU) (https://www.vu.nl/en)
Website for additional job details: https://www.itn-emuse.com/
Specific Requirements - Eligibility Criteria
The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 2 years.
Additionally, Vrije Universiteit Amsterdam offers excellent fringe benefits and various schemes and regulations to promote a good work/life balance, such as:
The ambition of Vrije Universiteit Amsterdam is clear: to contribute to a better world through outstanding education and ground-breaking research. We strive to be a university where personal development and commitment to society play a leading role. A university where people from different disciplines and backgrounds collaborate to achieve innovations and to generate new knowledge. Our teaching and research encompass the entire spectrum of academic endeavour – from the humanities, the social sciences and the natural sciences through to the life sciences and the medical sciences.
Vrije Universiteit Amsterdam is home to more than 26,000 students. We employ over 4,600 individuals. The VU campus is easily accessible and located in the heart of Amsterdam’s Zuidas district, a truly inspiring environment for teaching and research.
Diversity
We are an inclusive university community. Diversity is one of our most important values. We believe that engaging in international activities and welcoming students and staff from a wide variety of backgrounds enhances the quality of our education and research. We are always looking for people who can enrich our world with their own unique perspectives and experiences.
The Faculty of Science
The Faculty of Science inspires researchers and students to find sustainable solutions for complex societal issues. From forest fires to big data, from obesity to medicines and from molecules to the moon: our teaching and research programmes cover the full spectrum of the natural sciences. We share knowledge and experience with leading research institutes and industries, both here in the Netherlands and abroad.
Working at the Faculty of Science means working with students, PhD candidates and researchers, all with a clear focus on their field and a broad view of the world. We employ more than 1,250 staff members, and we are home to around 6,000 students.
About the department
The lab of VUA, in which the proposed work will be carried out, studies the molecular networks inside cells that give rise to cell behavior and fitness, in isolation and in interaction with other cells and their environment. The team focuses on the principles and general understanding of how those networks adapt in response to environmental and genetic changes and combine mathematical modelling, theory, and experiments. The approach is to apply the fundamental insights and methods in a biotechnological and biomedical setting.
The lead supervisor is prof. dr. B. Teusink (VU), the head of the Systems Bioinformatics group, which he runs together with prof. dr. F. Bruggeman (VU) who is also one of the co-supervisors. B. Teusink’s group currently houses 12 PhD students and 2 postdocs. Of previous students, 2 PhD and 3 PDs now have a faculty position at Dutch Universities; 2 PhDs and 5 PDs moved to R&D jobs in industry, 3 PhDs are currently postdocs elsewhere, and 3 PhDs work as data analysts for bank and insurance companies.The co-supervisors for this role are also dr D. Molenaar (VU) – member of prof. Teusink group who is specialist in microbiology, bioinformatics and data analysis and J. Van Impe (KUL) – the Division Head and founder of BioTeC (Chemical and Biochemical Process Technology and Control) research group at KU Leuven.
Are you interested in this position? Please apply via the application button and upload your curriculum vitae and cover letter until 15/04/2021, 23:59.
Applications received by e-mail will not be processed.
Vacancy questions
If you have any questions regarding this vacancy, you may contact:
Name: Prof.dr. B. Teusink
Position: group leader
E-mail: b.teusink@vu.nl
No agencies
In your application, please refer to Professorpositions.com