DC 5 PhD position

Do you want to combine biology and computation to make the world a better place by helping the protein transition towards plant-based foods?

JOB DESCRIPTION

The project of this PhD student aims at developing models to improve the prediction of strain-specific phenotypes. The models will handle different levels of granularity and combine genomic information, mechanistic knowledge (enzyme signatures, promoter architecture, context methods such as operon structures or co-expression, thermodynamic data) and phenotypic data with artificial intelligence and machine learning techniques. Phenotypic data will include data from available strain collections with sequenced strains and information on their phenotypic behaviour, as well as data from strains screened within FAIROmics for activities during plant-based fermentations.

The project will deliver insight to what extent integration of mechanistic knowledge and experimental data with AI/ML methods can lead to reliable predictions of variation in traits from variations in sequences. In the process, we will develop an inventory of relevant features and mechanisms and associated databases (or links thereto), methods and predictive models.

REQUIREMENTS

A Master in a relevant field, such as (bio)physics, systems biology, bioinformatics or computer science (with good understanding of biology)

Skills/Qualifications

• Strong in, and affinity with, the use of computational methods in biological contexts
• Problem solving
• Independent but willing to ask for help
• Curious
• Communicative in word and text

CONDITIONS OF EMPLOYMENT

Fixed-term contract: 1 year.

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So in return for your efforts, we offer you:

• a salary of minimum € 2.770,00 (PhD) and maximum € 3.539,00 (PhD) gross per month, on a full-time basis. This is based on UFO profile PhD candidate.
• a position for 1 FTE. Your employment contract will initially last one year, and will be extended to three years upon positive evaluation.

We also offer you attractive fringe benefits and regulations. Some examples:

• A full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
• 8% holiday allowance and 8.3% end-of-year bonus
• contribution to commuting expenses
• discount on (and occasionally exclusive access to) theater performances and courses at the Griffioen Cultural Center
• a wide range of sports facilities which staff may use at a modest charge

EMPLOYER

Vrije Universiteit Amsterdam

This project is part of the FAIROmics docteral training network financed by the EU, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims at developing doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities and social sciences.

The Systems Biology Lab 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. We focus on the principles and general understanding of how those networks adapt in response to environmental and genetic changes. We combine mathematical modelling, theory, and experiments. We apply the fundamental insights and methods in a biotechnological and biomedical setting.

Faculty of Science
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely. - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility. Over 5,500 staff work at the VU and over 30,000 students attend academic education.

Diversity
Diversity is the driving force of the VU. The VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

ADDITIONAL INFORMATION

Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application.

Submitting a diploma is part of the application process.

https://www.dn-fairomics.eu/open-phd-positions/dc-5-phd-position

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.