DC 5 PhD position

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

Salary Benefits:

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

De Boelelaan 1108