PhD: AI Models to Identify Disease Correlates of Pathogens

Wageningen University & Research’s Animal Sciences Group (ASG) is launching a new investment programme centred on the digital transformation of the animal sciences. The programme initiative aims to further strengthen knowledge and methods in data-driven research, data science and artificial intelligence (AI). Seven PhD tracks form the core of the programme and will be carried out jointly by Wageningen BioVeterinary Research (WBVR), Wageningen Livestock Research (WLR) and Wageningen Marine Research (WMR), in close collaboration with the graduate school WIAS and Wageningen University

The PhDs work under a single theme: “Digital Biology – Integrating Behaviour, Health and Biodiversity in Animal Science”.

The ‘Digital Biology’ programme focuses on developing and applying digital technologies (AI, sensors, modelling, data fusion) to better understand and predict the behaviour, health and biodiversity of animals.

Together, the PhD candidates strive for a better understanding of the ‘digital physiology’ of animals: how behaviour, genetic predisposition, pathogens, health and environmental stimuli jointly determine how animals function, adapt and contribute to ecosystems.

PhD: Development and implementation of AI tools for identification of correlates of disease to pathogens
Understanding the virulence mechanisms of complex pathogens is still needed because these pathogens circulate in livestock and wild animal populations. Effective vaccines or intervention strategies are lacking, urging the need for new perspectives on pathogen control. Within this project these perspectives will be explored.

To predict correlates of disease against these complex pathogens, you will develop and use AI-driven tools capable of predicting protein structure and folding to assess antigenicity and immunogenicity. These predicted proteins will be experimentally validated in vitro. Ultimately, this work will contribute to future vaccine and immunological assay development.

You will:

1. Identify and implement the AI-driven tools required for the assessment of antigenicity, epitope accessibility, and immune-relevant structures
2. Integrate genomic, proteomic, and structural features to generate ranked lists of candidate virulence-associated proteins.
3. Initiate the development of machine-learning models capable of analysing the potential of selected antigens as potential vaccine candidate and/or diagnostic target.

You will work here

The research is embedded within Wageningen Bioveterinary research located in Lelystad embedded with the chair Adaptation Physiology of the animal science group , and topic resilience of animals, which is led by Prof. Annemarie Rebel . You will be co-supervised by Dirkjan Schokker

You are an accurate, structured, and collaborative professional. You thrive in a team environment. You are highly curious and motivated to improve animal health and to advance your skills in AI/ML and data workflows. Your Learning goals: combining advanced data analysis techniques with AI methods and techniques. Affinity with microbiology (virus; bacteria) and host response (immunology), health and welfare.

You also possess:

• A MSc degree with specialization in Data Science (Bioinformatics, Computer Science, Data Science, Artificial Intelligence, Computational Biology) or Life Sciences with strong affinity to Data Science.
• Experience with different programming languages / environments, such as, Python, Rand experience working with High Performance Computing.
• Basic knowledge of machine-learning concepts (classification, regression, cross-validation).
• Knowledge of statisticsand machine-learning techniques
• Ability to work in multidisciplinary teams.
• Pro-active, collaborative, flexible, and result-oriented.

For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here.

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

• Partially paid parental leave;
• working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
• a fixed year-end bonus of 8.3%;
• excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.
The gross salary for the first year is € 3.059,- per month rising to € 3.881,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

Wageningen University & Research offers plenty of opportunities for growth and development, with a strong internal recruitment policy and excellent training programmes.

The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 7,600 employees (6,700 fte) and 13,100 students and over 150,000 participants to WUR’s Life Long Learning, Wageningen University & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.

Read the 5 reasons why your future colleagues enjoy working at WUR and watch the video below to get an idea of our green campus!

We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated.

Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.

Because we expect you to work and live in the Netherlands our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.

Feeling welcome also has everything to do with being well informed. We can assist you with any additional advice and information about for example helping your partner to find a job, housing, or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.