PhD Researcher in Artificial Intelligence for Detecting Epistasis in ALS

Tilburg School of Economics and Management and Tilburg School of Humanities and Digital Sciences at Tilburg University (TiU) is recruiting a doctoral candidate in the domain of genomic data science. The PhD researcher will contribute to the research project “Artificial Intelligence for Detecting Epistasis in ALS”, a collaboration between Tilburg University and UMC Utrecht. This project is led by dr. Marleen Balvert, TiSEM, TiU, who will be the promotor. The researcher will be co-supervised by dr. Sharon Ong, TSHD, TiU and Prof. dr. Jan Veldink, UMC Utrecht. 

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease with a genetic foundation. Some of the mutations in our DNA – also called variants – that lead to ALS are known. However, it is still unknown which genetic variants have led to the disease for the majority of patients. Recent research has found that there are variants that sometimes do and sometimes do not lead to ALS. A likely explanation is found in so-called epistasis: two (or three or more) genetic characteristics only lead to disease if an individual has all of them. Finding groups of genetic characteristics that cause ALS paves the way for further understanding the disease and for treatment development. This project aims to develop new methods that can identify groups of ALS-causing variants from the Project MinE data – a large dataset containing the genomic information of over a hundred thousand individuals with and without ALS.

Your position
The PhD researcher will, together with the supervision team:

• develop and apply classification models that can determine whether an individual is an ALS patient or not, based on their genomic information. This model should handle population structure and data sparsity;
• develop a model interpreter that can explain which genetic features the classification model uses to determine whether an individual is an ALS patient;
• publish results in scientific journals and present results at (international) conferences.

Firstly, we understand that no candidate will meet every single requirement. If you are excited about this position but do not tick every box, we still encourage you to apply. In your application, tell us not only about the qualifications you bring but also about the areas you are eager to develop further and how you foresee doing that. We invite candidates of all genders, ethnicities and orientations.

Your qualifications

• Master’s degree in Data Science, Artificial Intelligence, Computational Biology, Bioinformatics. Mathematics, Operations Research or a closely related field.
• Programming Skills in Python and R.
• Research or coding experience in machine learning and deep learning techniques.
• Good command of English (spoken and written).
• High desirable: bachelor/master’s degree in Biological Sciences or a closely related field, some knowledge of mechanisms implicated in ALS pathogenesis, experience with analyzing biological data (e.g. data from GWAS, NGS, RNA-seq) 

Tilburg University offers excellent benefits in a pleasant working environment:

• Employment of 1.0 fte (40 hours per week).
• A salary of minimum €3,059 and maximum €3,881 gross per month for full-time employment, based on UFO profile PhD student and salary scale P.
• You will be given a temporary employment contract for the duration of 1 year. Upon positive outcome of the first-year evaluation, you will receive a subsequent employment contract that will be extended for an additional 3 years.
• Vacation pay of 8% and a year-end bonus of 8.3%.
• Over 8 weeks of vacation leave.
• Reimbursement sustainable commuting: walking, cycling, and public transport.
• Options model for additional leave, pension, a bicycle or personal training.
• Moving allowance (subject to conditions).
• 30% rule for international employees (if applicable).
• Pension through ABP.
• Support for your personal development and career, and a broad package of fringe benefits (including excellent technical infrastructure, savings schemes and excellent sport facilities).
• Inclusive work culture: everyone welcome, equal opportunities.
• A green, inviting campus that’s easily accessible by public transport.

For more information, please see our website and the CLA Dutch Universities.

Tilburg University is an academic, inclusive, and engaged community. Together with nearly 3,000 employees, we are committed to broad prosperity, sustainably, and inclusion. For current and future generations. We develop and share knowledge for the requirements of people and our society. This is how we contribute to solving complex social issues and help society move forward.

We educate our 19,500 students of 110 nationalities to become responsible leaders with knowledge, skills, and character. With our education and research for broad prosperity, we exceedingly focus on themes such as mental and preventive care, an inclusive labor market, the energy transition, and digitalization.

About the Research Center for Cognitive Science and Artificial Intelligence 

The Research Center for Cognitive Science and Artificial Intelligence at Tilburg University is part of the Tilburg School of Humanities and Digital Sciences. The center emphasizes innovative cutting-edge research in those areas of cognitive science that bring together psychological and computational theories and methodologies. The group is responsible for the Bachelor and the Master program Cognitive Science & Artificial Intelligence, is co-responsible for the university-wide data science Master program Data Science & Society and is affiliated with the Jheronimus Academy of Data Science (http://www.jads.nl). Researchers in the Cognitive Science and Artificial Intelligence center have access to computer clusters, experimental lab facilities, and the virtual and mixed reality DAF Technology Lab and its sensing technologies (https://www.tilburguniversity.edu/campus/experiencing-virtual-reality/ ). Moreover, researchers play an important role in Mind Labs (http://www.mind-labs.eu ), an initiative that fosters collaborations between knowledge institutions and corporations in the field of interactive technologies and behavior. 

About Deep Learning for Perception Research Unit  

You will be embedded in the Deep Learning for Perception Research Unit, which focuses on developing deep learning methods in contexts hallmarked by a high degree of complexity and uncertainty. In our research, we study generative models of perception. We also address transparency and explainability of deep learning models, in combination with techniques designed to reduce complexity of deep learning architectures.

Want to know more?

Would you like to know more before applying? Feel free to contact dr. Marleen Balvert at m.balvert@tilburguniversity.edu