PhD Position in Systems Biology: improved metabotyping through hybrid modeling of multi-omics data

Ever wondered how your metabolism really ticks? Help us build smarter tools to find out!

Job Description
At the Maastricht Centre for Systems Biology (MaCSBio) we focus on connecting the dots between different types of biological data. A key part of our mission involves developing computational and modeling tools that go beyond simple classification to explore the complex intricacies of metabolism. By doing so, we aim to uncover the subtle nuances of how our bodies process nutrients and respond to interventions, ultimately leading to personalized health strategies and better disease prevention.

In this PhD role, you will develop and apply hybrid approaches that blend the knowledge-driven biological precision of genome-scale metabolic modeling with the adaptive, data-driven power of machine learning. In doing so, you will focus on leveraging multi-omics data—spanning genomics, epigenomics, transcriptomics, and possibly more. Thus, you will be at the forefront of creating cutting-edge tools that not only enhance metabotyping but also provide deeper insights into the complexities of human metabolism.
Your research will aim to maximize the insights gained from multi-omics data, enhancing our understanding of variations in metabolic phenotypes and the prediction of responses to metabolic interventions. A specific area of interest will be the development of methods to study the genetic and epigenetic regulation of metabolism, uncovering how these mechanisms shape individual metabolic responses.

You’ll be joining a dynamic, interdisciplinary team, collaborating with experts in molecular biology, bioinformatics, and systems biology. Your research will contribute to ongoing projects in molecular cardiology and precision nutrition, offering a unique opportunity to explore and innovate within a well-supported and data-rich environment.

Responsibilities and tasks:

• Develop innovative frameworks that integrate genome-scale metabolic models with machine learning;
• Create computational and modeling methods to incorporate and analyze multi-omics data within these paradigms;
• Investigate how genetic and epigenetic factors contribute to metabolic regulation;
• Contribute to advancements in precision nutrition and molecular cardiology through impactful research;
• Collaborate with nutritionists and clinicians with the potential to translate your findings into practical, individualized health strategies;
• Present findings at scientific conferences and publish in peer-reviewed journals.

Requirements
We are looking for a highly motivated candidate with strong analytical skills and a passion for interdisciplinary research. You should be an effective communicator, able to work both independently and as part of a team, and have a strong interest in the intersection of multi-omics, metabolism, and systems biology. Our ideal candidate has:

• A MSc in Biomathematics, Biostatistics, Biomedical Engineering, Bioinformatics, Systems Biology or equivalent (required);
• Experience with genome-scale metabolic modelling and/or machine learning methods (e.g. elastic net, neural networks, random forests) (required);
• Excellent data analysis skills (required);
• Proficiency in the English language (required);
• Familiarity with multi-omics data integration and regulatory genomics is a plus;
• Strong interest in working at the interface between biology and technology;
• Excellent communication skills;
• Programming experience in R and Matlab, Java, Python or equivalent languages.

What we offer
As PhD Position in Systems Biology: improved metabotyping through hybrid modeling of multi-omics data at Faculty of Science & Engineering, you will be employed by the most international university in the Netherlands, located in the beautiful city of Maastricht. In addition, we offer you:

• Good employment conditions. The position is graded in scale P according to UFO profile PhD, with corresponding salary based on experience ranging from €2872,00 and €3670,00 gross per month (based on a full-time employment of 38 hours per week). In addition to the monthly salary, an 8.0% holiday allowance and an 8.3% year-end bonus apply.
• An employment contract for a period of 12 months with a scope of 1,0 FTE. Upon a positive evaluation, an extension of 3 years will follow.
• At Maastricht University, the well-being of our employees is of utmost importance, we offer flexible working hours and the possibility to work partly from home if the nature of your position allows it. You will receive a monthly commuting and internet allowance for this. If you work full-time, you will be entitled to 29 vacation days and 4 additional public holidays per year, namely carnival Monday, carnival Tuesday, Good Friday, and Liberation Day. If you choose to accumulate compensation hours, an additional 12 days will be added. Furthermore, you can personalize your employment conditions through a collective labor agreement (CAO) choice model.
• As Maastricht University, we offer various other excellent secondary employment conditions. These include a good pension scheme with the ABP and the opportunity for UM employees to participate in company fitness and make use of the extensive sports facilities that we also offer to our students.
• Last but certainly not least, we provide the space and facilities for your personal and professional development. We facilitate this by offering a wide range of training programs and supporting various well-established initiatives such as 'acknowledge and appreciate'.

The terms of employment at Maastricht University are largely set out in the collective labor agreement of Dutch Universities. In addition, local provisions specific to UM apply. For more information, click here.

Maastricht University
Why work at Maastricht University?

At Maastricht University (UM), everything revolves around the future. The future of our students, as we work to equip them with a solid, broad-based foundation for the rest of their lives. And the future of society, as we seek solutions through our research to issues from all around the world. Our six faculties combined provide a comprehensive package of study programmes and research.

In our teaching, we use the Problem-Based Learning (PBL) method. Students work in small groups, looking for solutions to problems themselves. By discussing issues and working together to draw conclusions, formulate answers and present them to their peers, students develop essential skills for their future careers.

With over 22,300 students and more than 5,000 employees from all over the world, UM is home to a vibrant and inspiring international community.

Are you drawn to an international setting focused on education, science and scholarship? Are you keen to contribute however your skills and qualities allow? Our door is open to you! As a young European university, we value your talent and look forward to creating the future together.

Click here for more information about UM.

Faculty of Science and Engineering
At the Faculty of Science and Engineering (FSE), we focus on themes such as circularity and sustainability, future farming, digitisation and (scientific) instrument development. FSE's leading projects, like the Einstein Telescope Pathfinder, are sure to grab anyone's attention. The faculty is a vibrant hub of education and research in Science, Technology, Engineering, and Mathematics (STEM) and Liberal Arts and Sciences (LAS). At FSE, over 450 staff members and 3700 students gather to explore e exciting interdisciplinary research and educational programmes. Feel welcome, be part of our team and put your brilliant mind to work!

FSE at the Brightlands Campuses
Maastricht, Sittard-Geleen, Heerlen, and Venlo, the home of four creative Brightlands campuses, are bustling with 30,000 entrepreneurs, researchers, and students working diligently to solve global challenges. The Faculty of Science and Engineering is active on all four Brightlands campuses, and this is where our impact reaches its peak. To give you an idea of what is happening at each campus: Sittard-Geleen is home to the largest chemical site in the Euregion, while Venlo is a large hub for agri-food innovation. Maastricht is the site of the Health Campus, and Heerlen is the place to be for Smart Services.

Department
Launched in 2015, the Maastricht Centre for Systems Biology (MaCSBio) aims to develop a set of computational and mathematical models and methods that will advance our understanding of biological systems, and predict the progression and treatment of complex diseases over time.
MaCSBio strives to perform cutting edge research in the interdisciplinary field of Systems Biology to create a “Digital Twin”, a set of computational and mathematical models based on biological evidence that will help to understand and predict human systems. Research projects at MaCSBio focus on modelling across multiple scales of time and space, tackling areas that are highly relevant for society: systems biomedicine, computational neuroscience and systems toxicology.

Curious?
Are you interested in this exciting position but still have questions? Feel free to contact Michiel Adriaens michiel.adriaens@maastrichtuniversity.nl for more information. Any questions regarding the procedurecan also be directed there.

Applying?
Or are you already convinced and ready to become our new PhD candidate? Apply now, no later than the 22nd of September for this position.

Please upload your CV, motivation letter, grade list and contact information of 2 referees.

The vacancy is open for internal and external candidates. In case of equal qualifications, internal candidates will be prioritized.

Maastricht University is committed to promoting and nurturing a diverse and inclusive community. We believe that diversity in our staff and student population contributes to the quality of research and education at UM, and strive to enable this through inclusive policies and innovative projects led by teams of staff and students. We encourage you to apply for this position.

38 hours per week

Paul-Henri Spaaklaan 1