PhD Position: Automated Knowledge Graphs for Kidney Physiology and Pathology

This vacancy represents an exciting opportunity for ambitious individuals to join the department of Cell Biology-Inspired Tissue Engineering (cBITE) at the MERLN Institute for Technology-inspired Regenerative Medicine at Maastricht University in the Netherlands as part of the ERC STG project “AUTOMATHIC”, under the supervision of dr. Aurélie Carlier. This 5-year interdisciplinary project aims to perform cutting-edge research in developing new methodologies for the automated modeling of the dynamic behavior of large biological networks. The project also involves engaging with national and international stakeholders. 

In silico models aim to capture and elucidate the complex and emergent interactions of biological systems, with the goal of expediting research and potential clinical translation. For example, ordinary differential equation (ODE) models of toxin and drug transport are being developed to bring safer therapies to chronic kidney disease patients. Despite recent progress, these cutting-edge ODEs only model transport in steady state and remain limited regarding the amount and complexity of dynamic transport mechanisms as it is often not clear which kinetic relation is most suitable. This limitation is due to the manual and labor-intensive approaches to construct the ODEs, which critically hinder their application in quantitative toxicity assessment in key industrial settings like drug development. In AUTOMATHIC, we aim to develop an integrated framework for automated ODE structure identification, parameter estimation and model evaluation and explore the capabilities of the developed framework for toxin and drug transport in the kidney. 

Requirements and key expertise 

• Master’s degree in mathematical biology, computational mathematics, biomedical engineering, numerical optimization, biophysics, systems biology, bioinformatics, computer science or equivalent
• Demonstrated ability to work independently as well as in a team
• Excellent programming skills (for example Matlab, Python, R)
• Expertise in systems biology and data integration (for example disease maps, knowledge graphs, network biology, SBML) is a plus
• Background in biology or biomedical sciences (or equivalent) is a plus
• Good oral and written English communication

Additional training opportunities will be provided based on your skills.

Project description: 

• Development of an integrated workflow for automatic extraction of information from literature, biological datasets, databases, and existing maps, including LLM-assisted reasoning and combining them into a physiological map/knowledge graph, using a graphical editor such as for example CellDesigner
• Construction of a kidney physiology and pathology map 
• Network analysis of the obtained map

Project embedding:
The project will be coordinated by the MERLN Institute for Technology-Inspired Regenerative Medicine (http://merln.maastrichtuniversity.nl/) as part of the ERC STG project “AUTOMATHIC”. The computational group at MERLN focuses on multiscale computational modelling of biological processes, with a particular interest in bone tissue engineering applications, kidney physiology and pathology and cell-biomaterial interactions and using a range of data-driven to mechanistic modelling approaches (https://www.carlier-insilico-lab.com/who-are-we). 

What we offer
As PhD Position: Automated Knowledge Graphs for Kidney Physiology and Pathology at Faculty of Health, Medicine and Life Sciences, 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 €2901,00 and €3707,00 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 Health, Medicine and Life Sciences
At the Faculty of Health, Medicine and Life Sciences (FHML), everything revolves around healthy living. Our research and education are not solely focused on recovery, but place a strong emphasis on prevention, health preservation, and health promotion. Our aim is to use our knowledge and expertise to genuinely contribute to the well-being of individual people as well as society in total. 

In, research, and healthcare, FHML is closely collaborating with the academic hospital in Maastricht, together forming the Maastricht University Medical Center (MUMC+).  FHML is strongly connected in education, research, and care with the Maastricht academic hospital, together with which it forms the Maastricht University Medical Centre (MUMC+). 

FHML, which is the largest faculty of Maastricht University, is formed by an (inter)national community of employees and students. The faculty offers a wide range of Dutch and English-taught bachelor's and master's programs in innovative educational concepts in which the emphasis is always on building bridges to practice.
 

The multidisciplinary research of the FHML focuses on a number of carefully chosen topical current themes. In addition to research aimed at gaining new insights, it also concerns research whose results can be directly translated into concrete applications and innovations. The implementation of the various research programs is organized in our six graduate schools and two institutes.

 
Curious?
Are you interested in this exciting position but still have questions? Feel free to contact A. Carlier at a.carlier@maastrichtuniversity.nl for more information.

Applying?
Or are you already convinced and ready to become our new PhD Position: Automated Knowledge Graphs for Kidney Physiology and Pathology? Apply now, no later than November 24, 2024, for this position.

The application should contain:

• Cover letter with motivation, fit and preferred starting date
• CV 
• Contact information of two references

The selection process will consist of multiple interviews (technical and non-technical).

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.