PhD Candidate in Transcriptomic data Analysis with a Focus on Adverse Outcome Pathways (AOPs)

PhD Candidate in Transcriptomic data Analysis with a Focus on Adverse Outcome Pathways (AOPs)

Published Deadline Location
11 Jun 30 Jun Maastricht

Job description

Enhance human and environmental safety by joining our fully funded PhD position at Maastricht University! Become a key player in exploring applications of transcriptomic data linked to Adverse Outcome Pathways to shape the future of toxicological research through the innovative TXG-MAP project.

Job Description
As the successful candidate for this open science PhD position, your primary responsibility will be to lead the analysis and interpretation of large-scale transcriptomic data within the TXG-MAP project. Your role involves selecting and generating Adverse Outcome Pathway (AOP) networks related to liver, kidney, lung, and neuronal toxicity. Through innovative gene mapping strategies, you will develop and evaluate new analytical strategies to evaluate transcriptomic data in the context of AOPs and use those to validate the TXG-MAPr toolbox, integrating gene sets with Key Events (KEs) and advancing our understanding of toxicological processes. Your work will culminate in the quantification of AOP activity, establishing a framework that enhances human and environmental safety assessments for chemicals. As part of your PhD position, you will be writing your PhD thesis, taking part in education, and participating in activities by the research school NUTRIM (Institute of Nutrition and Translational Research in Metabolism).

Situated within the Department of Bioinformatics (BiGCaT) at Maastricht University, this position offers a collaborative and dynamic research environment as part of a dynamic, multidisciplinary team. This project extends beyond borders, working with (inter)national partners from various backgrounds contributing to different aspects of the TXG-MAP project. As a key player in this initiative, you will have the opportunity to collaborate with experts, enhancing your research capabilities and contributing to the collective success of the project.

In summary, this position involves the following tasks and responsibilities:
  • Develop and evaluate new analytical methods for transcriptomic data and interpret the results in the context of molecular adverse outcome pathways.
  • Contribute to the selection and generation of Adverse Outcome Pathway (AOP) networks relevant to liver, kidney, lung, and neuronal toxicity
  • Curate molecular pathways based on scientific literature and existing knowledge resources
  • Implement innovative gene mapping strategies to link genes to Key Events (KEs)
  • Employ quantitative (including statistical) techniques to quantify Adverse Outcome Pathway (AOP) and Key Event (KE) activity
  • Compare outputs with traditional transcriptomic data analysis methods, including pathway overrepresentation analysis and Gene Ontology enrichment
  • Ensure effective integration of gene sets, KEs, and molecular pathways
  • Develop a framework needed to evaluate the TXG-MAPr toolbox

The vacancy requires a candidate to possess a diverse set of soft skills. Effective communication and collaboration skills are essential, as the successful candidate will need to work closely with a multidisciplinary team of researchers and engage with international partners. Strong problem-solving and critical thinking abilities are crucial for navigating complex research challenges. Adaptability and a proactive attitude towards learning and skill development are highly valued. Additionally, exceptional organizational and time-management skills are necessary to meet project milestones and reporting deadlines. Furthermore, a commitment to attention to detail, and an ability to work independently while
also seeking guidance when needed demonstrate a well-rounded set of soft skills for this PhD position in a European-funded project.

As we recognize the pivotal role of soft skills, the following enumeration delves into the specific hard skills essential for excelling in this dynamic PhD position within the TXG-MAP project.
  • Proficiency in coding languages, particularly R and/or Python
  • Strong analytical skills for tasks involving the analysis and interpretation of large-scale transcriptomic data
  • In-depth knowledge of transcriptomic data analysis, as the position involves tasks related to gene mapping, AOP network development, and molecular pathway modeling using transcriptomic datasets
  • Knowledge of biology, toxicology, chemical risk assessment, and Adverse Outcome Pathways (AOPs) will be an advantage
  • Proficiency in semantic web technologies and/or data integration is useful

What we offer
As PhD Candidate in Transcriptomic data Analysis with a Focus on Adverse Outcome Pathways (AOPs) 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 €2770,00 and €3539,00 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.

Are you interested in this exciting position but still have questions? Feel free to contact Egon Willighagen at or Marvin Martens at for more information.

Or are you already convinced and ready to become our new PhD Candidate in Transcriptomic data Analysis with a Focus on Adverse Outcome Pathways (AOPs)? Apply now, no later than June 30, 2024, for this position.

Please upload your CV and motivation letter.

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.


Maastricht University (UM)


  • PhD
  • Health
  • €2770—€3539 per month
  • University graduate
  • 1004


Maastricht University (UM)

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P. Debyelaan 25, 6229HX, Maastricht

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Application procedure

Application procedure

Make sure to apply no later than 30 Jun 2024 23:59 (Europe/Amsterdam).