What will you do
Research Fellowship 3 (RF3): Functional markers of MN status
Duration: 48 months
Supervisors:
- Dr Angelique de Man (Amsterdam UMC)
- Dr Maurits de Rotte (Amsterdam UMC)
- Dr Frans van der Horst (Reinier Haga Medical Diagnostic Center)
- Dr Lennard Dekker (Reinier Haga Medical Diagnostic Center)
Doctoral enrolment: Amsterdam UMC Doctoral School
Project description:
Micronutrient deficiencies are common in critically ill patients and may significantly delay recovery. However, current diagnostic methods are often insufficient, and clinical care typically relies on fixed-dose supplementation rather than personalised treatment strategies.
Within the Marie Skłodowska-Curie Actions–funded BIO-MICRO project, this PhD position aims to enhance the diagnostic armamentarium for assessing functional micronutrient status through innovative analytical approaches. Improved diagnostics may enable the identification of patient subphenotypes that are most likely to benefit from targeted micronutrient therapy.
The aim of this PhD study is to develop and validate new functional biomarkers to identify deficiencies in micronutrients, like vitamins and trace elements. Firstly, with the use of relevant databases, like www.hmdb.ca, metabolic pathways are to be identified, that depend on enzymes, that have selected vitamins and trace elements as cofactor. Based on a literature study, the concentration behaviour of metabolites, within these selected metabolic pathways, has to be identified in relation with deficiencies of vitamins or trace elements.
Based on the concentration patterns of the micronutrients and of the metabolic pathways within the physiological compartments of patients, it has to be explored whether these patterns can be related to type and severity of deficiencies and to the type of the physiological status (e.g. type of disease). The PhD student has to set up these semantic FAIR-models with internationally established packages in addition to the deployment of LC-MS/MS, ICP-MS methods for the measurement of the relevant biomarkers in the different body compartments. In addition, the PhD student will perform these new measurements in samples from ICU patients that will be enrolled in a multicentre, prospective, observational clinical study. This data driven semantic model will be used to explore the possibility to predict deficiencies of micronutrients in ICU patients, based on patterns of selected biomarkers.
Your main tasks and responsibilities in this project are:
1. Pathway and cofactor Mapping
2. Semantic FAIR data modeling
3. LC-MS/MS, ICP-MS method development
4. Measurements of new functional markers in samples from IC patients
5. Predictive modeling for clinical applications
What do we expect
We are looking for a highly motivated and proactive researcher who is able to work both independently and collaboratively within an interdisciplinary team. You have strong analytical and problem-solving skills, with the ability to integrate multidisciplinary data. You have excellent communication skills for disseminating research findings. You have a collaborative mindset, with experience in interdisciplinary teams (e.g., clinicians, bioinformaticians, analytical chemists). The position includes intersectoral secondments in Delft and Appingedam, of 6 months each. The project should result in the successful completion of a PhD thesis.
To be eligible for this position, applicants must meet the Marie Skłodowska-Curie admission requirements:
- You must not already hold a doctoral degree.
- You must comply with the MSCA mobility rule: you must not have resided in or carried out your main activity (work, studies, etc.) in the Netherlands for more than 12 months during the three years immediately prior to recruitment.
Required qualifications and experience
- A Master’s degree in biochemistry, molecular biology, bioinformatics, or analytical chemistry
- Excellent command of English, both written and spoken; proficiency in Dutch is an advantage
- Adequate knowledge of metabolic pathway analysis, semantic data modeling, and LC-MS-based metabolomics, with a strong commitment to FAIR data principles and translational research statistics
Desirable skills (not essential)
- Experience with medical or scientific writing
- Laboratory experience
Your working environment
You will work in a highly stimulating and interdisciplinary research environment spanning Amsterdam UMC, Reinier Haga Medical Diagnostic Center, and Diagnotix. At the Intensive Care department of Amsterdam UMC, you will join a large and dynamic research group consisting of approximately 40 PhD candidates and 5 postdoctoral researchers, supervised by 7 principal investigators across two locations (AMC and VUmc).
What we offer
This PhD position is funded by the Marie Skłodowska-Curie Actions (MSCA) of the European Union’s Europe 2024 research and innovation program under grant agreement No 101226686. You will be appointed as fulltime PhD student for 4 years at Amsterdam UMC.
Salary scale: Market competitive based on a 36 hour week, depending on qualifications and experience. Successful candidates will receive an attractive base-salary in accordance with the Marie Skłodowska-Curie Actions, for 48 months. The exact (net) salary depends on the EU-defined country correction factor, and on local tax regulations (for additional information see EU MSCA website). Exact salary will be confirmed upon appointment.
Doctoral candidates will receive a living allowance of €4010/month (correction factor to be applied per country, and local employer’s contribution and tax regulations). They will also benefit from a monthly mobility allowance of €710. In addition a family monthly allowance of €660 (if applicable) is on offer to fellows with a spouse &/or child/children. Successful applicants are eligible for parental leave in compliance with the Dutch legislature.
In addition to your local PhD training, you will participate in a comprehensive and attractive educational programme specifically designed for the 13 Research Fellows within the BIO-MICRO consortium. The BIO-MICRO training programme offers a blended learning approach that combines monthly interactive live online sessions (60–90 minutes) with in-person workshops. The online curriculum covers essential topics in clinical research, including epidemiology, biostatistics, observational and clinical trial design, statistical computing, and scientific writing. In addition, four intensive three-day in-person workshops are dedicated to the development of both academic and transferable skills. In addition, all fellows will carry out 12 months of secondments and will be enabled to participate in relevant international scientific conferences. Together, this structured training programme is designed to optimally prepare you for a successful career as a critical care researcher.
If you don’t have the nationality of an EU/EEA country or Switzerland, you will need a residence permit to live and work in the Netherlands.
How to apply for this position
Follow the link to apply for this job: https://werkenbij.amsterdamumc.org/en/vacatures/research/msca-dn-phd-position-functional-markers-of-micronutrient-status#questions
