PhD candidate for tracer-based metabolomics to study Gaucher disease

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Ronan M.T. Fleming

May 10, 2023, 3:05:05 AMMay 10
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Dear All,
here is a new Recon4IMD vacancy that might suit someone interested in analytical chemistry and modelling.

The Metabolomics & Analytics Centre at the Leiden Academic Centre for Drug Research (LACDR) at Leiden University is looking for a:

PhD candidate for tracer-based metabolomics to study Gaucher disease

The Metabolomics and Analytics Center (MAC) seeks to hire a PhD student for the study and optimization of treatment of Gaucher disease using tracer-based metabolomics and advanced metabolomics and lipidomics methods. You will be part of a larger EU project (Reconstruction and Computational Modelling for Inherited Metabolic Diseases; for accelerating the diagnosis and personalize the management of inherited metabolic diseases, and especially of Gaucher disease. You will develop a tracer-based metabolomics workflow using liquid chromatography (LC) coupled to high resolution mass spectrometry (MS) and using advanced MS/MS methods (such as electron activation dissociation technology). The data acquisition workflow will be integrated with a computational workflow to process data; a first version of such a workflow has been recently developed at MAC. You will use the workflow to study in-vitro models of Gaucher disease to better guide patient management and predict treatment response. For this you will be supported by colleague researchers developing computational metabolic models for Gaucher disease in the EU project, and by integrating your metabolomics data with other transcriptomics or proteomics data. You will work together with a large group of clinicians, experts on inherited metabolic diseases, omics and computational modelling using reconstructed metabolic networks. The aim of your project is to develop methods, apply them to support development of better treatment, and apply these to be ultimately translated into clinical care.

Key responsibilities 
You will focus on 1) developing advanced tracer-based metabolomics technologies and methods, 2) applying your methods to analyze disease pathways and interventions in in-vitro models, and 3) screening for novel metabolites and lipids involved in Gaucher's disease. You will integrate and interpret your data using computational reconstructed metabolic networks and using multi-omics data integration in collaboration with other researchers. 

Selection criteria 
•    Recent Master degree in Chemistry, Biochemistry, Biopharmaceutical Sciences, Life Sciences, Biomedical Sciences, preferably with a Major in Analytical Chemistry or Biochemistry 
•    Interest in the field of metabolomics, lipidomics, mass spectrometry, in-vitro cell culture experiments, biochemistry and computational modeling
•    Independent and creative team player with good communicative skills
•    Proficient in spoken and written English
Our organization 
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. The research carried out at the Faculty of Science is very diverse, ranging from mathematics, information science, astronomy, physics, chemistry and bio-pharmaceutical sciences to biology and environmental sciences. The faculty is located at the heart of Leiden’s Bio Science Park, one of Europe’s biggest science parks, where university and business life come together. 

The LACDR is one of the eight research institutes of the Faculty of Science. LACDR is an international leading drug research institute, and Leiden University consistently ranks within the top-20 world-wide within the subject-based QS Ranking in Pharmacology and Pharmacy. At LACDR, we develop innovative scientific concepts in fundamental and translational research underlying the discovery and optimization of drugs, and personalized medicines. 

The ambition of the Metabolomics and Analytics Centre (MAC) at the LACDR is to develop innovative analytical strategies for metabolomics-driven health monitoring and systems biology studies. Understanding the intricate balance between health, disease and adaptation to challenges relies on the identification of systematic changes during time. We believe that health monitoring and personalized medicine approaches can be achieved with clinical studies involving multiple patient samples, often in combination with stem cell derived in-vitro or organ-on-a-chip models. MAC has been a pioneer in Metabolomics since early 2000, and combines advanced metabolomics technologies, innovative sample preparation and robotics for clinical and in-vitro samples, and computational and FAIR digital twinning expertise’s. MAC houses a beyond-state-of-the-art metabolomics and mass spectrometry lab with automated and robotic sample preparation, access to state-of-the-art cell culture and advanced imaging facilities. MAC is involved in many national and international exciting academic and industrial collaborations.

Terms and conditions  
We offer a full-time appointment of initially one year. After a positive evaluation of the progress of the research, teaching evaluations, personal capabilities and compatibility, the appointment will be extended for another three years. You will be appointed in accordance with the Collective Labour Agreement for Dutch Universities. The salary ranges from € 2.541,- to € 3.247,-  gross per month depending on experience (pay scale P)
Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development. Our individual choices model gives you some freedom to assemble your own set of terms and conditions. For international spouses we have set up a dual career program. Candidates from outside the Netherlands may be eligible for a substantial tax break. For more information, see the website:

All our PhD students are embedded in the Leiden University Graduate School of Science. Our graduate school offers several PhD training courses at three levels: professional courses, skills training and personal effectiveness. In addition, advanced courses to deepen scientific knowledge are offered by the research school.

Diversity and work-life balance              
Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups. LACDR is a highly diverse institute, in culture, background, and gender. We stand for excellence in a caring Institute. We wish to reflect society in all aspects, as we believe that this improves the dynamics in our organization. Therefore, we support and understand the need for a work/life/family balance and consequent varying working hours and places. We believe that doing good science is fun, and goes hand in hand with a friendly culture.

Enquiries can be made to Prof. dr. Thomas Hankemeier, e-mail:   
If you have any questions about the procedure, please contact Mrs. Ina Hazejager (e-mail:, telephone: +31 71 527 4220).  
Instructions for applications 
To apply for this vacancy, please send an email to The closing date is 7 June 2023. Please ensure that you include the following additional documents quoting the vacancy number:
•    Motivation letter;
•    Full curriculum vitae;
•    A list of grades;
•    Two references.

Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
Associate Professor,
School of Medicine,
National University of Ireland, Galway.
Assistant Professor,
Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)
Peer-reviewed publications:
Mobile:  +353 852 109 806
Skype: ronan.fleming
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