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Postdoc in the field of computational modelling of metabolism

A computational biologist is sought to join an interdisciplinary collaborative Horizon 2020 project, entitled “Systems Medicine of Mitochondrial Parkinson’s …

ongeveer 2 jaar geleden


J.H. Oortweg, Leiden, Zuid-Holland
Tijdelijk contract / Tijdelijke opdracht
Uren per week:
38 uur
€ 2588 - € 4048 per maand


A computational biologist is sought to join an interdisciplinary collaborative Horizon 2020 project, entitled “Systems Medicine of Mitochondrial Parkinson’s Disease” (sysmedpd.eu/). The candidate will be responsible for generation and analysis of personalized constraint-based computational models of human metabolism. Specifically, the candidate will integrate an established constraint-based computational model of human dopaminergic neuronal metabolism, with metabolomic, transcriptomic, proteomic and biochemical phenotypic data previously generated on multiple in vitro cultures of monogenic Parkinson’s disease patient-derived cell lines and isogenic controls. The candidate will develop a data-driven, mechanistic computational modelling approach to systematically characterize and biochemically interpret the metabolic consequences of mitochondrial dysfunction in monogenic Parkinson’s disease patients, then predict targets to reduce this dysfunction. Top ranked predictions will subsequently be tested on in vitro and rodent models by experimental collaborators within SysMedPD.

The responsibilities of the position include:

  • Constraint-based computational modelling of dopaminergic neuronal metabolism;
  • Characterise and biochemically interpret metabolic changes associated with monogenic Parkinson’s disease with mitochondrial dysfunction;
  • Close collaboration with experimental, bioanalytical and bioinformatics experts responsible for generation, analysis and preprocessing of experimental data, respectively;
  • Close collaboration with experimental drug discovery experts, responsible for prioritization, selection and testing of candidate therapeutic compounds.


  • An undergraduate degree in computer science, computational engineering, bioengineering or related disciplines;
  • A master’s degree in computational biology, bioinformatics, bioengineering, or related disciplines;
  • A PhD in data-driven computational modeling of biochemical networks, including development and application of novel modeling methods to successfully address biological questions;
  • Demonstrable programming skills, e.g. open-source contributions to projects in Matlab, Julia, Python, or the like;
  • Experience with collaborative software development tools, e.g. git, etc;
  • Good written and verbal English communication skills are important;
  • Experience with goal-oriented team science is essential;
  • Knowledge of biology and biochemistry is essential, ideally energy metabolism.


We offer a one-year term position, with the possibility of renewal for up to three more years. Salary range from €2,588 to €4,084 gross per month (pay scale 10 in accordance with the Collective Labour Agreement for Dutch Universities).

Leiden University offers an attractive benefits package with additional holiday (8%) and end-of-year bonuses (8.3 %), training and career development and sabbatical leave. 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 programme. Candidates from outside the Netherlands may be eligible for a substantial tax break. More at https://www.universiteitleiden.nl/en/working-at/job-application-procedure-and-employment-conditions.

Leiden University is strongly committed to diversity within its community and especially welcomes applications from members of underrepresented groups.

Additional information

Enquiries can be made to Dr. Ronan Fleming, email r.m.fleming@lacdr.leidenuniv.nl, coordinator of SysMedPD. If you have any questions about the procedure, please contact Mrs. Loes Beijersbergen, email l.beijs@lacdr.leidenuniv.nl.

To apply for this vacancy, please send no later than 15 June 2018, an email to Dr. R. Fleming: r.m.fleming@lacdr.leidenuniv.nl. Please ensure that you upload the following additional documents quoting the vacancy number:

  • A detailed CV;
  • A cover letter mentioning the reference number;
  • List of publications;
  • Description of past research experience and how future interests complement the proposed role;
  • Name and addresses of three referees.