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  3. PhD candidate: Mathematical modeling of host‐pathogen‐drug interactions to optimize antibiotic therapy, ESR 15

PhD candidate: Mathematical modeling of host‐pathogen‐drug interactions to optimize antibiotic therapy, ESR 15

PhD candidate: Mathematical modeling of host‐pathogen‐drug interactions to optimize antibiotic therapy, ESR 15

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Einsteinweg, Leiden, Zuid-Holland
Tijdelijk contract / Tijdelijke opdracht


Leiden University has available an Early Stage Researcher / PhD candidate position on Translational pharmacology of antimicrobial drug effects (ESR 15) as part of the Innovative Training Network (ITN) Training towards Innovative Personalized Antibiotic Therapy (TIPAT).

In this PhD project the ESR will develop mathematical models to characterize population dynamics of pathogens considering the interaction between pathogens, antimicrobial agents and the host (patient) immune system. The ultimate goal of these models is to enable immune response biomarker-guided treatment optimization in patients, and to aid in translation between preclinical model organisms and patients. Model development will in part be guided by developing theoretical/conceptual models to guide design of experiments, and in part based on data generated in the TIPAT project. An ability to effectively collaborate with other PhD students in TIPAT is therefore important. We primarily aim to develop mathematical models based on ordinary differential equations, although we also have an interest to incorporate individual-based or stochastic modeling approaches to understand within-host population dynamics and heterogeneity in bacterial populations under treatment with antimicrobial agents.

This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 861323.

Key responsibilities

  • Develop mathematical models for host-pathogen-drug interaction based on both theoretical and data-driven approaches;
  • Actively participate in the TIPAT international and inter-disciplinary training program, which includes regular webinars and presentations, network-wide training events, and several short international secondments to receive further training;
  • Reporting of results at project meetings and conferences;
  • Writing of progress reports and scientific manuscripts;
  • Contribution to educational activities;
  • Contribute to a collaborative, open and positive working atmosphere in the research group.


  • Master degree in the field of pharmacology, pharmacometrics, (computational/mathematical) biology, chemical engineering, (bio-) physics or a related degree (graduation date before project start date);
  • Experience in mathematical modeling in pharmacology or biology using ODEs;
  • Experience in use of scripting languages (R, Python, MatLab);
  • Experience in specifically PK-PD modeling is of added value;
  • Solid understanding biology;
  • Knowledge of immunology and/or pharmacology is of added value;
  • Interest in antimicrobial drug research;
  • Experience in individual-based or stochastic modeling techniques (CA, ABM) of added value
  • Good communication and interpersonal skills to organize research with both academics and professionals;
  • Good communication (verbal and writing) skills in English;
  • Confirmed capacity to write high-level scientific reports and papers;
  • Interested in participating in educational tasks;
  • Independent and creative team player.

At the time of commencing their employment, researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of their (recruiting) host organization for more than 12 months in the 3 years prior to their recruitment.

Applicants must be in the first four years (full-time equivalent research experience) of their research career and have not been awarded a doctoral degree at the first day of their employment contract. This research experience is measured from the date when they obtain the degree which formally entitles them to embark on a doctorate (either in the country in which the degree was obtained or in the country in which the researcher is recruited), even if a doctorate was never started or envisaged. Research experience is measured to the first day of the employment contract of the researcher.

Usual MSCA eligibility criteria apply and will be verified during the application process. For more information on MSCA, please see the website


We offer a one year term position, with the possibility of an extension by a further three years, based on a positive evaluation of the progress of the thesis, personal capabilities and compatibility. Salary range from € 2,325.- to € 2,972.- gross per month (pay scale P in accordance with the Collective Labour Agreement for Dutch Universities). Special agreements as a Marie Curie early stage researcher you will be entitled to extra allowances based on EU funding. These allowances are explained at a later stage. The planned start of employment: Between 01-09-2020 and 01-11-2020

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. Candidates from outside the Netherlands may be eligible for a substantial tax break (30% of gross salary exempt from income taxation).

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.

In addition to their individual scientific projects, TIPAT ESRs will collaborate with world-leading research groups and industries within the consortium through secondments. All ESRs will benefit from further extensive and varied continuing education, completing a series of carefully designed training modules and transferable skills courses; they will participate in symposia, workshops, and international conferences and will have meaningful exposure to the industrial environment through TIPAT industrial partners.

Additional information

Questions about this position can be send to Coen van Hasselt, email coen.vanhasselt@lacdr.leidenuniv.nl


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