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

Wetenschappelijke functies, PhD-posities
Omvang (fte)
Geplaatst op
21 april 2020
27 mei 2020

Solliciteer vandaag

The Faculty of Science and the Leiden Academic Centre for Drug research are looking for a

PhD candidate: Mathematical modeling of hostpathogendrug interactions to optimize antibiotic therapy, ESR 15

Project description
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.

Selection criteria

  • 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.

Our organisation
The Faculty of Science is a world-class faculty where staff and students work together in a dynamic international environment. It is a faculty where personal and academic development are top priorities. Our people are committed to expand fundamental knowledge by curiosity and to look beyond the borders of their own discipline; their aim is to benefit science, and to make a contribution to addressing the major societal challenges of the future. 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 research activities are organised in eight institutes. These institutes offer eight bachelor’s and twelve master’s programmes. The faculty has grown strongly in recent years and now has more than 2.200 staff and almost 4,200 students. We are 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 Innovative Training Network (ITN) Training towards Innovative Personalized Antibiotic Therapy (TIPAT) has started March 1, 2020. TIPAT offers a cutting-edge training-by-research program for 15 Early stage researchers (ESRs) / PhD candidates.  TIPAT is part of the Marie Skłodowska-Curie International Training Network (ITN) of the European Commission. ESRs in TIPAT will be part of an international network of universities, hospitals and companies.  To enable development of innovative personalized antibiotic treatment strategies, quantitative understanding of the interplay between drug, pathogen and host is crucial. The TIPAT network will train inter-disciplinary specialists optimally equipped with a skill set to address this challenge. Central to the TIPAT research and training program of ESRs is the combination of state-of-the art quantitative modelling with approaches in clinical pharmacology, immunology and microbiology, which enables development of innovative methodology to personalized antibiotic therapies.

Terms and conditions
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.

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

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

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

You application should be send to tipat@lacdr.leidenuniv.nl and to applications@tipat.eu. When applying, please use the following email subject title: TIPAT ESR15 - Your Name. In your application please include the following files:

  • A motivation letter (1 page maximum), please include in your letter alternative ESR TIPAT positions of interest to you if not selected, if any;
  • A CV according to the Europass format;
  • Two reference letters (at least one from your Master thesis supervisor);
  • An up-to-date of grades in your bachelor and master programs;
  • Optional: English proficiency test results (TOEFL, IELTS).

Please submit online your application no later than May 27, 2020.

We may extend this deadline depending on the developments of the COVID19 pandemic.

Applicants are notified if they are invited for video-conferencing interviews by May 30.
Please note these dates may change if the application deadline is extended.

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