PhD student modelling of human microbiota

PhD student modelling of human microbiota

Published Deadline Location
24 Apr 28 May Leiden

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Job description

Are you looking for a PhD opportunity and are you interested in a challenging research project in human microbiota? Then the role as PhD student ‘modelling of human microbiota’ might be for you.

As a PhD candidate in the Department of the Medical Statistics and Bioinformatics you will be part of a project aimed to gain more insight on the functional and compositional properties of the microbial ecosystems of our body (human microbiota). In this multifaceted project you will work at the interface between mathematics, ecology, bioinformatics and medical statistics. 

The Project

Human health is profoundly impacted by the microbial populations residing on and within the human body (human microbiota). Several diseases are associated with an imbalance (dysbiosis) in these microbiota. The aim of this PhD project is to adapt and extend existing quantitative approaches drawn from systems ecology, to identify the topologies of microbial interaction networks that characterize such imbalance. This knowledge may ultimately be used for directed therapeutic interventions.

Within this project, you will apply a mesh of mechanistic and statistical modelling techniques on a multitude of metagenomics datasets from different anatomical sites of the human body (i.e. gut, respiratory tract). By using different network inference techniques, you will characterize the dynamics and reconstruct the network of microbial interactions. You will apply concepts of complexity theory to investigate the presence of possible alternative stable states and uncover the mechanisms that govern microbiota stability and resilience to disease.

This requires a multidisciplinary approach covering a broad spectrum of expertise. For this purpose, an interdisciplinary consortium of twelve experts from different institutes and universities has been formed specifically for this project and they will work synergically with you during the entire duration of the PhD track.


Leiden University Medical Center (LUMC)


You are highly motivated and enthusiastic candidate. You hold a master degree in mathematics, theoretical ecology, bioinformatics or a similar discipline. You are interested in microbial communities and have affinity with complex network theory. You possess strong analytical skills, like to work with large datasets and are fluent in at least one programming language (C, C++, Matlab, Python, R). You are well able to communicate with researchers from other disciplines and are a good team player. We also expect you to have excellent written and oral communication skills in English. Recognize yourself in this profile? Then do not hesitate to apply.

Conditions of employment

Fixed-term contract: four years.

You are employed on the basis of a 36-hour week. Appointment will lead to a PhD thesis and is for a maximum duration of four years. Your salary depends on your qualifications and experience, with a maximum of € 2.279 gross per month in the first year, amounting to € 2.919 gross per month in the fourth year based on a full-time position (scale for PhD students, Collective Labor Agreement for University Hospitals).

The terms of employment offered by the LUMC are highly favorable. For example, you will receive 8% holiday remuneration, a year-end bonus, and a pension arrangement with the National Civil Pension Fund. Also, as employee of one of the University Hospitals in the Netherlands, you can benefit from our collective health insurance policy.

Moreover, the LUMC offers excellent facilities in the area of education, child-care center, and career advice.



At the Leiden University Medical Centre (LUMC), we are continually seeking to improve the quality of healthcare. The LUMC aims for excellence in patient care, research, teaching, training and continuing education.


Biomedical Data Sciences

The LUMC is a center for medical innovation that aims to improve patient care through leading international research. So as to also provide our patients with a safe and friendly environment, we need doctors, medical care specialists, support staff and academic researchers. You will work at the department of Biomedical Data Sciences at the LUMC. This department is specialized in combining expertise in the fields of medical statistics, molecular epidemiology, bio-informatics and data management. Furthermore, you will also work closely with our partner in this project, namely: the RIVM. The center of Epidemiology and Surveillance of Infectious Diseases at the RIVM analyses and protects the health of the Dutch in the domain of infectious diseases and investigates the effectiveness of control measures. The department Infectious Diseases Modelling is specialized in developing mathematical en statistical models to solve epidemiological research questions. Lastly, as a PhD student, you will collaborate and regularly communicate with the other members of the consortium at the VUMC, Wageningen University, TNO, UMCU, MUMC and Spaarne Gasthuis.


  • PhD; Research, development, innovation; PhD scholarship
  • Health
  • max. 36 hours per week
  • €2279—€2919 per month
  • University graduate
  • D.18.MV.MP.13


Leiden University Medical Center (LUMC)

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Albinusdreef 2, 2333 ZA, Leiden

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