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Theoretical Biology & Bioinformatics

We have several open PhD positions

A PhD position at Utrecht University means that you will be employed by the University for 4 years. You will spend most of your time doing research, and a limited amount of time attending and giving courses. You will receive a gross salary starting at approximately 2000 Euro per month. We are a Theoretical Biology & Bioinformatics group: please apply only if you have a relevant background in (bio)mathematical modeling, computational modeling and/or bioinformatics.

PhD position in evolutionary immuno-epidemiology

The evolution of host-pathogen interactions is a topic receiving considerable recent attention. Questions in this field have mainly been addressed from an epidemiological point of view, assuming that pathogens evolve in a homogeneous population of hosts. However, a hallmark of the immune system is that hosts differ genetically, and mount different immune responses even to the same pathogen. Therefore, pathogens evolve in highly heterogeneous host populations, and in each newly infected host a pathogen has to cope with immune responses that differ from the responses that it has learned to cope with in previous hosts. We argue that this has important implications for host-pathogen co-evolution, in particular the balance between virulence and transmission. In this project we hope to shed light on questions as to why some pathogens induce acute infections that are cleared in several days (e.g., influenza A/hepatitis B in adults), while others lead to long-lasting chronic infections (e.g., HIV/hepatitis B in infants). We take an interdisciplinary approach linking immunological and epidemiological modeling of host-pathogen co-evolution, using agent-based approaches and mathematical models based on the Price equation. The models to be developed track the immune response of each host, the evolution of the pathogen quasi-species within that host, and the evolutionary dynamics on the population level. Focusing on data from hepatitis B, HIV, and influenza A, we will build models that are simple but nevertheless operate in a realistic parameter regime both at the immunological and epidemiological level.

Project organization. The project emanates from a collaboration between the department of Theoretical Biology and Bioinformatics of Utrecht University (Prof. Dr. Rob de Boer) and the Centre for Infectious Disease Control of the National Institute for Public Health and the Environment (Dr Michiel van Boven). The person to be hired will be formally appointed by Utrecht University, but spend a sizeable fraction of their time at both institutions. Utrecht University and the National Institute for Public Health and the Environment are less than 5km apart.

Qualifications. We are looking for highly motivated individuals with experience, or an interest in biology and a training in mathematical modeling and computer simulation. Ideally, we are looking for a computational biologist. The person to be hired should communicate easily in English, both verbally and in writing. The candidate is offered a full-time position for four years.

Additional information about this vacancy can be obtained from: Prof. Dr. Rob J de Boer: R.J.DeBoer@uu.nl.

PhD postion in a NWO TOP-GO project entitled "Evolutionary cell biology of signal transduction networks from primitive eukaryotes to higher plants"

Snel Lab, Theoretical Biology and Bioinformatics, Utrecht University
Project Description.
Plants and other eukaryotes have complicated signaling networks to regulate growth. Preliminary results suggest that in Plants these systems are the result of a combination of the emergence of novel pathways and adaptation of pre-existing pathways from the primitive eukaryotic ancestor. The aim is reconstruct the evolution of these systems, first from the common eukaryotic ancestor to animals, fungi and primitive algae and secondly from algae to primitive plants (such as mosses and ferns) and higher plants (such as the plant model organism Arabidopsis thaliana). The methods for this reconstruction are comparative genomics to study the gene loss, gain and duplication of the core pathway components as well as integrative bioinformatics to study the rewiring of the network. The candidates are offered a full-time position for four years.
Qualifications
We are looking for highly motivated individuals with experience, or an interest, in biology and training in bioinformatic analysis. Applicants should possess hands on experience with sequence analysis or expression data analysis, as well as experience with a scripting language (such as perl or python). The persons to be hired should communicate easily in English, both verbally and in writing.
How to apply
Please send your CV, along with a cover letter outlining your specific qualifications for the preferred positions including contact information for at least two references to Dr. Berend Snel, b.snel@uu.nl

Theoretical Biology & Bioinformatics / Last modified on 11 May 2012 / Webmaster: R.J.DeBoer@uu.nl