Do you want to pursue a PhD in computational biology? Are you interested
in the genome diversity of bacteriophages across space and time? And do
you want to combine bioinformatics and mathematical modelling to study
the evolutionary factors that impact bacteriophage diversity? Then we
are looking for you!

  Job description  

Viruses that infect bacteria - bacteriophages - are the most
abundant biological entities on Earth. They contribute significantly
to bacterial ecology and evolution and hence impact the function of all
ecosystems. Due to their parasitic lifestyle, phages are constantly under
selection, resulting in an enormous phage genome diversity. Metagenomics,
i.e., bulk sequencing the genetic content of environmental samples, has
recently revealed a surprising amount of phage diversity. Particularly,
the within-species diversity of phages varies to a large extent in natural
populations, and little is known about the distribution of phage diversity
across space and time, and which factors drive this diversity.

In this project, you will combine bioinformatics and modelling to untangle
the drivers of phage diversity across space and time. Potential factors
influencing phage diversity are host diversity, presence of other phages,
and environmental factors like spatial structure. You will compare phage
diversity in different types of environments, such as marine and soil
environments. Particularly, you will develop bioinformatics pipelines
to analyze public phage genome and metagenome data with the aim to
estimate phage diversity. Additionally, you will formulate mathematical
and computational models of phage evolution to explain observed patterns
of diversity. You will refine these models based on the observations
from the genomic data.

Beyond the scientific and potential application merits, you will build
a network for your future career both within and outside Wageningen
University.

  Your qualities  

You have:

* a successfully completed MSc degree in bioinformatics, evolutionary
  biology, applied mathematics, or another related field;

* proficiency in programming (e.g., python) ;

* experience in high-throughput sequencing data analysis and comparative
  genomics or strong interest to develop it;

* strong affinity with the development of mathematical models and their
  application to genomic data;

* fascination for the evolution of microbes and their viruses and a
  quantitative mindset;

* a proactive attitude and teamwork skills and you are committed to
  obtaining a PhD ;

* a very good level of oral and written English.

A PhD is a learning trajectory. If you do not yet have a track-record
showing all the requirements but do have a strong motivation to acquire
the skills necessary to make this project a success, we would like to
encourage you to apply.

  Supervision and Training  

The research is embedded in two chair groups at Wageningen University:
the Bioinformatics group led by prof. Dick de Ridder and the Laboratory
of Genetics led by prof. Bas Zwaan. Your daily supervisors will be
dr. Hilje Doekes and dr. Anne Kupczok, with complementary expertise:
mathematical biology and evolutionary modelling (Hilje Doekes) and
bioinformatics and comparative genomics (Anne Kupczok). The position
is for four years, and you will join the Dutch graduate school PE&RC,
which offers PhD training and other activities.

  Offer  

The gross salary for the first year is  euro  2.770 - per month rising to
 euro  3.539,-  in the fourth year. This is based on a full-time working
week of 38 hours. We offer a temporary contract for 18 months which will
be extended to a total of four years if you perform well.

Employee benefits include

* a fixed holiday bonus of 8% and December bonus of 8.3%;

* working hours that can be discussed and arranged so that they allow
  for the best possible work-life balance;

* reduced fees for the use of on-campus sports facilities;

* partially paid parental leave;

* excellent pension scheme.

  More information  

If you have questions about this position, please contact Hilje Doekes:
hilje.doekes@wur.nl.

To apply (deadline: Aug 26):
https://www.wur.nl/en/vacancy/phd-position-in-spatiotemporal-diversity-of-phages.htm

"Doekes, Hilje" <hilje.doekes@wur.nl>

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