PhD Student “Modelling causal interactions between marine microbes”: the Netherlands

The Department of Marine Microbiology and Biogeochemistry (MMB; Principal Investigator dr. Julia Engelmann), is looking for a highly motivated PhD student with a background in bioinformatics, computational biology, molecular ecology, computer science, (bio-)statistics, applied mathematics or physics with an interest in microbiology; or a PhD student with a background in microbiology, marine science or related fields with strong computational skills.

The research

The research team of dr. Julia Engelmann applies bioinformatic and network biology approaches to marine genomic, meta-barcoding, meta-genomic and transcriptomic data. Rather than merely describing which microbial species are present at a given location, we want to find out how the individual species interact and form communities, for example by providing nutrients to each other. We use modern network modelling techniques to infer these interactions. The PhD student will be trained in applying and improving on network methodology.

The project

The project is concerned with elucidating marine microbial inter-species interactions based on high-throughput genomic data by applying network modelling. Microbes in the oceans, sediment and in microbiomes of higher organisms, form communities which keep the element and nutrient cycles in the seas and on land running. Different microorganisms have different metabolic capabilities. The product of one species can be the substrate for another. Besides dependencies based on individual nutrients, more complex interactions, such as symbiosis, predator-prey and competition for limited resources among marine microbes, will be elucidated in this project. Moreover, the impact of changing environmental conditions due to climate change on microbial communities will be assessed. To do so, causal network modelling will be applied to microbial abundance data and measurements of environmental parameters such as temperature and salinity to predict causal effects of species and environmental parameters on other species. The PhD student will then perform follow-up experiments in the lab to validate predicted interactions.

The candidate

  • We like to get into contact with a PhD student holding an MSc degree in Bioinformatics, Computational Biology, Computer Science, Mathematics, (Bio-)Statistics, Physics, Microbiology, Molecular Biology, Microbial Ecology or related fields.
  • You are highly organized, motivated, and fluent in oral and written English.
  • Experience with Unix is mandatory. Candidates need to have a proven record of their bioinformatics and programming skills. Candidates with good command of R, Bash and Python are preferred.
  • If your background is in Biology-related fields, you will need to catch up with some mathematics and statistics.
  • The ideal candidate also has experience in the analysis of high-throughput genomic data, including metagenomic data.

For additional information about this vacancy, please contact Dr. Julia Engelmann (tenure-track scientist).

For additional information about the procedure, please contact Jolanda Evers (senior HR advisor).

Please note this job advertisement is a repeated call. The original advert has been posted by the Royal NIOZ earlier in 2018, under Vacancy ID 2018 – 010. Candidates that have applied for this vacancy cannot enter the current procedure.

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