Theoretical Biology & Bioinformatics

tree of life
Basten snoek

Basten Snoek

Home | Publications | Projects for internships | LettuceKnow | SoilPros | CropXR


The research in my group is defined by the following key words: systems genetics, multi-omics, data integration, network biology and bioinformatics. There are two main questions we focus on:

  • How does genetic variation lead to phenotypic variation?
  • What are the interactions between the (soil) microbiome and the environment?

The link between Genotype and Phenotype

Genetic variation is known to be a major driver of phenotypic variation, however the genes and mechanisms underlying the variation in most (complex) traits are still to be uncovered. Advances in -omics technologies, such as transcriptomics, proteomics, metabolomics and phenomics combined with systems genetics enable the discovery of these genes and mechanisms on a massive scale. This approach has been applied to different phenotypes in Arabidopsis thaliana, C. elegans, Tomato, Lettuce, and Lolium. Currently most of our genetic research is focused on Lettuce and Lactuca species, which is part of the LettuceKnow TTW perspective project.

The link between Soil Biodiversity and Function

Soil is the most biodiverse ecosystem on earth and vital to our existence. It provides services such as a substrate to grow food, store water and capture green-house gases. A relatively unexplored part of the soil is the microbiome. Both bacteria and fungi play an important role in the dynamics of the soil ecosystem and the interactions with the biotic and abiotic environment. We combine various data sources, such as functional gene content, microbiome profiles, soil characteristics and even satellite images to predict changes in soil biodiversity and function. Currently this research is part of the SoilPros TTW perspective project.

Internship opportunities, and potential collaborations

We are open to internships and collaborations related to our main research questions. We offer experience with techniques such as Genome Wide Association Studies (GWAS), Quantitative Trait Locus (QTL) mapping, RNA-sequencing analysis, metabolomics, hyperspectral imaging, (multi-omics) data integration and visualization, machine learning and AI, and many more. From nucleotide to ecosystem if the data is available, we can integrate and investigate it.

Internship opportunities, and potential collaborations:

Projects for internships


Laura Dijkhuizen (Lecturer - PhD education)
Sarah Mehrem (PhD Candidate)
Bram van Eijnatten (PhD Candidate)
Rens Dijkhuizen (Junior Researcher)
Eleni Manousou (Visiting Scientist)
Frank Okyere (Post Doc; shared with Guido van den Ackerveken and Sanne Abeln)

Margarita Bikineeva (MSc)
Coen Micklei (MSc)
Anne Zeil (MSc)
Ruben van Diest (MSc)

Former Members

Laurens Janssen (MSc)
Martijn van Tuijl (MSc)
Luc van Zon (MSc)
Kevin Boelhouwer (MSc)
Justin Pelle (BSc)
Coen Micklei (BSc)
Rens Dijkhuizen (MSc)
Niels Peeters (MSc)
Rutger Ballieux (BSc)
Nimrod de Wit (MSc)
Myrthe de Haan (MSc)
Matthijs Kon (MSc)
Bram van Eijnatten (MSc)
Douwe ten Bulte (MSc)
Tom Schermer (MSc)
Rodrigo Rosas (MSc)
Cas Blaauw (BSc)
Daan Stolker (BSc)
Eli Heule (BSc)