Timeline

2020 – 2024

Group and collaboration

Dr. Bas E. Dutilh, Metagenomics Group, Theoretical Biology and Bioinformatics
Institute for Biodynamics and Biocomplexity (IBB), Science for Life, Utrecht University (UU), Utrecht Bioinformatics Centre (UBC)
Dr. Ronnie de Jonge, Plant-Microbe Interactions, Institute for Environmental Biology (IEB), Science for Life, UU
Prof. Dr. Marion Koopmans, Viroscience, Erasmus Medical Centre
PhD Student: Ling-Yi Wu

Project description

One Health research often depends on the accurate and sensitive detection of microbes and viruses in environmental sequencing datasets (metagenomes). Identifying viral sequences in metagenomes is like searching for a needle-in-a-haystack, because their sequences cannot be recognised with commonly used homology-based search tools. In this PhD-project researchers will integrate innovative machine learning and statistical approaches into a sensitive virus detection tool. “We will apply the tool to important plant, human, and other NCOH datasets. Our novel computational tools for virus identification in a range of biomes – including healthy and diseased humans, farm animals and wildlife – will lead to a better understanding of the role of viruses in human, plant, animal, and environmental systems.”

Tasks

1. Benchmark a collection of state-of-the-art virus identification and interpretation tools and integrate the best ones into a robust and user-friendly computational pipeline for virus studies. Recommendations on how to use the pipeline for best practice will be given so biologists can use it based on their specific interests.
2. Apply the developed pipeline to plant, human and animal related virus metagenomic datasets to study the interactions between viruses, microbes, and higher organisms. Specific attention will be paid to how the interactions between viruses and microbes influence their higher organisms’ health.