Metagenomes represent the genetic content of all community members in a specific environment and contain unprecedented information on the genetic variation that exists within all the community members. Our research focuses on viral and microbial evolution. To this end, we develop and apply approaches (i) to reconstruct viruses from metagenomic and metatranscriptomic data and (ii) to infer microbial population genetic processes from genomic and metagenomic data.
- We are looking for a PhD student to join our team - get in touch if you are a bioinformatician who wants to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns
- New preprint is out - Large-scale investigation of orphan genes in the human gut microbiome elucidates their evolutionary origins
- A new Msc thesis student started - Laurens Klinkien will work on using protein structures to investigate orphan proteins (in co-supervision with Aalt-Jan van Dijk)
- The conference season is starting. You can find us at BioSB, NLSEB, and ViBiom
- Our short perspective on pangenome evolution is accepted in GBE
- Joran Schorlemmer successfully finished his Msc thesis on the surface proteins of phages (in co-supervision with Aalt-Jan van Dijk). Congratulations!
- Elma van Wieren successfully finished her Msc thesis on the evolution of auxiliary metabolic genes. Contratulations!
- Devin van Valkengoed sucessfully finished his Msc thesis in co-supervision with Astrid Bryon from the WUR Virology group. Congratulations! We are happy that he stays around a bit longer to wrap up the project.
- Nikolai Matviiets sucessfully finished his Msc thesis in co-supervision with Anna Alekseeva from the WUR Genetics group. Congratulations!
- Another Msc thesis student started: Gian Passania will work on integrated viral elements
- Dimitris Karapliafis finished his research practice and is ready to start his PhD in the group in February, huge congratulations! Looking forward to explore the evolution of plant viruses!
- New paper on phage recombination: Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000915
- Three new thesis students are starting: Joran Schoorlemmer, Jori de Leuw, and Elma van Wieren. Welcome!
- New paper published in collaboration with the Virology Goup on Arabidopsis latent virus 1: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18466
- Two new thesis students are starting: Devin van Valkengoed and Dimitris Karapliafis. Both will work on the virus evolution, welcome!
- Amanda van de Ligt has successfully defended her Msc thesis, congratulation!
- New papper published :) Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids: https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac121/6663764
- New paper published :) Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance: https://academic.oup.com/gbe/article/14/7/evac098/6613374
- Nikolai Matviiets started his Msc thesis on Meta-omics analysis of fermented milk communities, in co-supervision with Anna Alekseeva from the WUR Genetics group. Welcome Nikolai!
- Matthijs Kon has finished his Msc thesis entitled Pipeline comparison for covert virus detection in Spodoptera exigua using high throughput sequencing data. Congratulations Matthijs!
New preprint available: Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids https://www.biorxiv.org/content/10.1101/2022.01.07.475421v1
Joliese Teunissen started her PhD co-supervised with Stefan Geisen at the WUR Nematology group. She will investigate the microbiome in intercropping. Welcome Joliese!
New preprint available: Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance https://www.biorxiv.org/content/10.1101/2021.11.12.468352v1
Jan Baijens joined as a PhD student to work on genome evolution of plant viruses. Welcome Jan!
We are looking for a PhD student in deciphering the soil microbiome in intercropping! Forward the announcement to suitable candidates and apply here: https://www.wur.nl/en/vacancy/PhD-Deciphering-the-soil-microbiome-for-optimized-intercropping.htm Feel free to contact me for questions!
Matthijs Kon has started his Msc thesis on insect virus discovery in sequencing data, in co-supervision with Astrid Bryon. Welcome Matthijs!
Jun Liu started his PhD project in China co-supervised by Jing He at the Energy Microbiology Center of the Chinese Academy of Agricultural Sciences. Welcome Jun!
We are looking for a PhD student in plant virus genomics! Forward the announcement to suitable candidates and apply here: https://www.academictransfer.com/en/303862/phd-position-virus-diversity-and-evolution-in-natural-plant-ecosystems/ Feel free to contact me for questions!
The PhD project “Deciphering the soil microbiome for optimized intercropping” is funded by the plant science group at WUR. This will establish a novel a collaboration between Stefan Geisen and me. The project is embedded in a larger consortium of young tenure trackers at WUR. Stay tuned!
The PhD project “Virus diversity and genome evolution in natural plant ecosystems (V-GENE)” has been awarded funding by the graduate school EPS: https://www.graduateschool-eps.info/3-projects-awarded-in-eps-wu-young-tenure-track-call/ Let’s celebrate (now) and look for a candidate (after the holidays)!
Nikolaos Vakirlis started as a postdoc at Kiel University on a project that I acquired during my time there. We will work in close colaboration. Welcome Nikos!
Department of Plant Sciences
Wageningen University & Research
Wageningen, The Netherlands