Lab members
Assistant professor / PI
Isabel Rathmann
Postdoc Since February 2024
Predicting evolution in nematodes and bacteria
Joined with Thomas Blankers
Shijia Li
PhD student Since October 2021
Dynamic data analysis and metabolic models of the gut microbiome
Joined with Johan Westerhuis, Remco Kort and Stanley Brul
Pim van Leeuwen
PhD student Since January 2020
Interactions in the human gut microbiome
Joined with Jurgen Seppen, Stanley Brul and Wouter de Jonge
Nienke Koopman
PhD student Since May 2019
The human gut microbiome in Inflammatory Bowel Disease
Joined with Jurgen Seppen, Stanley Brul and Wouter de Jonge
Dana Sluis
MSc student Biomedical Sciences VU Since February 2024
Project: Predicting bacterial evolution based on prior genetic alterations
Past members
Postdocs
Yuliia Orlova February 2021 - January 2023
Project: Evolution of metabolic networks in the Origin of Life
Next position: Consultant SURF Research Cloud
Research assistants
Roel van der Ploeg November 2020 - June 2021
Project: Building a analysis pipeline to study evolution in the infant gut from timeseries metagenome data
Next position: PhD student at the University of Amsterdam
MSc Students
Archontis Goumagias Bioinformatics and Systembiology Joint Degree VU-UvA September 2022 - October 2023
Thesis: Functional consequences of genomic and single-nucleotide variation in infant gut microbiome time series
Leonardo Claudin Bioinformatics and Systembiology Joint Degree VU-UvA January 2023 - August 2023
Thesis: Evolutionary response of bacterial strains to drug therapy
Bodine Slegte Biomedical Sciences UvA October 2021 - July 2022
Thesis: How do resistant and sensitive TEM-1 ß-lactam bacteria coexist in conditions with cefotaxime and glycerol concentrations?
Pjotr van der Jagt Biomedical Sciences UvA January 2021 - July 2021
Thesis: Unravelling the metabolic potential of a three-species gut bacteria composition using genome-scale metabolic models
Next position: PhD Sainsbury Laboratory - Renske Vroomans group
Agathe Meulenbelt-Zumer Sorbonne Université January 2021 - July 2021
Thesis: Evolution of antibiotic resistance in E. coli under nematode predation
Randi Stoop Biomedical Sciences UvA December 2020 - August 2021
Thesis: The influence of predator-prey induced evolved Escherichia coli on Caenorhabditis elegans
Luca Rieger Biological Sciences UvA July 2020 - April 2021
Thesis: Recreating evolution in the lab
BSc Students
Jordi de Theye Biomedical Sciences UvA September 2023 - February 2024
Thesis: Combined growth and metabolite analysis of E. coli, E. faecalis and L. lactis can provide insight into interbacterial interactions
Isabel Verhijde Biomedical Sciences UvA February 2023 - June 2023
Thesis: A co-culture of E. coli and E. cloacae stimulates the growth of C. parapsilosis
Carlijn Schutte Biomedical Sciences VU February 2023 - May 2023
Thesis: Evolution of Escherichia coli in a Predator-Prey Model: Colonization and Survival of Caenorhabditis elegans
Laura Hannema Bèta-gamma UvA February 2021 - June 2021
Thesis: Investigating the limits of a species interaction model with metabolite mediated toy models
Annemieke Willms Bèta-gamma UvA September 2020 - February 2021
Thesis: Predicting dynamics of human gut microbiota using species interaction mathematical modelling