Members
Berend Snel
Professor
Kirsten ten Tusscher
Professor
Rob de Boer
Professor
Ronald Bontrop
Professor
Paulien Hogeweg
Honorary professor
Bas E Dutilh
Visiting Professor
Basten Snoek
PI
Bram van Dijk
PI
Working on: Simulating complex microbial ecosystems to identify their fundamental rules
Can Kesmir
PI
Daniel Tamarit
PI
Working on: archaeal and bacterial genome evolution
Erika Tsingos
PI
Working on: Modelling animal development using multicellular models
Michael F Seidl
PI
Monica Garcia-Gomez
PI
Woking on: Multi-scale modeling of lateral root development
Rutger Hermsen
PI
Vivek Bhardwaj
PI
Working on: Developing new bioinformatics tools and methods for quantitative genomics
Leonie van Steijn
Lecturer
Lecturer on Programming and Statistics for MBLS
Laura Dijkhuizen
Lecturer
Working on: PhD courses from basic programming to more advanced techniques like RNAseq, microbiome data analysis, and advanced data visualisation
Bas van den Herik
Post-Doc
Working on: Regulation of sucrose/water transport and tuber growth by the StSWEET11/StSP6A interaction in potato (supervisor: Kirsten ten Tusscher)
Benjamin Planterose Jimenez
Post-Doc
Working on: Modelling cellular fate decision making in the postembryonic M lineage of C. elegans (Supervisors: Erika Tsingos, Kirsten ten Tusscher)
Carlos Santana-Molina
Post-Doc
Working on: Evolution and diversification of eukaryotic metabolisms. (Supervisor: Berend Snel)
Chrats Melkonian
Post-Doc
Working on: modeling plant-microbiome interactions in the rhizosphere in response to plant stress. Part of the MiCRop project (supervisor: Bas Dutilh)
Lotte de Vries
Post-Doc
Working on: Modeling the evolution of ageing when conflict and cooperation are important, e.g. during evolutionary transitions (supervisor: Rutger Hermsen)
Paula Gomez-Zapata
Post-Doc
Working on: investigating the genomic features that drive the switch between the heteroecious and autoecious forms in the rust fungus Cronartium pini (supervisor: Michael Seidl)
Anouk van Westerhoven
PhD candidate
Working on: Genome analysis of fungal banana pathogens to detect pathogenicity genes (supervisor: Michael Seidl)
Bram van Eijnatten
PhD Candidate
Working on: High throughput phenotyping of lettuce for GWAS using machine learning (supervisor: Basten Snoek)
David Giron Villalobos
PhD Candidate
Working on: Metagenomics of urobiomes in health and disease (supervisor: Michael Seidl, Bas Dutilh)
Erdem Sanal
PhD candidate
Working on: Mathematical models of the immune system and T cell dynamics (supervisor: Rob de Boer)
Jeroen Meijer
PhD candidate
Working on: the evolution of microbial ecosystems in multilevel models (supervisors: Bas E Dutilh, Paulien Hogeweg)
Jeroen Saccheri
PhD candidate
Working on: Multi-Scale models of carbon, nitrogen, and phosphorus regulation in Arabidopsis thaliana (supervisor: Kirsten ten Tusscher)
Josje Romeijn
PhD candidate
Working on: the role of transposable elements in fungal genome evolution (supervisor: Michael Seidl)
Laura van Rooijen
PhD candidate
Working on: evolution of the kinetochore complex (supervisor: Berend Snel)
Lingyi Wu
PhD candidate
Working on: tools for viral identification from metagenomic data (Supervisor: Bas Dutilh)
Mara Vizitiu
PhD candidate
Working on: drawing evolutionary inferences based on the architecture of microbial genomes (supervisor: Daniel Tamarit)
Max Raas
PhD candidate
Working on: The evolution of the kinetochore (supervisors: Berend Snel, Geert Kops)
Meine D Boer
PhD candidate
Working on: Analysis and modelling of metagenomic and metabolomic data from the Caribbean Sea (supervisor: Bas Dutilh)
Petros Skiadas
PhD candidate
Working on: high-quality genomes of spinach downy mildew isolates to identify effectors (supervisor: Michael Seidl)
Rick Beeloo
PhD candidate
Supervisor: Bas Dutilh
Sarah Mehrem
PhD candidate
Working on: understanding the genetic and phenotypic variation in Lettuce via GWAS, QTL mapping and multi-omics data integration. (LettuceKnow project, supervisor: Basten Snoek)
Sultan Nazir
PhD candidate
Working on: Multiscale models of phage evolution and bacterial pathogenicity (supervisor: Bram van Dijk)
Thijs van Loo
PhD candidate
Working on: Mechanistic modelling of heat and drought stress in Arabidopsis Thaliana. (supervisors: Kirsten ten Tusscher, Monica Garcia Gomez)
Tina Hauptfeld
PhD candidate
Working on: environmental metagenomics, phage-host interaction (supervisor: Bas Dutilh)
Xin Zhang
PhD candidate
Working on: gene family evolution in fungi (supervisor: Michael F Seidl)
Eleni Manousou
Visiting Researcher
Working on: linking amplicon data to the function of microbial communities (supervisor: Bram van Eijnatten)
Anne van der Grinten
MSc student
Working on: Comparing foldome-based clustering to sequence trees with the aim of improving orthogroup assignment for highly divergent sequences (supervisor: Berend Snel)
Anne Zijl
MSc student
Working on: the LettuceKnow project using RNA-seq data and hyperspectral imaging to find patterns between genotype and phenotype in lettuce (supervisor: Sarah Mehrem)
Bingqing Qi
MSc student
Working on: Using R language to develop a multicellular model of SHR intracellular trafficking in the root apex (supervisor: Monica Garcia)
Cristina Serra Melendez
MSc student
Working on: Chemical and molecular interaction between phyllosphere yeast and mycotoxigenic Fusarium graminearum using genomic data (WGS) and metabolomic data (supervisor: Chrats Melkonian)
Daan Bossche
MSc student
Working on: identifying factors that influence the TCR of Treg population within humans using the TiRP (supervisor: Can Kesmir)
Gabe van den Hoeven
MSc student
Working on: A T-cell receptor repertoire analysis to find out why some sequences lack a D-segment from VDJ-recombination (supervisor: Rob de Boer)
Griffin Kutler Dodd
MSc student
Working on: Investigating evolution of MHC genes in primates using in silico epitope prediction methods (supervisor: Can Kesmir)
Kyran Wissink
MSc Student
Working on: setting up a framework for creating and analysing microbial pangenomes and then using this framework to analyse a new Fusarium race (supervisor: Anouk van Westerhoven)
Lorenzo Caranti
MSc student
Working on: genome-scale modelling of phyllosphere yeast metabolism with the aim of improving the computational tool to perform this task (supervisor: Chrats Melkonian)
Manu Ayllon Gavilan
MSc student
Working on: Automating biomarker identification and validation for immunotherapies: Non-canonical peptides presented on MHC molecules (supervisor: Can Kesmir)
Markos Polos
MSc student
Working on: Using AI, I am trying to predict the spatial distribution of viral communities using metagenomic data (supervisor: Lingyi Wu)
Timo Westerdijk
MSc student
Working on: reviewing the impact of mathematical modelling on the understanding of and the development of treatment for HIV (supervisor: Rob de Boer)
Wouter van Etteger
MSc student
Working on: building structural-functional models in order to investigate carbon/nitrogen feedback loops in Arabidiosis thalania (supervisor: Bas van den Herik)
Loek de Jonge
BSc student
Working on: using machine learning to predict T cell type from the T cell receptor sequence (supervisor: Can Kesmir)
Maarten Wunderink
BSc student
Working on: Modelling the replicative history of memory T cells based on TREC contents (supervisor: Rob de Boer)
Nikki de Mol
BSc Student
Working on: How the application of a pangenome graph as reference can improve short read mapping and variant calling (supervisor: Anouk van Westerhoven)
