Koen Rademaker

PhD student with Tim Coorens at the European Bioinformatics Institute (EMBL-EBI) and the University of Cambridge, UK. I focus on computational analysis of single-cell and spatial mutational data to uncover human development and cancer origins.

[email protected]

Experience

Oct 2026 - Present Predoctoral Fellow (PhD student), Coorens group, European Bioinformatics Institute (EMBL-EBI) (Cambridge, UK)
Computational analysis of single-cell and spatial mutational data to investigate human development and cancer origins.

Feb 2024 - Aug 2026 Bioinformatician, Bayraktar group (Cellular Genomics), Wellcome Sanger Institute (Cambridge, UK)
Computational analysis of single-cell and spatial omics data to uncover cellular changes during human neurodevelopment and disease. Analysed 10x Genomics Xenium and scRNA-seq/snRNA-seq datasets and adapted computational workflows to emerging spatial platforms. Research included autism-associated genes in neurodevelopment, spinal cord injury and glioblastoma.

Apr 2023 - Oct 2023 Bioinformatics Research Intern, Computational Genomics and Systems Genetics group (Oliver Stegle), German Cancer Research Center (DKFZ) (Heidelberg, Germany)
Research project jointly conducted with the Bayraktar group at the Wellcome Sanger Institute. Modelled cell type-specific expression changes in neurodevelopmental disorders using 10x Genomics Visium spatial transcriptomics data. Supervised by Oliver Stegle and Alexander Aivazidis.

May 2022 - Jun 2022 Teaching Assistant, University of Amsterdam
Assisted with online and on-campus computer practicals, supported teaching staff, and helped with grading for Image Processing and Quantitative Data Analysis (with Dr. Marten Postma).

Sep 2021 - Feb 2022 MSc internship, Chromatin Genomics group (Bas van Steensel), Netherlands Cancer Institute (Amsterdam)
Developed a pipeline for mapping genomic rearrangement experiments and downstream analyses. Supervised by Prof. Dr. Bas van Steensel, Dr. Lise Dauban and Mathias Eder MSc.

Jan 2021 - May 2022 Teaching Assistant, Vrije Universiteit Amsterdam
Assisted with online and on-campus computer practicals, supported teaching staff, and helped with grading for:

Sep 2020 - Jun 2022 Peer Mentor, Vrije Universiteit Amsterdam
Helped groups of new students (2020/2021 and 2021/2022 cohorts) navigate the MSc program in Bioinformatics & Systems Biology through regular informal meetings.

Feb 2019 - Sep 2019 BSc internship, Department of Translational Neuroscience, UMC Utrecht
Identified neuronal cells involved in schizophrenia by integrating scRNA-seq and GWAS data using cell type enrichment methods DEPICT, MAGMA, LDSC and FUMA. Supervised by Dr. Bochao Lin.

Sep 2017 - Jan 2018 BSc internship, Translational Metabolic Laboratory, Radboudumc (Nijmegen)
Applied bioinformatics to glycopeptide profiling to study congenital disorders of glycosylation. Supervised by Dr. Hans Wessels.

Education

2019-2023 MSc Bioinformatics and Systems Biology, Vrije Universiteit Amsterdam / University of Amsterdam
Thesis: “Mapping cell type-specific differential expression of trisomy 21 in spatially resolved fetal brain development”.
Supervisors: Prof. Dr. Oliver Stegle (German Cancer Research Center), Dr. Alexander Aivazidis (Wellcome Sanger Institute).
Courses: Fundamentals of Bioinformatics, Introduction to Systems Biology, Algorithms in Sequence Analysis, Biosystems Data Analysis, Signal Transduction in Health and Disease, Structural Bioinformatics, Bioinformatics for Translational Medicine, Statistics with R, Machine Learning, Deep Learning, Genomics and Gene Expression, and Gene Finding: GWAS and Beyond.

2015-2019 BSc Bioinformatics, HAN University of Applied Sciences
Thesis: “Targeting brain cell types underlying schizophrenia”.
Supervisor: Dr. Bochao Lin, UMC Utrecht.

Publications

Publications are also listed on ORCID.

Peer-reviewed publications

Preprints