Koen Rademaker
MSc student Bioinformatics and Systems Biology, Vrije Universiteit Amsterdam / University of Amsterdam.
Experience
Apr 2023 - Sep 2023
MSc internship, Computational Genomics and System Genetics group (Oliver Stegle), German Cancer Research Center (Heidelberg)
Statistical modelling of cell type-specific expression changes in neurodevelopmental disorders from 10x Genomics Visium spatial transcriptomics data. Supervised by prof. Dr. Oliver Stegle and Dr. Alexander Aivazidis (Wellcome Sanger Institute) in collaboration with Bayraktar group (Sanger).
May 2022 - Jun 2022 Teaching Assistant, University of Amsterdam
Assisting with online and on-campus computer practicals for students, and supporting teaching staff with practical issues and grading for the course(s):
- 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 pipeline for mapping genomic rearrangement experiments and downstream analyses. Supervised by prof. Dr. Bas van Steensel, Dr. Lise Dauban, Mathias Eder MSc.
Jan 2021 - May 2022 Teaching Assistant, Vrije Universiteit Amsterdam
Assisting with online and on-campus computer practicals for students, and supporting teaching staff with practical issues and grading for the course(s):
- Structural Bioinformatics (2021 edition, with Dr. Anton Feenstra)
- Bioinformatics for Translational Medicine (2021 and 2022 editions, with Dr. Evert Bosdriesz)
- Introduction to Bioinformatics (2022 edition, with Dr. Evert Bosdriesz)
Sep 2020 - Jun 2022 Peer Mentor, Vrije Universiteit Amsterdam
I helped groups of new students (2020/2021 and 2021/2022 cohorts) to navigate their way around the MSc program in Bioinformatics & Systems Biology through regular informal meetings.
Feb 2019 - Sep 2019
BSc internship, Department of Translational Neuroscience, UMC Utrecht
Identification of neuronal cells involved in schizophrenia through integration of scRNA-seq and GWAS data for cell type enrichment methods DEPICT, MAGMA, LDSC and FUMA. Supervision by Dr. Bochao Lin.
Sep 2017 - Jan 2018
BSc internship, Translational Metabolic Laboratory, Radboudumc (Nijmegen)
Application of bioinformatics for 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, Genomes and gene expression, Gene Finding: GWAS and beyond, Literature review on experimental and computational methods for multimodal single-cell sequencing.
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
2022
M. Olislagers, K. Rademaker, R. A. H. Adan, B. D. Lin & J. J. Luykx., ‘Comprehensive analyses of RNA-seq and genome-wide data point to enrichment of neuronal cell type subsets in neuropsychiatric disorders’. Mol Psychiatry, 27, 947–955 (2022); doi: 10.1038/s41380-021-01324-6.
Pre-prints
M. Olislagers, K. Rademaker, R. A. H. Adan, B. D. Lin & J. J. Luykx. ‘Comprehensive analyses of RNA-seq and genome-wide data point to enrichment of neuronal cell type subsets in neuropsychiatric disorders’. bioRxiv, doi: 10.1101/2021.05.06.442982 (July 20 2021).