Leiden University

LIACS Thesis Repository

Leiden University


These webpages contain theses and reports by students affiliated with the various bachelor and master programmes offered at the Leiden Institute of Advanced Computer Science (LIACS), the computer science and artificial intelligence department of Leiden University.
Note: this thesis repository might be incomplete for certain programmes and years.


Bachelor Bioinformatica


2024-2025
Student Thesis Content
Bouwman, E.C.T.D. (Emma)Comparing Neurodegenerative Disorders: Discovering Patterns Through Protein-Protein Interaction Network Analysis
Zee, D.F. (Daniel)Integrating ARISE Fungal ITS Data in the MycoDiversity Database for Biodiversity Analysis

2023-2024
Student Thesis Content
Bijl, I. (Imaan)Measuring the Performance of Different Convolutional Neural Networks and a Swin-transformer Model in Pollen Classification Using 3D Sequential Data
Bijsterveld, J. van (Jens) & Benthum, S.W. van (Sybe)Automating VAST Imaging for High Throughput and Fluorescence
Deen, L. (Luuk)ZebraVishualizer: A Tool for 3D Cell Trajectory Annotation and Visualization
Gijsbert, R. (Robert) Zebrafishualizer
Konijn, T. (Tijs)The Performance of RetinaNet and Faster R-CNN with Classification on 3D Pollen Images

2022-2023
Student Thesis Content
Benthum, S.W. van (Sybe) [samen met van Bijsterveld]Automating VAST imaging for high throughput and fluorescence
Bijsterveld, J. van (Jens) [samen met van Benthum]Automating VAST imaging for high throughput and fluorescence
Boer, A.M. de (Aster)Identifying Overlapping Processes of Alzheimer’s and Huntington’s Disease with a Protein-Protein Interaction Network Analysis
Bos, A. (Aaron)A tool for manual 3D cell track annotation through time
Brouwer, B. (Benthe)Impact of GO evolution on covid-19 results
Grondelle, K. van (Kim)A Comparative Omics Approach To Understanding Huntington’s Disease Network Interactions
Haaf, L. ten (Lena)Localized Information Comparison and Analysis for MycoDiversity Database
Laauwen, S. (Sanne)Analysis of the 3D Distribution of Granulomas in Adult Zebrafish
Meyer, T. (Tomke)Early Detection of Celiac Disease in Children
Onderwater, J. (Jurian)High throughput acquisition of zebrafish larvae using VAST
Osenbruggen, L.C.A.W. van (Lucas) Variant Algebra based Star Allele Calling
Plas, S. van der (Sofie)Optimizing the segmentation of zebrafish imaged with optical projection tomography
Rademaker, N. (Nikki) [samen met Smid]Studying Anatomy of Organisms through Virtual Reality
Sebastian, S. (Shreya)Enhancing Pollen Classification Accuracy through the Use of Whole Stack Images in 3D Convolutional Neural Networks
Smid, Y. (Yanna) [samen met Rademaker]Studying Anatomy of Organisms through Virtual Reality
Wel, T. van (Tijmen)Novel Way for the Calculation of Sarcomere Length in Human Pluripotent Stem Cell Derived Cardiomyocytes
Yousufi, N. (Noria)Functional profiling of Alzheimer’s through a consensus network

2021-2022
Student Thesis Content
Aydin, A. (Aylin)Ethical Discussion on Current Protocols for Crohn’s Disease in the Use of CAM Therapies
Burg, K. (Koen) van derIdentifying key genes in CRC patients to predict efficacy of CAPOX treatment
Jiang, C.J.R. (Chen)Finding Consensus Knowledge in the Huntington’s Disease Pathway
Lin, D. (David)Gradual OverPy: A Proof of Concept of Applying a Gradual Method on the Overwatch Workshop
Silié, A-J. 3D mesh optimization strategy for images acquired from Bioimaging
Thiel, H. van (Haike) Speeding up the multiscale access in the MycoDiversity DataBase
Venemans, W.R.D. (Willem)Classifying Protein Topology Matrices Using AI
Versluis, R. (Robbert)Comparing and Improving Different Analysis Workflows for High Compound Screening Data
Yarim, M. (Metin)Bioinformatics Analysis of the Core Hallmarks of Cancer Genes

2020-2021
Student Thesis Content
Belle, N. (Niels) vanThe Bioinformatic Search for ENOD40 Genes in the Rosales Order and Possible Insertions of Transposable Elements
Biesot, N. (Nienke)Actionable Pharmacogenomic Variation Present in the General Population
Boonstra, N.J.L. (Niels)Is the Linux Completely Fair Scheduler Ready for Serverless Workloads?
Faas, M. (Marije)Training Logical Operations through Gameplay
Freeke, K. (Karl)Exploring Hallmark Connections through Pathway Enrichment in a Cancer Gene PPI-network
Homma, R. (Rutger)Exploring the Feasibility of Pharmacogenomic Data Analysis
Kossen, D. (Dylan)Network Analysis of polyQ Proteins in the Human Brain
Vijfvinkel, D. (Daan)Discovery of ENOD40 RNA in Poaceae

2019-2020
Student Thesis Content
Cheung, M. (Menco)Mining Structural Patterns in a Non-coding RNA Related to Influenza Virus Infection and Cancer Development
Engwegen, L.R. (Laurens)Investigating the Hallmarks of Cancer Using Protein-Protein Interaction Networks
Heijnen, L.S.E.M. (Lucas)Revisiting the Evolution and Function of Polyglutamine Repeats
Janssens, L.M.I. (Luka)A Network Analysis Approach to Studying PolyQ Protein Interactions
Nuijten, P. (Pascal)The Relationship Between Prognostic Genes in Human and Mouse Cancer

2018-2019
Student Thesis Content
Boer, W.F.H. (Wilco) deEvaluation and Improvement of Methods and Models for Segmentation of Zebrafish Larvae
Dekker, L. (Loes)Optimization of High-Throughput Zebra sh Imaging on a Distributed Computer
Paul, V. (Valerie)Predicting the Discharge Date of Patients using Classification Techniques
Wesselman, S. (Sjoerd)The Intestinal Flora of the Zebrafish

2017-2018
Student Thesis Content
Spaink, H.A.J. (Hermes)Age Classification of Zebrafish Larvae using Machine Learning from HOG Features