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M.J.T. Reinders

85 records found

Grounding Large Language Models (LLMs) in chemical knowledge graphs (KGs) offers a promising way to support synthesis planning, but reliably retrieving information from these complex structures remains a challenge. Therefore, this work addresses that gap by constructing a biparti ...

From Latent to Blatant Space

Coupling Biological Systems to Neural Networks for Improved Model Interpretability

Deep Neural Networks (DNNs) are renowned for their high accuracy and versatility, which has led to their application in many fields of research, including biology. However, this accuracy often comes at the expense of interpretability, making it challenging to reason about the inn ...
Single-cell RNA sequencing (scRNAseq) is a measuring technique of gene expressions in single cells that has allowed researchers to tackle Alzheimer’s disease (AD) in many ways. Single-cell data has been joined with machine learning to classify brain cells as affected by AD. Howev ...

Improving and Interpreting Epigenetic Age Predictors

A Machine Learning Approach to Improving Epigenetic Age Predictors and Understanding How DNA Methylation Affects Aging

Understanding the mechanisms of aging can help us live longer and healthier lives. Epigenetic age predictors are machine learning models that use methylation levels at CpG sites to predict the biological age of the cell. Horvath’s linear clock uses 353 CpGs with a median absolute ...
The aim of this research is to investigate whether physical gene characteristics can predict age-related changes in gene expression. Specifically, we analyze gene length, GC content, distance to the ends of the chromosome, and similar features to determine their connection with d ...
Online databases contain extensive collections of (bio)chemical reactions serving as valuable resources for a variety of applications. However, these large datasets often suffer from incomplete reaction data missing, for example, co-reactants and by-products. Machine learning can ...

Improving Single-Cell Transcriptomic Aging Clocks

Enhancing Accuracy and Biological Interpretability

Biological aging clocks estimate age from molecular data and provide insights into age-related functional decline. While aging clocks based on bulk transcriptomic data are well-studied, their single-cell counterparts remain limited and underexplored. In this study, we replicate a ...
Alzheimer’s Disease is a complex neurodegenerative disorder marked by the abnormal build-up of proteins in the brain. As no cure currently exists, understanding the disease’s cellular mechanisms is essential for advancing diagnostics and treatment. To this end, single-cell RNA se ...
Aging is the biological process that changes the body over time. When we age our bodies become more prone to disease and other health risks. But not everyone experiences these changes at the same age. This is because the age of our cells (biological age) does not always match our ...
A deeper understanding of Multiple Sclerosis (MS) symptom progression is required for diagnostic accuracy and patient care. Remote monitoring through smartphones can provide continuous insights in the well-being of MS patients. This research aims to explore differences between MS ...

Unmasking the Unexpected

Towards Reliable Time Series Anomaly Detection

The integration of wearable technology into healthcare is revolutionizing health monitoring by enabling continuous tracking of vital metrics like heart rate and blood sugar. Devices such as smartwatches and glucose monitors empower proactive interventions, reducing hospital visit ...
Antimicrobial resistance (AMR), termed a "silent pandemic" has caused 4.95 million deaths in 2019, with numbers expected to rise. AMR spans human, animal, and environmental sectors, requiring a One Health approach to address this multifaceted global challenge. This dissertation f ...
The shift to precision medicine in cancer focuses on providing therapies targeting vulnerabilities of each individual patient tumor. This approach involves identifying cancer subtypes and discovering targets, such as genetic interactions, to treat patients who lack effective ther ...

Characterizing bacterial genetic diversity

In species' pangenomes and microbial communities

Bacteria are everywhere and play essential roles in Earth's diverse ecosystems and human health. For example, humans harbor a complex and essential gut microbial community comprising thousands of bacterial species (in addition to numerous viruses, fungi, and microbial eukaryotes) ...
In summary, the contributions within this thesis advance Alzheimer's research by introducing new computational tools and methods to better understand the genetics of the disease and cellular mechanisms. Additionally, showing that single-cell gene expression can be effectively ana ...
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology has transformed molecular biology by enabling a strategy for precise, efficient, and relatively simple genome editing. Guided by a small strand of RNA, CRISPR locates specific DNA sequences within the g ...
The intensive care unit (ICU) is a hospital department where critically ill patients requiring organ support or intensive monitoring are admitted. Nowadays, the care provided in an intensive care unit has advanced so that more patients are being discharged alive. Advances in ICU ...
Alzheimer’s disease (AD) is a neurodegenerative disorder prevalent in older adults, leading to loss in memory, cognitive, and executive function. A characteristic feature of AD is the accumulation of amyloid-beta (Aβ) plaques, which are extracellular deposits of Aβ protein primar ...