Using metagenomic Hi-C data to discover broad host-range plasmids conferring antimicrobial resistance

Horizontal gene transfer (HGT) trough plasmids is one of the main contributors to the rapid increase of antimicrobial resistance (AMR). Studying wastewater from wastewater treatment plants (WWTPs) allows us new insights into HGT as bacteria from different sources come together. Currently the analysis of HGT is limited, as plasmids cannot be...

Reference-free biomarker mining in metagenomic data using language embedding

Metagenomic Next-Generation Sequencing (mNGS) presents a promising avenue to generate massive volume of sequence reads in a short period of time. This has opened opportunities for disease diagnosis based on individual variations and mutations by considering the microbiome profile of each patient. However, the effective use of this data requires...

Host- Microbiome Omics Integration for Cancer Analysis and Diagnostics: Investigating the added value of integrating microbial and host omics information for cancer diagnostics using prediction models

Cancer is one of the leading causes of death in the world. While there have been many studies investigating the development and progression of cancer in human tissues using host omics data or microbial data, there is a lack of research combining both types of data, even though both modalities have been shown to affect cancer morphology and...

Explainable AI for metabolic engineering

Metabolic engineering is an important field in biotechnology, aimed at optimizing cellular processes to produce desired compounds. In this thesis, we focus on predicting the metabolome from the proteome, as understanding this relationship is crucial for understanding cellular metabolism. We investigate the usage of additional biological...

Batch correction of taxonomic data of the human gut microbiome for generalization of case-control classification

Next-Generation Sequencing (NGS) has made it possible to perform metagenomic sequencing of environmental microbiome samples. Colorectal cancer (CRC) benefits from early detection, and many studies find correlations between disease presence and abundance of species in samples of the microbiome. However, these studies are hard to reproduce and...

Benchmarking of viral quasispecies assembly algorithms

Viral quasispecies refers to viral populations that comprises of numerous viral strains closely related to each other due to within-host evolution or co-infection. The reconstruction of viral strain-specific genomes using sequencing reads is referred to as viral quasispecies assembly, and it is also crucial to determine the relative abundances...

Explainable artificial intelligence in forensics: realistic explanations for number of contributor predictions of DNA profiles

Using machine learning to determine the number of contributors (NOC) in short tandem repeat (STR) mixture DNA profiles has been shown to obtain good accuracy. However, the models used so far are not transparent to users as they only output a prediction without any reasoning for that conclusion. Therefore, we leverage techniques from the field of...

A Bayesian approach to haplotype-aware de novo genome assembly for polyploid organisms

Capturing all genetic variation within a polyploid organism is a challenge. Most current de novo assemblers have no notion of the concept “ploidy”. Consequently, when assembling the genome of diploid or higher ploidy organisms, the assembler mixes reads coming from either chromosome copy and builds a single DNA sequence representing an arbitrary...

Population graph for Mycobacterium Tuberculosis

In recent years, cheap sequencing has resulted in hundreds or thousands of individual genomes available for many species. Therefore, it is logical to rethink the concept of the reference genome; as consisting of a population of genomes rather than being a single one. The term pan-genome describes a population of genomes of the same species or a...

Population graph of Mycobacterium Tuberculosis

In recent years, cheap sequencing has resulted in hundreds or thousands of individual genomes available for many species. Therefore, it is logical to rethink the concept of the reference genome; as consisting of a population of genomes rather than being a single one. The term pan-genome describes a population of genomes of the same species or a...

Detecting mixed Mycobacterium tuberculosis infections and differences in drug susceptibility with WGS data

Tuberculosis is a pulmonary disease caused by the pathogen Mycobacterium tuberculosis and is the second leading cause of death from an infectious disease. Individuals infected by multiple strains referred to as a mixed infection are associated with poor treatment outcomes when the infecting strains differ in their susceptibility against...