We now need more than ever to make genome analysis more intelligent. We need to read,
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …

Pangenomes reduce reference bias by representing genetic diversity better than a single
reference sequence. Yet when comparing a sample to a pangenome, variants in the …

We propose a polynomial algorithm computing a minimum plain-text representation of k-mer
sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of …

A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer
assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications …

Aim. Due to the growing availability of genomic datasets, machine learning models have
shown impressive diagnostic potential in identifying emerging and reemerging pathogens …

As a single reference genome cannot possibly represent all the variation present across
human individuals, pangenome graphs have been introduced to incorporate population …

K-mers have become ubiquitous in modern bioinformatics pipelines. A key factor in their
success is the ability to filter out erroneous k-mers by removing those with low abundance …

This paper provides a comprehensive survey of data structures for representing k-mer sets,
which are fundamental in high-throughput sequencing analysis. It categorizes the methods …

In this dissertation, I present four projects covering two main research objectives. The first
objective of my dissertation is to optimize storage usage of sequence analysis tools and …

Using long k-mers to find sequence matches is increasingly used in many bioinformatic
applications, including metagenomic sequence classification. The accuracy of these …