In this article, we introduce the Conway–Bromage–Lyndon (CBL) structure, a compressed,
dynamic and exact method for representing k-mer sets. Originating from Conway and …

The exponential growth of genome databases calls for novel space-efficient algorithms for
data compression and search. State-of-the-art approaches often rely on k-merization for data …

The exponential growth of DNA sequencing data calls for efficient solutions for storing and
querying large-scale k-mer sets. While recent indexing approaches use spectrum …

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 …

Unitigs are a central construct in many subfields of bioinformatics, including genome
assembly and the compact representation of k-mer spectra. In both of these subfields, using …

Abstract The Shortest Superstring problem is an NP-hard problem, in which given as input a
set of strings, we are looking for a string of minimum length that contains all input strings as …

The exponential growth of genomic data calls for novel space-efficient algorithms for
compression and search. State-of-the-art approaches often rely on tokenization of the data …

The rapid advancements in DNA sequencing technology have led to an unprecedented
increase in the generation of genomic datasets, with modern sequencers now capable of …

The exponential growth of DNA sequencing data calls for efficient approaches for their
compression and search [1, 2]. Modern bioinformatics increasingly uses k-merization as a …