Motivation The amount of sequencing data from high-throughput sequencing technologies
grows at a pace exceeding the one predicted by Moore's law. One of the basic requirements …

Motivation The size of a genome graph—the space required to store the nodes, node labels
and edges—affects the efficiency of operations performed on it. For example, the time …

A directed multigraph is called Eulerian if it has a circuit which uses each edge exactly once.
Euler's theorem tells us that a weakly connected directed multigraph is Eulerian if and only if …

Pangenomic studies have enabled a more accurate depiction of the human genome
landscape. Genome graphs are suitable data structures for analyzing collections of …

The nearest-neighbor chain algorithm was proposed in the eighties as a way to speed up
certain hierarchical clustering algorithms. In the first part of the dissertation, we show that its …

Given $ d $ strings over the alphabet $\{0, 1,\ldots,\sigma {-} 1\} $, the classical Aho--
Corasick data structure allows us to find all $ occ $ occurrences of the strings in any text $ T …

Textually represented data–text–is one of the most common types of preserved information.
It occurs in many forms, eg, source code, markup languages and plain text. Also, DNA and …

The shortest superstring problem for a given set of strings is to find a string of minimum
length such that each input string is a substring of the resulting string. This problem is known …

Hand-crafted heuristics for solving NP-hard optimization problems are fast and often
effective; yet they lack theoretical guarantees and often fail to generalize across problem …