Background De novo genome assembly relies on two kinds of graphs: de Bruijn graphs and
overlap graphs. Overlap graphs are the basis for the Celera assembler, while de Bruijn …

One of the most computationally intensive tasks in computational biology is de novo genome
assembly, the decoding of the sequence of an unknown genome from redundant and …

Indexing huge collections of strings, such as those produced by the widespread sequencing
technologies, heavily relies on multistring generalizations of the Burrows–Wheeler transform …

Spurred by a widening gap between hardware accelerators and traditional processors,
numerous bioinformatics applications have harnessed the computing power of GPUs and …

In the all-pairs suffix-prefix (APSP) problem [Gusfield et al., Inf. Process. Lett. 1992], we are
given a dictionary R of r strings, S₁,…, S_r, of total length n, and we are asked to find the …

Graph pangenomics is a new emerging field in computational biology that is changing the
traditional view of a reference genome from a linear sequence to a new paradigm: a …

In the all-pairs suffix-prefix (APSP) problem, we are given a dictionary R of k strings, S1,...,
Sk, of total length n, and we are asked to find the length SPLi, j of the longest string that is …

The Lyndon factorization of a word has been largely studied and recently variants of it have
been introduced and investigated with different motivations. In particular, the canonical …

Automated software diversity promises to reduce an attacker's ability to reuse exploits across
application instances. However, many questions remain regarding the efficacy of and …

The Lyndon factorization of a word has been extensively studied in different contexts and
several variants of it have been proposed. In particular, the canonical inverse Lyndon …