Various graphs such as web or social networks may contain up to trillions of edges.
Compressing such datasets can accelerate graph processing by reducing the amount of I/O …

Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

We propose a generic approach to replace the canonical sequence representation of
genomes with graph representations, and study several applications of such extensions. We …

We propose new succinct representations of ordinal trees and match various space/time
lower bounds. It is known that any n-node static tree can be represented in 2 n+ o (n) bits so …

We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …

Abstract The famous Burrows–Wheeler Transform (BWT) was originally defined for a single
string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs …

The de Bruijn graph plays an important role in bioinformatics, especially in the context of de
novo assembly. However, the representation of the de Bruijn graph in memory is a …

Variation graphs, which represent genetic variation within a population, are replacing
sequences as reference genomes. Path indexes are one of the most important tools for …

The analysis of biological sequencing data has been one of the biggest applications of
string algorithms. The approaches used in many such applications are based on the …

Grammar-based compression, where one replaces a long string by a small context-free
grammar that generates the string, is a simple and powerful paradigm that captures …