Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …

The recent advances in sequencing technologies enable the assembly of individual
genomes to the quality of the reference genome. How to integrate multiple genomes from …

Two decades ago, a breakthrough in indexing string collections made it possible to
represent them within their compressed space while at the same time offering indexed …

Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …

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

The wavelet tree is a versatile data structure that serves a number of purposes, from string
processing to computational geometry. It can be regarded as a device that represents a …

A well-known fact in the field of lossless text compression is that high-order entropy is a
weak model when the input contains long repetitions. Motivated by this fact, decades of …

High-throughput sequencing has revolutionised the field of biological sequence analysis. Its
application has enabled researchers to address important biological questions, often for the …

The exponential increase in sequencing data calls for conceptual and computational
advances to extract useful biological insights. One such advance, minimizers, allows for …