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 …

Post-Sanger sequencing methods produce tons of data, and there is a generalagreement
that the challenge to store and process them must be addressedwith data compression. In …

White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and
providing genomics resources for this commercially valuable tree will help improve forest …

Large datasets can be screened for sequences from a specific organism, quickly and with
low memory requirements, by a data structure that supports time-and memory-efficient set …

We address the problem of designing, implementing, and experimenting with compressed
data structures that support rank and select queries over a dictionary of integers. We shine a …

High-throughput sequencing technologies have led to explosive growth of genomic
databases; one of which will soon reach hundreds of terabytes. For many applications we …

This article presents an O (n)-time algorithm called SACA-K for sorting the suffixes of an
input string T [0, n-1] over an alphabet A [0, K-1]. The problem of sorting the suffixes of T is …

In recent years, the focus of bioinformatics research has moved from individual sequences to
collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform …

In this paper we describe algorithms for computing the Burrows-Wheeler Transform (bwt)
and for building (compressed) indexes in external memory. The innovative feature of our …

Large-scale genomics demands computational methods that scale sublinearly with the
growth of data. We review several data structures and sketching techniques that have been …