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

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 …

Motivation: PacBio single molecule real-time sequencing is a third-generation sequencing
technique producing long reads, with comparatively lower throughput and higher error rate …

Information retrieval (IR) has changed considerably in recent years with the expansion of the
World Wide Web and the advent of modern and inexpensive graphical user interfaces and …

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

This newly expanded and updated second edition of the best-selling classic continues to
take the" mystery" out of designing algorithms, and analyzing their efficacy and efficiency …

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 consider the indexable dictionary problem, which consists of storing a set S⊆{0,…, m−
1} for some integer m while supporting the operations of rank (x), which returns the number …

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 …

In 1990, Manber and Myers proposed suffix arrays as a space-saving alternative to suffix
trees and described the first algorithms for suffix array construction and use. Since that time …