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

In this paper we develop optimal algorithms in the binary-forking model for a variety of
fundamental problems, including sorting, semisorting, list ranking, tree contraction, range …

Presenting the fundamental algorithms and data structures that power bioinformatics
workflows, this book covers a range of topics from the foundations of sequence analysis …

Dynamic analyses are a standard approach to analyzing and testing concurrent programs.
Such techniques observe program traces σ and analyze them to infer the presence or …

The suffix array, one of the most important data structures in modern string processing,
needs to be augmented with the longest-common-prefix (LCP) array in many applications …

Abstract In the Range Minimum Query (RMQ) problem, we are given an array A of n
numbers and we are asked to answer queries of the following type: for indices i and j …

In this paper we study the offline (batched) range minima query (RMQ) problem in the
external memory (EM) and cache-oblivious (CO) models. In the static RMQ problem, given …

Abstract The Range Minimum Query problem consists in answering efficiently the simple
question:“what is the minimal element between two specified indices of a given array?”. In …

A string is a sequence of symbols derived from a given alphabet Σ. The early stages of the
research focused on ordinary pattern matching and several associated variants. For …

Computing an optimal chain of fragments is a classical problem in string algorithms, with
important applications in computational biology. There exist two efficient dynamic …