Background Orthology analysis is an important part of data analysis in many areas of
bioinformatics such as comparative genomics and molecular phylogenetics. The ever …

Orthology is a powerful refinement of homology that allows us to describe more precisely the
evolution of genomes and understand the function of the genes they contain. However …

A comprehensive survey of a rapidly expanding field of combinatorial optimization,
mathematically oriented but offering biological explanations when required. From one cell to …

One of the challenges in the Comparative Genomics field is to infer how close two
organisms are based on the similarities and differences between their genetic materials …

This paper describes a general hybrid metaheuristic for combinatorial optimization labelled
Construct, Merge, Solve & Adapt. The proposed algorithm is a specific instantiation of a …

Background Genome median and genome halving are combinatorial optimization problems
that aim at reconstructing ancestral genomes as well as the evolutionary events leading from …

String comparison is a fundamental problem in computer science, with applications in areas
such as computational biology, text processing or compression. In this paper we address the …

Computing the edit distance between two genomes is a basic problem in the study of
genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most …

We address the problem of homology identification in complex multidomain families with
varied domain architectures. The challenge is to distinguish sequence pairs that share …

The assignment of orthologous genes between a pair of genomes is a fundamental and
challenging problem in comparative genomics, since many computational methods for …