Annelyse Thévenin

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A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogenetic tree. A large number of such measures has been proposed in the recent past: number of reversals, number of breakpoints, number of common or conserved intervals, SAD etc. In their initial definitions, all(More)
Comparing genomes of different species is a fundamental problem in comparative genomics. Recent research has resulted in the introduction of different measures between pairs of genomes: for example, reversal distance, number of breakpoints, and number of common or conserved intervals. However, classical methods used for computing such measures are seriously(More)
The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. Orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. Here we present PoFF, an extension(More)
The comparison of relative gene orders between two genomes offers deep insights into functional correlations of genes and the evolutionary relationships between the corresponding organisms. Methods for gene order analyses often require prior knowledge of homologies between all genes of the genomic dataset. Since such information is hard to obtain, it is(More)
Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clustering of genes by function, except for(More)
Comparing genomes of different species is a crucial problem in comparative genomics. Different measures have been proposed to compare two genomes: number of common intervals, number of adjacencies, number of reversals, etc. These measures are classically used between two totally ordered genomes. However, genetic mapping techniques often give rise to(More)
Comparing genomes of different species has become a crucial problem in comparative genomics. Recent research have resulted in different genomic distance definitions: number of breakpoints, number of common intervals, number of conserved intervals, Maximum Adjacency Disruption number (MAD), etc. Classical methods (usually based on permutations of gene order)(More)
Many methods in computational comparative genomics require gene family assignments as a prerequisite. While the biological concept of gene families is well established, their computational prediction remains unreliable. This paper continues a new line of research in which family assignments are not presumed. We study the potential of several family-free(More)
—Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a(More)