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The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent…
Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the genomes in comparative genomics studies.…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the…
The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
A number of fields, including the study of genome rearrangements and the design of interconnection networks, deal with the connected problems of sorting permutations in "as few moves as possible", using a given set of allowed operations, or…
This paper presents two new approaches to prove termination of rewrite systems with the Knuth-Bendix order efficiently. The constraints for the weight function and for the precedence are encoded in (pseudo-)propositional logic and the…
In the context of the genome rearrangement problem, we analyze two well known models, namely the block transposition and the prefix block transposition models, by exploiting the connection with the notion of permutation pattern. More…
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…
The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be exactly computed thanks to a pioneering approach of Hannenhalli and Pevzner from 1995. In…