Related papers: A new 1.375-approximation algorithm for Sorting By…
The Transposition Distance Problem (TDP) is a classical problem in genome rearrangements which seeks to determine the minimum number of transpositions needed to transform a linear chromosome into another represented by the permutations…
Sorting a Permutation by Transpositions (SPbT) is an important problem in Bioinformtics. In this paper, we improve the running time of the best known approximation algorithm for SPbT. We use the permutation tree data structure of Feng and…
In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is,…
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…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $\pi$…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
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…
We present a deterministic (1+sqrt(5))/2-approximation algorithm for the s-t path TSP for an arbitrary metric. Given a symmetric metric cost on n vertices including two prespecified endpoints, the problem is to find a shortest Hamiltonian…
Given a graph $G=(V,E)$ with $V=\{1,\ldots,n\}$, we place on every vertex a token $T_1,\ldots,T_n$. A swap is an exchange of tokens on adjacent vertices. We consider the algorithmic question of finding a shortest sequence of swaps such that…
Given a generator set $S$ of the symmetric group ${\rm{Sym}}_n$, every permutation $\pi\in {\rm{Sym}_n}$ is a word (product of elements) of $S$. A positive integer $d(\pi)$ is associated with each $\pi\in{\rm{Sym}_n}$ taking the length of…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
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…
Homomorphic permutation is fundamental to privacy-preserving computations based on batch-encoding homomorphic encryption. It underpins nearly all homomorphic matrix operations and predominantly influences their complexity. Permutation…
An upper dominating set is a minimal dominating set in a graph. In the \textsc{Upper Dominating Set} problem, the goal is to find an upper dominating set of maximum size. We study the complexity of parameterized algorithms for \textsc{Upper…
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…
Some of the most fundamental and well-studied graph parameters are the Diameter (the largest shortest paths distance) and Radius (the smallest distance for which a "center" node can reach all other nodes). The natural and important…
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…
The Traveling Salesman Problem (TSP) is a classic and extensively studied problem with numerous real-world applications in artificial intelligence and operations research. It is well-known that TSP admits a constant approximation ratio on…
We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation…