Related papers: A simple framework on sorting permutations
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and…
In this paper we generalize permutations to plane permutations. We employ this framework to derive a combinatorial proof of a result of Zagier and Stanley, that enumerates the number of $n$-cycles $\omega$, for which $\omega(12\cdots n)$…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…
We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of…
Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
In this paper we prove new lower bounds for the maximal size of permutation codes by connecting the theory of permutation codes with the theory of linear block codes. More specifically, using the columns of a parity check matrix of an…
A wide range of applications, most notably in comparative genomics, involve the computation of a shortest sorting sequence of operations for a given permutation, where the set of allowed operations is fixed beforehand. Such sequences are…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
A permutation may be represented by a collection of paths in the plane. We consider a natural class of such representations, which we call tangles, in which the paths consist of straight segments at 45 degree angles, and the permutation is…
Motivated by Bourque and Pevzner's simulation study of the parsimony method for studying genome rearrangement, Berestycki and Durrett used techniques from random graph theory to prove that the minimum parsimony distance after iterating the…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
The aim of this paper is to provide an overview of recent development related to Bregman distances outside its native areas of optimization and statistics. We discuss approaches in inverse problems and image processing based on Bregman…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
A permutation is called {\it {block-wise simple}} if it contains no interval of the form $p_1\oplus p_2$ or $p_1 \ominus p_2$. We present this new set of permutations and explore some of its combinatorial properties. We present a generating…
In a previous work, B\'ona and Pantone studied permutations that avoided all but one pattern of length $k$ that began with a length $k-1$ increasing subsequence. We draw the connection between that idea and distant patterns, first discussed…
We examine an error-correcting coding framework in which each coded symbol is constrained to be a function of a fixed subset of the message symbols. With an eye toward distributed storage applications, we seek to design systematic codes…
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…
A set of linearly constrained permutation matrices are proposed for constructing a class of permutation codes. Making use of linear constraints imposed on the permutation matrices, we can formulate a minimum Euclidian distance decoding…
Given a permutation pi, the application of prefix reversal f^(i) to pi reverses the order of the first i elements of pi. The problem of Sorting By Prefix Reversals (also known as pancake flipping), made famous by Gates and Papadimitriou…