Related papers: Permutation patterns in genome rearrangement probl…
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-…
A pattern class is a set of permutations closed under the formation of subpermutations. Such classes can be characterised as those permutations not involving a particular set of forbidden permutations. A simple collection of necessary and…
We collect open problems in permutation patterns on four themes: rank-unimodality in the permutation pattern poset, Wilf-equivalence and shape-Wilf-equivalence, the enumeration of derangements in permutation classes, and sorting by stacks…
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.…
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…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
A $k$-universal permutation, or $k$-superpermutation, is a permutation that contains all permutations of length $k$ as patterns. The problem of finding the minimum length of a $k$-superpermutation has recently received significant attention…
We define the operation of composing two hereditary classes of permutations using the standard composition of permutations as functions and we explore properties and structure of permutation classes considering this operation. We mostly…
There are several approaches to study occurrences of consecutive patterns in permutations such as the inclusion-exclusion method, the tree representations of permutations, the spectral approach and others. We propose yet another approach to…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
Motivated by the problem of constructing bijective maps with low differential uniformity, we introduce the notion of permutation resemblance of a function, which looks to measure the distance a given map is from being a permutation. We…
Drawing on a problem posed by Hertzsprung in 1887, we say that a given permutation $\pi\in\mathcal{S}_n$ contains the Hertzsprung pattern $\sigma\in\mathcal{S}_k$ if there is factor $\pi(d+1)\pi(d+2)\cdots\pi(d+k)$ of $\pi$ such that…
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…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
We consider here the morphogenesis (pattern formation) problem for some genetic network models. First, we show that any given spatio-temporal pattern can be generated by a genetic network involving a sufficiently large number of genes.…
A brief presentation of basic definitions and notation used in permutation patterns research.
Prime number multiplet classifications and patterns are extended to negative integers. The extension from prime numbers to single prime powers is also studied. Prime number septets at equal distance are given. It is also shown that each…
In the last decade a huge amount of articles has been published studying pattern avoidance on permutations. From the point of view of enumeration, typically one tries to count permutations avoiding certain patterns according to their…
We consider the problem of packing fixed-length patterns into a permutation, and develop a connection between the number of large patterns and the number of bonds in a permutation. Improving upon a result of Kaplansky and Wolfowitz, we…
We introduce the notion of crossings and nestings of a permutation. We compute the generating function of permutations with a fixed number of weak exceedances, crossings and nestings. We link alignments and permutation patterns to these…