Related papers: Permutation patterns in genome rearrangement probl…
We explore a new type of replacement of patterns in permutations, suggested by James Propp, that does not preserve the length of permutations. In particular, we focus on replacements between 123 and a pattern of two integer elements. We…
Permutation testing in linear models, where the number of nuisance coefficients is smaller than the sample size, is a well-studied topic. The common approach of such tests is to permute residuals after regressing on the nuisance covariates.…
Motivated by some problems in genome assembling, we investigate properties of spacings from absolutely continuous distributions. Several results on the asymptotic behavior of the maximal uniform and non-uniform $k$-spacings are presented.…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Following a question of J. Cooper, we study the expected number of occurrences of a given permutation pattern $q$ in permutations that avoid another given pattern $r$. In some cases, we find the pattern that occurs least often, (resp. most…
Two permutations $s$ and $t$ are $k$-similar if they can be decomposed into subpermutations $s^1, \ldots, s^k$ and $t^1, \ldots, t^k$ such that $s^i$ is order-isomorphic to $t^i$ for all $i$. Recently, Dudek, Grytczuk and Ruci\'nski posed…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
We consider uniform random permutations in proper substitution-closed classes and study their limiting behavior in the sense of permutons. The limit depends on the generating series of the simple permutations in the class. Under a mild…
Numerical evidence suggests that certain permutation patterns of length k are easier to avoid than any other patterns of that same length. We prove that these patterns are avoided by no more than (2.25k^2)^n permutations of length n. In…
The subject of pattern avoiding permutations has its roots in computer science, namely in the problem of sorting a permutation through a stack. A formula for the number of permutations of length n that can be sorted by passing it twice…
The problem of genealogy of permutations has been solved partially by Stefan (odd order) and Acosta-Hum\'anez & Bernhardt (power of two). It is well known that Sharkovskii's theorem shows the relationship between the cardinal of the set of…
We describe some configurations of conjugate permutations which may be used as a mathematical model of some genetical processes and crystal growth.
Mutations are typically classified by their effects on the nucleotide sequence and by their size. Here, we argue that if our main aim is to understand the effect of mutations on evolutionary outcomes (such as adaptation or speciation), we…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Permutation codes, in the form of rank modulation, have shown promise for applications such as flash memory. One of the metrics recently suggested as appropriate for rank modulation is the Ulam metric, which measures the minimum…
A descent $k$ of a permutation $\pi=\pi_{1}\pi_{2}\dots\pi_{n}$ is called a big descent if $\pi_{k}>\pi_{k+1}+1$; denote the number of big descents of $\pi$ by $\operatorname{bdes}(\pi)$. We study the distribution of the…
In this paper we present a novel tool to evaluate problem solving systems. Instead of using a system to solve a problem, we suggest using the problem to evaluate the system. By finding a numerical representation of a problem's complexity,…
The boolean elements of a Coxeter group have been characterized and shown to possess many interesting properties and applications. Here we introduce "prism permutations," a generalization of those elements, characterizing the prism…