Related papers: Permutation patterns in genome rearrangement probl…
For each integer k >= 2, let F(k) denote the largest n for which there exists a permutation \sigma \in S_n, all of whose patterns of length k are distinct. We prove that F(k) = k + \lfloor \sqrt{2k-3} \rfloor + e_k, where e_k \in {-1,0} for…
Random permutations with distribution conditionally uniform given the set of record values can be generated in a unified way, coherently for all values of $n$. Our central example is a two-parameter family of random permutations that are…
We study the mixing properties of permutations obtained as a product of two uniformly random permutations of fixed cycle types. For instance, we give an exact formula for the probability that elements $1,2,...,k$ are in distinct cycles of…
This is a brief survey of some open problems on permutation patterns, with an emphasis on subjects not covered in the recent book by Kitaev, \emph{Patterns in Permutations and words}. I first survey recent developments on the enumeration…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
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…
This work gives a mathematical foundation for bifurcation from a stable equilibrium in the genome. We construct idealized dynamics associated with the genome. For this dynamics we investigate the two main bifurcations from a stable…
We consider a large family of equivalence relations on permutations in Sn that generalise those discovered by Knuth in his study of the Robinson-Schensted correspondence. In our most general setting, two permutations are equivalent if one…
We discuss a model of genome as a program with functional architecture and consider the approach to Darwinian evolution as a learning problem for functional programming. In particular we introduce a model of learning for some class of…
We discuss efficient methods for unranking derangements and m\'enage permutations. That is, we will provide an algorithm to efficiently extract the $k$-th earliest such permutation under the lexicographic ordering. We will show that this…
We develop a new, powerful method for counting elements in a multiset. As a first application, we use this algorithm to study the number of occurrences of patterns in a permutation. For patterns of length 3 there are two Wilf classes, and…
Constraint programming (CP) is a powerful tool for modeling mathematical concepts and objects and finding both solutions or counter examples. One of the major strengths of CP is that problems can easily be combined or expanded. In this…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
In this paper we study the inverse of so-called unfair permutations, and explore various properties of them. Our investigation begins with comparing this class of permutations with uniformly random permutations, and showing that they behave…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Analyzing the computational complexity of evolutionary algorithms for binary search spaces has significantly increased their theoretical understanding. With this paper, we start the computational complexity analysis of genetic programming.…
Permutation patterns and pattern avoidance are central, well-studied concepts in combinatorics and computer science. Given two permutations $\tau$ and $\pi$, the pattern matching problem (PPM) asks whether $\tau$ contains $\pi$. This…
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,…
Every k entries in a permutation can have one of k! different relative orders, called patterns. How many times does each pattern occur in a large random permutation of size n? The distribution of this k!-dimensional vector of pattern…