Related papers: Permutation patterns in genome rearrangement probl…

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…

In this paper, we propose a general framework that extends the theory of permutation patterns to higher dimensions and unifies several combinatorial objects studied in the literature. Our approach involves introducing the concept of a…

Packing density is a permutation occurrence statistic which describes the maximal number of permutations of a given type that can occur in another permutation. In this article we focus on containment of sets of permutations. Although this…

Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…

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…

Let $\pi=(\pi_1,\pi_2,\hdots,\pi_n)$ be permutation of the elements $1,2,\hdots,n. $ Positive integer $k\leq2^{n-1}$ we call index of $\pi,$ if in its binary notation as $n$-digital binary number, the 1's correspond to the ascent points. We…

In a highly simplified view, a disease can be seen as the phenotype emerging from the interplay of genetic predisposition and fluctuating environmental stimuli. We formalize this situation in a minimal model, where a network (representing…

A {\it superpattern} is a string of characters of length $n$ that contains as a subsequence, and in a sense that depends on the context, all the smaller strings of length $k$ in a certain class. We prove structural and probabilistic results…

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…

Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…

For a given permutation or set partition there is a natural way to assign a genus. Counting all permutations or partitions of a fixed genus according to cycle lengths or block sizes, respectively, is the main content of this article. After…

In this paper we give a bijection between the class of permutations that can be drawn on an X-shape and a certain set of permutations that appears in [Knuth] in connection to sorting algorithms. A natural generalization of this set leads us…

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 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…

An occurrence of a classical pattern p in a permutation \pi is a subsequence of \pi whose letters are in the same relative order (of size) as those in p. In an occurrence of a generalized pattern, some letters of that subsequence may be…

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…

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…

Recently, Babson and Steingrimsson have introduced generalised permutation patterns that allow the requirement that two adjacent letters in a pattern must be adjacent in the permutation. We consider pattern avoidance for such patterns, and…

Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…

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…