Related papers: Permutation patterns in genome rearrangement probl…
It is known that the set of permutations, under the pattern containment ordering, is not a partial well-order. Characterizing the partially well-ordered closed sets (equivalently: down sets or ideals) in this poset remains a wide-open…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…
In this article we generalize packing density problems from permutations to patterns with repeated letters and generalized patterns. We are able to find the packing density for some classes of patterns and several other short patterns.
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Baxter permutations are a class of permutations which are in bijection with a class of floorplans that arise in chip design called mosaic floorplans. We study a subclass of mosaic floorplans called $HFO_k$ defined from mosaic floorplans by…
We construct generating trees with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation,…
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…
We study a nonlinear recombination model from population genetics as a combinatorial version of the Kac-Boltzmann equation from kinetic theory. Following Kac's approach, the nonlinear model is approximated by a mean field linear evolution…
In the last years, different types of patterns in permutations have been studied: vincular, bivincular and mesh patterns, just to name a few. Every type of permutation pattern naturally defines a corresponding computational problem: Given a…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
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…
In this paper, we explore the theory and expand upon the practice of fitness landscape analysis for optimization problems over the space of permutations. Many of the computational and analytical tools for fitness landscape analysis, such as…
We consider the question of computing the distribution of a permutation statistics over restricted permutations via enumeration schemes. The restricted permutations are those avoiding sets of vincular patterns (which include both classical…
Permutation clones generalise permutation groups and clone theory. We investigate permutation clones defined by relations, or equivalently, the automorphism groups of powers of relations. We find many structural results on the lattice of…
We describe a new method for finding patterns in permutations that produce a given pattern after the permutation has been passed once through a stack. We use this method to describe West-3-stack-sortable permutations, that is, permutations…
We review a recent development at the interface between discrete mathematics on one hand and probability theory and statistics on the other, specifically the use of Markov chains and their boundary theory in connection with the asymptotics…
Let $G_{k,n}$ be a group of permutations of $kn$ objects which permutes things independently in disjoint blocks of size $k$ and then permutes the blocks. We investigate the probabilistic and/or enumerative aspects of random elements of…
A permutation of size $n$ can be identified to its diagram in which there is exactly one point per row and column in the grid $[n]^2$. In this paper we consider multidimensional permutations (or $d$-permutations), which are identified to…
Detecting and counting copies of permutation patterns are fundamental algorithmic problems, with applications in the analysis of rankings, nonparametric statistics, and property testing tasks such as independence and quasirandomness…