Related papers: Genome Halving by Block Interchange
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
The evaluation of the minimum distance of linear block codes remains an open problem in coding theory, and it is not easy to determine its true value by classical methods, for this reason the problem has been solved in the literature with…
We present a computational study of finite-time mixing of a line segment by cutting and shuffling. A family of one-dimensional interval exchange transformations is constructed as a model system in which to study these types of mixing…
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…
Upcoming many core processors are expected to employ a distributed memory architecture similar to currently available supercomputers, but parallel pattern mining algorithms amenable to the architecture are not comprehensively studied. We…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
In this paper, we propose a distributed algorithm to solve planar minimum time multi-vehicle rendezvous problem with non-identical velocity constraints on cyclic digraph (topology). Motivated by the cyclic alternating projection method that…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
Learning intersections of halfspaces is a central problem in Computational Learning Theory. Even for just two halfspaces, it remains a major open question whether learning is possible in polynomial time with respect to the margin $\gamma$…
Quantum computers provide an opportunity to efficiently sample from probability distributions that include non-trivial interference effects between amplitudes. Using a simple process wherein all possible state histories can be specified by…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
The clock synchronization problem is to determine the time difference $\Delta$ between two spatially separated clocks. When message delivery times between the two clocks are uncertain, $O(2^{2n})$ classical messages must be exchanged…
Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
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…
Given a bidirected ring with capacities and a demand graph, we present an approximation algorithm to the problem of finding the minimum $\alpha$ such that there exists a feasible unsplittable routing of the demands after multiplying each…
In the paper, we investigate Two Sets Intersection problem. Assume that we have two sets that are subsets of n objects. Sets are presented by two predicates that show which of n objects belong to these sets. We present a quantum algorithm…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…