Related papers: Genome Halving by Block Interchange
Quantum networks distributed over distances greater than a few kilometers will be limited by the time required for information to propagate between nodes. We analyze protocols that are able to circumvent this bottleneck by employing…
This paper explores the application of a new algebraic method of edge coloring, called complex coloring, to the scheduling problems of input queued switches. The proposed distributed parallel scheduling algorithm possesses two important…
In this paper we present an efficient algorithm for bivariate interpolation, which is based on the use of the partition of unity method for constructing a global interpolant. It is obtained by combining local radial basis function…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
Consider a problem where we are given a bipartite graph H with vertices arranged on two horizontal lines in the plane, such that the two sets of vertices placed on the two lines form a bipartition of H. We additionally require that H admits…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other ones. This problem has been shown to…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
Routing is a widespread approach to transfer information from a source node to a destination node in many deployed wireless ad-hoc networks. Today's implemented routing algorithms seek to efficiently find the path/route with the largest…
The key step of syndrome-based decoding of Reed-Solomon codes up to half the minimum distance is to solve the so-called Key Equation. List decoding algorithms, capable of decoding beyond half the minimum distance, are based on interpolation…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
In this paper we consider linear combinations of two trivariate homogeneous polynomials of second degree. We formulate and solve two problems: i) Characterization of polynomials for which all linear combinations are factorizable. ii) How…
In this note, we consider the problem of finding a step-by-step transformation between two longest increasing subsequences in a sequence, namely Longest Increasing Subsequence Reconfiguration. We give a polynomial-time algorithm for…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
The transfer or exchange of multipartite quantum states is critical to the realization of large-scale quantum information processing and quantum communication. A challenging question in this context is: What is the minimum resource required…
In several multiobjective decision problems Pairwise Comparison Matrices (PCM) are applied to evaluate the decision variants. The problem that arises very often is the inconsistency of a given PCM. In such a situation it is important to…
In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…
This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from probability theory. Crucially, this distance estimate provides a genuine metric on genome space. We develop the…