Related papers: Genome Halving by Block Interchange

We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…

Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…

In the bidirected minimum Manhattan network problem, given a set T of n terminals in the plane, we need to construct a network N(T) of minimum total length with the property that the edges of N(T) are axis-parallel and oriented in a such a…

We propose the interaction of two electrons in a triple quantum dot as a minimal system to control long range superexchange transitions. These are probed by transport spectroscopy. Narrow resonances appear indicating the transfer of charge…

We consider information diffusion on Web-like networks and how random walks can simulate it. A well-studied problem in this domain is Partial Cover Time, i.e., the calculation of the expected number of steps a random walker needs to visit a…

In this paper we deal with the restricted Block Relocation Problem. We present a new lower bound and a heuristic approach for the problem. The proposed lower bound can be computed in polynomial time and it is provably better than some…

We propose an algorithm using the Gaussian elimination method to find the minimal Hamming distance and decode received messages of linear codes. This algorithm is easy to implement as it requires no Gr\"obner bases to compute solutions for…

Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…

This paper introduces an efficient algorithm for computing the best approximation of a given matrix onto the intersection of linear equalities, inequalities and the doubly nonnegative cone (the cone of all positive semidefinite matrices…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

The paper describes a general glance to the use of element exchange techniques for optimization over permutations. A multi-level description of problems is proposed which is a fundamental to understand nature and complexity of optimization…

Interchange theorems between minimization and integration are useful in optimization, especially in optimal control and in stochastic optimization. In this article, we establish a generalized minimization interchange theorem, where…

Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…

The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be…

The construction of optimal linear block error-correcting codes is not an easy problem, for this, many studies describe methods for generating good error correcting codes in terms of minimum distance. In a previous work, we have presented…

It is $\mathsf{NP}$-hard to determine the minimum number of branching vertices needed in a single-source distance-preserving subgraph of an undirected graph. We show that this problem can be solved in polynomial time if the input graph is…

In 1996, Guigo et al. [Mol. Phylogenet. Evol., 6 (1996), 189-203] posed the following problem: for a given species tree and a number of gene trees, what is the minimum number of duplication episodes, where several genes could have undergone…

Given a graph where every vertex has exactly one labeled token, how can we most quickly execute a given permutation on the tokens? In (sequential) token swapping, the goal is to use the shortest possible sequence of swaps, each of which…

This paper introduces an algorithm designed to approximate quantum transformation matrix with a restricted number of gates by using the block decomposition technique. Addressing challenges posed by numerous gates in handling large qubit…

The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be exactly computed thanks to a pioneering approach of Hannenhalli and Pevzner from 1995. In…