Related papers: Genome Halving by Block Interchange
In the monotone integer dualization problem, we are given two sets of vectors in an integer box such that no vector in the first set is dominated by a vector in the second. The question is to check if the two sets of vectors cover the…
We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…
An interpolation-based decoding scheme for interleaved subspace codes is presented. The scheme can be used as a (not necessarily polynomial-time) list decoder as well as a probabilistic unique decoder. Both interpretations allow to decode…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
Tanglegrams are drawings of two rooted binary phylogenetic trees and a matching between their leaf sets. The trees are drawn crossing-free on opposite sides with their leaf sets facing each other on two vertical lines. Instead of minimizing…
A problem that arises in drawings of transportation networks is to minimize the number of crossings between different transportation lines. While this can be done efficiently under specific constraints, not all solutions are visually…
Given $n$ intervals on a line $\ell$, we consider the problem of moving these intervals on $\ell$ such that no two intervals overlap and the maximum moving distance of the intervals is minimized. The difficulty for solving the problem lies…
We present a genetic algorithm which is distributed in two novel ways: along genotype and temporal axes. Our algorithm first distributes, for every member of the population, a subset of the genotype to each network node, rather than a…
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…
Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced…
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
The main task in analyzing a switching network design (including circuit-, multirate-, and photonic-switching) is to determine the minimum number of some switching components so that the design is non-blocking in some sense (e.g., strict-…
The note derives an expression for the number of interchanges made by selection sort when the sorting elements are iid variates from geometric distribution. Empirical results reveal we can work with a simpler model compared to what is…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
List colouring is an NP-complete decision problem even if the total number of colours is three. It is hard even on planar bipartite graphs. We give a polynomial-time algorithm for solving list colouring of permutation graphs with a bounded…
We study the following variant of the 15 puzzle. Given a graph and two token placements on the vertices, we want to find a walk of the minimum length (if any exists) such that the sequence of token swappings along the walk obtains one of…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
This work aims at optimizing injection networks, which consist in adding a set of long-range links (called bypass links) in mobile multi-hop ad hoc networks so as to improve connectivity and overcome network partitioning. To this end, we…