Related papers: Orienting Ordered Scaffolds: Complexity and Algori…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
Ordered matchings, defined as graphs with linearly ordered vertices, where each vertex is connected to exactly one edge, play a crucial role in the area of ordered graphs and their homomorphisms. Therefore, we consider related problems from…
We examine ordered graphs, defined as graphs with linearly ordered vertices, from the perspective of homomorphisms (and colorings) and their complexities. We demonstrate the corresponding computational and parameterized complexities, along…
The orienteering problem (OP) is a combinatorial optimization problem that seeks a path visiting a subset of locations to maximize collected rewards under a limited resource budget. This article presents a systematic PRISMA-based review of…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Given a graph with edge costs and vertex profits and given a budget B, the Orienteering Problem asks for a walk of cost at most B of maximum profit. Additionally, each profit may be given with a time window within it can be collected by the…
Given an undirected graph G, the edge orientation problem asks for assigning a direction to each edge to convert G into a directed graph. The aim is to minimize the maximum out degree of a vertex in the resulting directed graph. This…
We introduce a variation of the scheduling with precedence constraints problem that has applications to molecular folding and production management. We are given a bipartite graph $H=(B,S)$. Vertices in $B$ are thought of as goods or…
Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…
We study the shared processor scheduling problem with a single shared processor where a unit time saving (weight) obtained by processing a job on the shared processor depends on the job. A polynomial-time optimization algorithm has been…
We study the \emph{order-finding problem} for Read-once Oblivious Algebraic Branching Programs (ROABPs). Given a polynomial $f$ and a parameter $w$, the goal is to find an order $\sigma$ in which $f$ has an ROABP of \emph{width} $w$. We…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
We study the partial search order problem (PSOP) proposed recently by Scheffler [WG 2022]. Given a graph $G$ together with a partial order over the set of vertices of $G$, this problem determines if there is an $\mathcal{S}$-ordering that…
In this paper, we define and study the new problem Simultaneous PQ-Ordering. Its input consists of a set of PQ-trees, which represent sets of circular orders of their leaves, together with a set of child-parent relations between these…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
The C-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired network class C. This problem arises, for example, when visualising evolutionary data, as popular methods…
Programmable arrays of optical traps enable the assembly of configurations of single atoms to perform controlled experiments on quantum many-body systems. Finding the sequence of control operations to transform an arbitrary configuration of…