Parameterized algorithms in bioinformatics: an overview
Bioinformatics regularly poses new challenges to algorithm engineers and theoretical
computer scientists. This work surveys recent developments of parameterized algorithms …
computer scientists. This work surveys recent developments of parameterized algorithms …
Complete assembly of circular and chloroplast genomes based on global optimization
This paper focuses on the last two stages of genome assembly, namely, scaffolding and gap-
filling, and shows that they can be solved as part of a single optimization problem. Our …
filling, and shows that they can be solved as part of a single optimization problem. Our …
New results about the linearization of scaffolds sharing repeated contigs
Solutions to genome scaffolding problems can be represented as paths and cycles in a
“solution graph”. However, when working with repetitions, such solution graphs may contain …
“solution graph”. However, when working with repetitions, such solution graphs may contain …
On the hardness of approximating Linearization of Scaffolds sharing Repeated Contigs
Solutions to genome scaffolding problems can be represented as paths and cycles in a
“solution graph”. However, when working with repetitions, such solution graph may contain …
“solution graph”. However, when working with repetitions, such solution graph may contain …
Instance guaranteed ratio on greedy heuristic for genome scaffolding
The Scaffolding problem in bioinformatics, aims to complete the contig assembly process by
determining the relative position and orientation of these contigs. Modeled as a …
determining the relative position and orientation of these contigs. Modeled as a …
On a greedy approach for genome scaffolding
Background Scaffolding is a bioinformatics problem aimed at completing the contig
assembly process by determining the relative position and orientation of these contigs. It can …
assembly process by determining the relative position and orientation of these contigs. It can …
Linearizing genomes: Exact methods and local search
In this article, we address the problem of genome linearization from the perspective of
Polynomial Local Search, a complexity class related to finding local optima. We prove that …
Polynomial Local Search, a complexity class related to finding local optima. We prove that …
New polynomial-time algorithm around the scaffolding problem
We describe in this paper an approximation algorithm for the scaffolding problem, which is
part of genome inference in bioinformatics. The aim of the problem is to find a maximum …
part of genome inference in bioinformatics. The aim of the problem is to find a maximum …