相关论文: Tractability results for the Double-Cut-and-Join c…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
The Genome Median Problem is an important problem in phylogenetic reconstruction under rearrangement models. It can be stated as follows: given three genomes, find a fourth that minimizes the sum of the pairwise rearrangement distances…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
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…
Establishing a distance between genomes is a significant problem in computational genomics, because its solution can be used to establish evolutionary relationships including phylogeny. The "double cut and join" (DCJ) model of chromosomal…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In…
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
The Generalized Discretizable Molecular Distance Geometry Problem is a distance geometry problems that can be solved by a combinatorial algorithm called ``Branch-and-Prune''. It was observed empirically that the number of solutions of YES…
In graph realization problems one is given a degree sequence and the task is to decide whether there is a graph whose vertex degrees match to the given sequence. This realization problem is known to be polynomial-time solvable when the…
Perfect Matching-Cut is the problem of deciding whether a graph has a perfect matching that contains an edge-cut. We show that this problem is NP-complete for planar graphs with maximum degree four, for planar graphs with girth five, for…
In this work, we explore heuristics for the Adjacency Graph Packing problem, which can be applied to the Double Cut and Join (DCJ) Distance Problem. The DCJ is a rearrangement operation and the distance problem considering it is a well…
Given a graph $G$ rooted at a vertex $r$ and weight functions, $\gamma, \tau: E(G) \rightarrow \mathbb{R}$, the generalized cable-trench problem (CTP) is to find a single spanning tree that simultaneously minimizes the sum of the total edge…
Let $\mathcal{D}$ be a set of straight-line segments in the plane, potentially crossing, and let $c$ be a positive integer. We denote by $P$ the union of the endpoints of the straight-line segments of $\mathcal{D}$ and of the intersection…
A graph $G$ is {\em matching-decyclable} if it has a matching $M$ such that $G-M$ is acyclic. Deciding whether $G$ is matching-decyclable is an NP-complete problem even if $G$ is 2-connected, planar, and subcubic. In this work we present…