Related papers: Heuristics based on Adjacency Graph Packing for DC…
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 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…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
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…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
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…
We investigate structural and algorithmic advantages of a directed version of the well-researched class of distance-hereditary graphs. Since the previously defined distance-hereditary digraphs do not permit a recursive structure, we define…
We investigate the statistical properties of cut sizes generated by heuristic algorithms which solve approximately the graph bisection problem. On an ensemble of sparse random graphs, we find empirically that the distribution of the cut…
Motivation: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution,…
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,…
Link prediction is a key problem for network-structured data. Link prediction heuristics use some score functions, such as common neighbors and Katz index, to measure the likelihood of links. They have obtained wide practical uses due to…
The {\em double-cut-and-join} (DCJ) operation, introduced by Yancopoulos \emph{et al.}, allows minimum edit distance to be computed by modeling all possible classical rearrangement operations, such as inversions, fusions, fissions,…
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 computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
One of the most important combinatorial optimization problems is graph coloring. There are several variations of this problem involving additional constraints either on vertices or edges. They constitute models for real applications, such…
The data arrangement problem on regular trees (DAPT) consists in assigning the vertices of a given graph G to the leaves of a d-regular tree T such that the sum of the pairwise distances of all pairs of leaves in T which correspond to edges…
In graph modification problems, one is given a graph G and the goal is to apply a minimum number of modification operations (such as edge deletions) to G such that the resulting graph fulfills a certain property. For example, the Cluster…
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…
Packing problems are in general NP-hard, even for simple cases. Since now there are no highly efficient algorithms available for solving packing problems. The two-dimensional bin packing problem is about packing all given rectangular items,…