Related papers: Pairwise Rearrangement is Fixed-Parameter Tractabl…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
We continue and extend previous work on the parameterized complexity analysis of the NP-hard Stable Roommates with Ties and Incomplete Lists problem, thereby strengthening earlier results both on the side of parameterized hardness as well…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
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…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
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 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…
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,…
We study the classical problem of computing geometric thickness, i.e., finding a straight-line drawing of an input graph and a partition of its edges into as few parts as possible so that each part is crossing-free. Since the problem is…
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…
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…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
Fixed-parameter tractability analysis and scheduling are two core domains of combinatorial optimization which led to deep understanding of many important algorithmic questions. However, even though fixed-parameter algorithms are appealing…
We argue that parameterized complexity is a useful tool with which to study global constraints. In particular, we show that many global constraints which are intractable to propagate completely have natural parameters which make them…
In extension problems of partial graph drawings one is given an incomplete drawing of an input graph $G$ and is asked to complete the drawing while maintaining certain properties. A prominent area where such problems arise is that of…
In Two-Sets Cut-Uncut, we are given an undirected graph $G=(V,E)$ and two terminal sets $S$ and $T$. The task is to find a minimum cut $C$ in $G$ (if there is any) separating $S$ from $T$ under the following ``uncut'' condition. In the…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
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…
The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other ones. This problem has been shown to…