相关论文: On sampling SCJ rearrangement scenarios

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.…

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 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…

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…

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…

Reconstructing ancestral gene orders is an important step towards understanding genome evolution. The Small Parsimony Problem (SPP) has been extensively studied in this regard. The problem aims at finding the gene orders at internal nodes…

Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies,…

We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. We compare the number of operations along the evolutionary trajectory to the DCJ distance of the genome from its ancestor…

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…

Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…

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 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,…

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…

We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…

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…

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…

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…