Related papers: On the Approximability of Comparing Genomes with D…
We introduce a new -as far as we know- problem, according to which we are asked to match sequences of two digits in matrices having entries among those two digits (but others too) and prove that this problem is NP-complete
Several statistical approaches based on reproducing kernels have been proposed to detect abrupt changes arising in the full distribution of the observations and not only in the mean or variance. Some of these approaches enjoy good…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
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…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
A matching is said to be disconnected if the saturated vertices induce a disconnected subgraph and induced if the saturated vertices induce a 1-regular graph. The disconnected and induced matching numbers are defined as the maximum…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
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.…
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…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
In multistage perfect matching problems we are given a sequence of graphs on the same vertex set and asked to find a sequence of perfect matchings, corresponding to the sequence of graphs, such that consecutive matchings are as similar as…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity multipartite graph. We present a model…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
Quantifying the similarity between two graphs is a fundamental algorithmic problem at the heart of many data analysis tasks for graph-based data. In this paper, we study the computational complexity of a family of similarity measures based…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
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…