Related papers: Sorting Genomes by Prefix Double-Cut-and-Joins
In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…
We are concerned with the problem of designing large families of subsets over a common labeled ground set that have small pairwise intersections and the property that the maximum discrepancy of the label values within each of the sets is…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
In nonadaptive group testing, the main research objective is to design an efficient algorithm to identify a set of up to $t$ positive elements among $n$ samples with as few tests as possible. Disjunct matrices and separable matrices are two…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
The well-known $k$-disjoint path problem ($k$-DPP) asks for pairwise vertex-disjoint paths between $k$ specified pairs of vertices $(s_i, t_i)$ in a given graph, if they exist. The decision version of the shortest $k$-DPP asks for the…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
Enumeration kernelization was first proposed by Creignou et al. [TOCS 2017] and was later refined by Golovach et al. [JCSS 2022] into two different variants: fully-polynomial enumeration kernelization and polynomial-delay enumeration…
A basic algorithm for enumerating disjoint propositional models (disjoint AllSAT) is based on adding blocking clauses incrementally, ruling out previously found models. On the one hand, blocking clauses have the potential to reduce the…
This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
Prolog's ability to return multiple answers on backtracking provides an elegant mechanism to derive reversible encodings of combinatorial objects as Natural Numbers i.e. {\em ranking} and {\em unranking} functions. Starting from a…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Following the footprints of what have been done with the algorithm Stacksort, we investigate the preimages of the map associated with a slightly less well known algorithm, called Queuesort. After having described an equivalent version of…
We extend the standard rough set-based approach to deal with huge amounts of numeric attributes versus small amount of available objects. Here, a novel approach of clustering along with dimensionality reduction; Hybrid Fuzzy C Means-Quick…
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…