Related papers: Linear-Time Superbubble Identification Algorithm f…
Recently we have developed a new method in graph theory based on the Regularity Lemma. The method is applied to find certain spanning subgraphs in dense graphs. The other main general tool of the method, beside the Regularity Lemma, is the…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
Sampling edges from a graph in sublinear time is a fundamental problem and a powerful subroutine for designing sublinear-time algorithms. Suppose we have access to the vertices of the graph and know a constant-factor approximation to the…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
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…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
The problem of finding the degeneracy of a graph is a subproblem of the k-core decomposition problem. In this paper, we present a (1 + epsilon)-approximate solution to the degeneracy problem which runs in O(n log n) time, sublinear in the…
Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…
Graph Convolutional Networks (GCNs) have been proved successful in the field of semi-supervised node classification by extracting structural information from graph data. However, the random selection of labeled nodes used by GCNs may lead…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
In this study, we explore how quantum pathfinding algorithm called Gaussian Amplitude Amplification (GAA) can be used to solve the DNA sequencing problem. To do this, sequencing by hybridization was assumed wherein short fragments of the…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
Uniform sampling of simple graphs having a given degree sequence is a known problem with exponential complexity in the square of the mean degree. For undirected graphs, randomised approximation algorithms have nonetheless been shown to…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…