Related papers: A memory-efficient data structure representing exa…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
Given a set of finite words, the Overlap Graph (OG) is a complete weighted digraph where each word is a node and where the weight of an arc equals the length of the longest overlap of one word onto the other (Overlap is an asymmetric…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
We present the first data structures that maintain near optimal maximum cardinality and maximum weighted matchings on sparse graphs in sublinear time per update. Our main result is a data structure that maintains a $(1+\epsilon)$…
The graph is one of the most widely used mathematical structures in engineering and science because of its representational power and inherent ability to demonstrate the relationship between objects. The objective of this work is to…
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.…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
An overlap representation is an assignment of sets to the vertices of a graph in such a way that two vertices are adjacent if and only if the sets assigned to them overlap. The overlap number of a graph is the minimum number of elements…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
An {\it overlap representation} of a graph $G$ assigns sets to vertices so that vertices are adjacent if and only if their assigned sets intersect with neither containing the other. The {\it overlap number} $\ol(G)$ (introduced by Rosgen)…
Subgraph matching query is a fundamental problem in graph data management and has a variety of real-world applications. Several recent works utilize deep learning (DL) techniques to process subgraph matching queries. Most of them find…
We study the problem of finding maximal exact matches (MEMs) between a query string $Q$ and a labeled graph $G$. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
Hypergraphs are generalisation of graphs in which a hyperedge can connect any number of vertices. It can describe n-ary relationships and high-order information among entities compared to conventional graphs. In this paper, we study the…