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Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
De Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…
The subgraph enumeration problem asks us to find all subgraphs of a target graph that are isomorphic to a given pattern graph. Determining whether even one such isomorphic subgraph exists is NP-complete---and therefore finding all such…
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…
DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
Graphs and their traversal is becoming significant as it is applicable to various areas of mathematics, science and technology. Various problems in fields as varied as biochemistry (genomics), electrical engineering (communication…
Subgraph queries also known as subgraph isomorphism search is a fundamental problem in querying graph-like structured data. It consists to enumerate the subgraphs of a data graph that match a query graph. This problem arises in many…
Spiking Neural Networks (SNN). SNNs are based on a more biologically inspired approach than usual artificial neural networks. Such models are characterized by complex dynamics between neurons and spikes. These are very sensitive to the…
Maximal Clique Enumeration (MCE) is a fundamental graph mining problem, and is useful as a primitive in identifying dense structures in a graph. Due to the high computational cost of MCE, parallel methods are imperative for dealing with…
Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph…
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…
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…
This paper presents a method to find new De Bruijn cycles based on ones of lesser order. This is done by mapping a De Bruijn cycle to several vertex disjoint cycles in a De Bruijn digraph of higher order and connecting these cycles into one…
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster.…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
Many studies have been conducted on seeking the efficient solution for subgraph similarity search over certain (deterministic) graphs due to its wide application in many fields, including bioinformatics, social network analysis, and…
Community search aims at finding densely connected subgraphs for query vertices in a graph. While this task has been studied widely in the literature, most of the existing works only focus on finding homogeneous communities rather than…