Related papers: Indexing Variation Graphs
The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information…
Pangenomes serve as a framework for joint analysis of genomes of related organisms. Several pangenome models were proposed, offering different functionalities, applications provided by available tools, their efficiency etc. Among them, two…
The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…
The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…
Graphs are commonly used to represent objects, such as images and text, for pattern classification. In a dynamic world, an object may continuously evolve over time, and so does the graph extracted from the underlying object. These changes…
The recently introduced class of Wheeler graphs, inspired by the Burrows-Wheeler Transform (BWT) of a given string, admits an efficient index data structure for searching for subpaths with a given path label, and lifts the applicability of…
Word-representable graphs, which are the same as semi-transitively orientable graphs, generalize several fundamental classes of graphs. In this paper we propose a novel approach to study word-representability of graphs using a technique of…
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…
In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these index structures far more complex than a single string, as was originally done with the FM-index…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Graph pattern matching is a fundamental operation for the analysis and exploration ofdata graphs. In thispaper, we presenta novel approachfor efficiently finding homomorphic matches for hybrid graph patterns, where each pattern edge may be…
Time-varying graph signals are alternative representation of multivariate (or multichannel) signals in which a single time-series is associated with each of the nodes or vertex of a graph. Aided by the graph-theoretic tools, time-varying…
Graphs are a fundamental abstraction for modeling relational data. However, graphs are discrete and combinatorial in nature, and learning representations suitable for machine learning tasks poses statistical and computational challenges. In…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Graph invariants provide a powerful analytical tool for investigation of abstract structures of graphs. They, combined in convenient relations, carry global and general information about a graph and its various substructures such as cycle…
The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory…
This paper presents a new graph isomorphism invariant, called $\mathfrak{w}$-labeling, that can be used to design a polynomial-time algorithm for solving the graph isomorphism problem for various graph classes. For example, all…
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can…