Related papers: The design and construction of reference pangenome…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
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…
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…
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…
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
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,…
Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
We associate all small subgraph counting problems with a systematic graph encoding/representation system which makes a coherent use of graphlet structures. The system can serve as a unified foundation for studying and connecting many…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…