Results 81 to 90 of about 1,282 (176)

Integrating Complex Pangenome Graphs

2024 IEEE 40th International Conference on Data Engineering Workshops (ICDEW)
Graph databases are increasingly used to handle complex data pipelines, in which interconnected data is exploited for visualization and analytics. We propose a novel method, PanGraph-DB, for performing complex inter-pangenomic analysis within a graph database. As a case study, we focus on the antibiotic resistance in sequenced genomes.
Arnoux, Jérôme, Bonifati, Angela, Calteau, A., Dumbrava, Stefania, Gautreau, Guillaume   +4 more
openaire   +2 more sources

Structure of the Enterobacter pan-genome is revealed using machine learning

Microbiology Spectrum
The growing availability of publicly accessible Enterobacter genomes offers an opportunity to reveal the structure of its pangenome, uncovering the catalog of genes across the genus and their distribution across the different species and subspecies of ...
Joshua T. Burrows, Gaoyuan Li, Jonathan M. Monk, Siddharth M. Chauhan, Bernhard O. Palsson   +4 more
doaj   +1 more source

PanCake: A Data Structure for Pangenomes.

, 2013
We present a pangenome data structure ("PanCake") for sets of related genomes, based on bundling similar sequence regions into shared features, which are derived from genome-wide pairwise sequence alignments. We discuss the design of the data structure, basic operations on it and methods to predict core genomes and singleton regions.
Ernst, Corinna, Rahmann, Sven
openaire   +3 more sources

Pangenome-aware DeepVariant

Abstract Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium, which has been shown to improve read mapping and structural variant ...
Mobin Asri, Pi-Chuan Chang, Juan Carlos Mier, Jouni Sirén, Parsa Eskandar, Alexey Kolesnikov, Daniel E. Cook, Lucas Brambrink, Glenn Hickey, Adam M. Novak, Lizzie Dorfman, Dale R. Webster, Andrew Carroll, Benedict Paten, Kishwar Shafin   +14 more
openaire   +3 more sources

Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

mSystems
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health.
Tommy H. Tran, Isabel F. Escapa, Ari Q. Roberts, Wei Gao, Abiola C. Obawemimo, Julia A. Segre, Heidi H. Kong, Sean Conlan, Matthew S. Kelly, Katherine P. Lemon   +9 more
doaj   +1 more source

Population structure, resistome, and virulome of Staphylococcus chromogenes strains from milk of subclinical bovine mastitis in South Africa

Frontiers in Cellular and Infection Microbiology
IntroductionStaphylococcus chromogenes are commonly found in intramammary infections associated with bovine subclinical mastitis in dairy cattle, yet their genomic diversity and antimicrobial resistance dynamics remain poorly characterized, particularly ...
N. G. Khasapane, S. J. Nkhebenyane, O. Thekisoe, T. Ramatla, K. E. Lekota   +4 more
doaj   +1 more source

On the optimization of copy number variations representation in pangenome graphs

Frontiers in Bioinformatics
Graph-based pangenome references often misrepresent Copy Number Variations (CNVs) and Variable Number Tandem Repeats (VNTRs) as alternative acyclic paths, which hinders downstream analyses, degrades alignment behavior, and reduces interpretability in ...
Mirko Coggi, Mirko Coggi, Lorenzo Basile, Beatrice Branchini, Beatrice Branchini, Gabriele Amodeo, Guido Walter Di Donato, Marco D. Santambrogio   +7 more
doaj   +1 more source

Modern Genomics Reshapes Soybean Cyst Nematode Research: Integrating Host Resistance, Nematode Virulence, and Functional Discovery

Molecular Plant-Microbe Interactions
The soybean cyst nematode (SCN), Heterodera glycines, remains the most damaging pathogen of soybean worldwide. Genomic advances over the past two decades have transformed our understanding of both the nematode and its host.
Esmaeil Miraeiz, Lucas Borges dos Santos, Matthew E. Hudson   +2 more
doaj   +1 more source

Graphical pangenomics

, 2018
Wellcome Trust PhD ...
openaire   +5 more sources

Integrative genomic analyses support the division of the extended Asfarviridae clade into multiple viral families

Journal of Virology
Giant viruses continue to challenge our understanding of virology, blurring boundaries of what a virus can be. The so-called “extended Asfarviridae”— such as African swine fever virus, faustovirus, kaumoebavirus, pacmanvirus, and AbALV—has long puzzled ...
Thiago Mendonça-Santos, Jônatas Abrahão, Luiz-Eduardo Del-Bem   +2 more
doaj   +1 more source