Results 51 to 60 of about 1,556 (147)
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs [PDF]
, 2021 Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were ...
Chang, Xian +6 more
core +1 more source
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs [PDF]
, 2023 Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were ...
Chang, Xian +6 more
core +1 more source
Pangenomes of multiple species for the "Cluster efficient pangenome graph construction with nf-core/pangenome" manuscript. [PDF]
<p>Pangenomes of multiple species for the "Cluster efficient pangenome graph construction with nf-core/pangenome" manuscript.</p> <p>Each pangenome is represented in a FASTA format file.
Heumos, Simon
core +1 more source
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 +4 more
openaire +2 more sources
BMC Bioinformatics, 2021 Background With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great ...
Jindan Guo +3 more
doaj +1 more source
The Plant Genome, 2022 Since the first reported crop pangenome in 2014, advances in high‐throughput and cost‐effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr ...
Silvia F. Zanini +8 more
doaj +1 more source
Adaptive Responses of Tropical Crops: A Multi‐Scale Omics Integrated Perspective
Advanced Science, EarlyView.Tropical crops integrate genomic, morphological, physiological, and ecological adaptations to thrive under extreme and variable environments. This review highlights how natural selection, domestication, and breeding shape stress resilience, resource‐use strategies, and productivity in sugarcane, banana, cassava, rubber and oil palm, offering new routes
Peilin Wang +11 more
wiley +1 more source
Popping Bubbles in Pangenome Graphs
CoRRIn this paper, we introduce flubbles, a new definition of "bubbles" corresponding to variants in a (pan)genome graph $G$. We then show a characterization for flubbles in terms of equivalence classes regarding cycles in an intermediate data structure we built from the spanning tree of the $G$, which leads us to a linear time and space solution for ...
Njagi Moses Mwaniki +2 more
openaire +2 more sources
iMetaOmics, EarlyView.This study identifies uterus weight as a heritable (h2 = 0.45) intermediate phenotype that independently associates with late‐life egg production and eggshell quality in aged laying hens. Genome‐wide association study (GWAS) reveals a genome‐wide significant locus on chromosome 3 and suggestive loci on chromosome 11 for uterus weight, mediation ...
Junnan Zhang +7 more
wiley +1 more source
Journal of Fish Diseases, EarlyView.ABSTRACT Monitoring antimicrobial resistance (AMR) in fish pathogens is essential for supporting sustainable aquaculture. In this study, susceptibility testing and genome sequencing were used to characterize the AMR profile of seven Flavobacterium psychrophilum originating from Danish rainbow trout farms (2019–2022).
Valentina L. Donati, Lone Madsen
wiley +1 more source