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Biology subjects

Knut Dagestad Rand

Publications and source records attributed to Knut Dagestad Rand.

2 recordsLinked to original sources

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome

Genome-wide, cell-type-specific profiles are being systematically generated for numerous genomic and epigenomic features. There is, however, no universally applicable analytical methodology for such data. We present GSuite HyperBrowser, the first comprehensive solution for integrative analysis of dataset collections across the genome and epigenome. The GSuite HyperBrowser is an open-source system for streamlined acquisition and customizable statistical analysis of large collections of genome-wide datasets. The system is based on new computational and statistical methodologies that permit comparative and confirmatory analyses across multiple disparate data sources. Expert guidance and reproducibility are facilitated via a Galaxy-based web-interface. The software is available at https://hyperbrowser.uio.no/gsuite

Genomics

Coordinates and Intervals in Graph-based Reference Genomes

MotivationIt has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as positions of genes, on graph-based reference genomes.\n\nResultsWe formalize offset-based coordinate systems on graph-based reference genomes and introduce a method for representing intervals on these reference structures. We show the advantage of our method by representing genes on a graph-based representation of the GRCh38 version of the human genome and its alternative loci for regions that are highly variable.\n\nConclusionMore complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of GRCh38 and potential future graph-based reference genomes. We illustrate our notation for genomic intervals, as well as the offset-based coordinate systems, through a web tool at: https://github.com/uio-cels/gen-graph-coords.

Bioinformatics