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Spectral clustering is a powerful approach for clustering, with applications across multiple disciplines, including bioinformatics. However, the way its computational complexity scales limits its application in analyzing large datasets. This complexity can be reduced using the Nyström method, which subsamples the input data in a way that preserves its representational diversity. There are different...
Spectral clustering has shown a superior performance in analyzing the cluster structure. However, the exponentially computational complexity limits its application in analyzing large-scale data. To tackle this problem, many low-rank matrix approximating algorithms are proposed, of which the Nyström method is an approach with proved lower approximate errors. The algorithms commonly combine two powerful...
Paired-end sequencing yields a read from each end of a DNA fragment, typically leaving a gap of unsequenced nucleotides in the middle. Closing this gap using information from other reads in the same sequencing experiment offers the potential to generate longer “pseudo-reads” using short read sequencing platforms. Such long reads may benefit downstream applications such as de novo sequence assembly,...
This past decade, genome sciences have benefitted from rapid advances in DNA sequencing technologies, and development of efficient algorithms for processing short nucleotide sequences played a key role in enabling their uptake in the field. In particular, reassembly of human genomes (de novo or reference-guided) from short DNA sequence reads had a substantial impact on health research. De novo assembly...
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