Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies
Sign Up to like & getrecommendations! Published in 2020 at "Virus Research"
DOI: 10.1016/j.virusres.2020.197963
Abstract: Abstract Next-generation sequencing (NGS) has revolutionized the scale and depth of biomedical sciences. Because of its unique ability for the detection of sub-clonal variants within genetically diverse populations, NGS has been successfully applied to analyze… read more here.
Keywords: unravel mutational; mutational landscape; viral quasispecies; next generation ... See more keywords
Inference of viral quasispecies with a paired de Bruijn graph
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa782
Abstract: MOTIVATION RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterise the quasispecies… read more here.
Keywords: bruijn graph; paired bruijn; graph based; viral quasispecies ... See more keywords
Viral quasispecies reconstruction via tensor factorization with successive read removal
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DOI: 10.1093/bioinformatics/bty291
Abstract: Motivation As RNA viruses mutate and adapt to environmental changes, often developing resistance to anti‐viral vaccines and drugs, they form an ensemble of viral strains‐‐a viral quasispecies. While high‐throughput sequencing (HTS) has enabled in‐depth studies… read more here.
Keywords: tensor factorization; quasispecies reconstruction; viral quasispecies;
De novo assembly of viral quasispecies using overlap graphs.
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DOI: 10.1101/gr.215038.116
Abstract: A viral quasispecies, the ensemble of viral strains populating an infected person, can be highly diverse. For optimal assessment of virulence, pathogenesis, and therapy selection, determining the haplotypes of the individual strains can play a… read more here.
Keywords: savage; overlap graphs; viral quasispecies; reference ... See more keywords