CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac182
Abstract: Abstract Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace… read more here.
Keywords: computational method; cherry computational; prediction; host prediction ... See more keywords
VIDHOP, viral host prediction with Deep Learning
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa705
Abstract: Abstract Motivation Zoonosis, the natural transmission of infections from animals to humans, is a far-reaching global problem. The recent outbreaks of Zikavirus, Ebolavirus, and Coronavirus are examples of viral zoonosis, which occur more frequently due… read more here.
Keywords: viral host; deep learning; host; host prediction ... See more keywords
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer
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DOI: 10.1093/bioinformatics/btad283
Abstract: Abstract Motivation As prevalent extrachromosomal replicons in many bacteria, plasmids play an essential role in their hosts’ evolution and adaptation. The host range of a plasmid refers to the taxonomic range of bacteria in which… read more here.
Keywords: hotspot; prediction assembled; host prediction; host ... See more keywords
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkab133
Abstract: Abstract Thousands of new phages have recently been discovered thanks to viral metagenomics. These phages are extremely diverse and their genome sequences often do not resemble any known phages. To appreciate their ecological impact, it… read more here.
Keywords: streamlining crispr; host predictions; crispr spacer; host ... See more keywords