Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection.
Sign Up to like & getrecommendations! Published in 2021 at "Biochimie"
DOI: 10.1016/j.biochi.2021.03.017
Abstract: G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming… read more here.
Keywords: infection; analyses viral; type; viral genomes ... See more keywords
R-loop-forming Sequences Analysis in Thousands of Viral Genomes Identify A New Common Element in Herpesviruses
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-63101-9
Abstract: R-loops are RNA-DNA hybrid sequences that are emerging players in various biological processes, occurring in both prokaryotic and eukaryotic cells. In viruses, R-loop investigation is limited and functional importance is poorly understood. Here, we performed… read more here.
Keywords: analysis; loop forming; sequences analysis; viral genomes ... See more keywords
ViPTree: the viral proteomic tree server
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx157
Abstract: Summary ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates… read more here.
Keywords: viptree viral; viral proteomic; tree server; proteomic tree ... See more keywords
A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level
Sign Up to like & getrecommendations! Published in 2020 at "GigaScience"
DOI: 10.1093/gigascience/giaa086
Abstract: Abstract Background Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the… read more here.
Keywords: reconstruction analysis; viral genomes; analysis viral; pipeline ... See more keywords
The complexity landscape of viral genomes
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DOI: 10.1093/gigascience/giac079
Abstract: Abstract Background Viruses are among the shortest yet highly abundant species that harbor minimal instructions to infect cells, adapt, multiply, and exist. However, with the current substantial availability of viral genome sequences, the scientific repertory… read more here.
Keywords: methodology; viral genome; complexity landscape; viral genomes ... See more keywords
In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Virology"
DOI: 10.1128/jvi.00250-21
Abstract: Defective viral genomes (DVGs) can have a significant impact on the production of infectious virus particles. DVGs have only been identified in cultured viruses passaged at high multiplicities of infection and RNA viruses collected from… read more here.
Keywords: dvgs; viral genomes; clinical specimens; defective viral ... See more keywords
Identification and Characterization of Defective Viral Genomes in Ebola Virus-Infected Rhesus Macaques
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Virology"
DOI: 10.1128/jvi.00714-21
Abstract: The study of filovirus pathogenesis is critical for understanding the consequences of infection and for the development of strategies to ameliorate future outbreaks. Defective viral genomes (DVGs) have been detected during EBOV infections in vitro;… read more here.
Keywords: presence; dvgs; viral genomes; infection ... See more keywords
Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection
Sign Up to like & getrecommendations! Published in 2023 at "mBio"
DOI: 10.1128/mbio.00250-23
Abstract: Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and… read more here.
Keywords: defective viral; generation; cov infection; viral genomes ... See more keywords
Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean
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DOI: 10.1128/msphere.00359-16
Abstract: Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral… read more here.
Keywords: environmental viral; biased toward; 352 nonredundant; host ... See more keywords
Adenovirus Remodeling of the Host Proteome and Host Factors Associated with Viral Genomes
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DOI: 10.1128/msystems.00468-21
Abstract: Viral infections induce myriad changes to the host cell proteome. As viruses harness cellular processes and counteract host defenses, they impact abundance, posttranslational modifications, interactions, or localization of cellular proteins. ABSTRACT Viral infections are associated… read more here.
Keywords: viral genomes; infection; associated viral; host ... See more keywords
Predicting host taxonomic information from viral genomes: A comparison of feature representations
Sign Up to like & getrecommendations! Published in 2020 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1007894
Abstract: The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have… read more here.
Keywords: information; host taxonomic; feature; host ... See more keywords