Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel. [PDF]
Nat Commun, 2020 Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the ...
Miller D +18 more
europepmc +3 more sources
The landscape of viral associations in human cancers [PDF]
Nature Genetics, 2020 Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and—for a subset—whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential ...
Alawi, Malik +14 more
core +4 more sources
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes [PDF]
Molecular biology and evolution, 2021 Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses.
M. Manni +4 more
semanticscholar +1 more source
Genome binning of viral entities from bulk metagenomics data
Nature Communications, 2021 Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood.
Joachim Johansen +10 more
semanticscholar +1 more source
Scientific Reports, 2021 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic threat worldwide and causes severe health and economic burdens.
Chieh-Wen Lo +8 more
semanticscholar +1 more source
WgLink: reconstructing whole-genome viral haplotypes using L0 + L1-regularization
bioRxiv, 2020 Many tools can reconstruct viral sequences based on next generation sequencing reads. Although existing tools effectively recover local regions, their accuracy suffers when reconstructing the whole viral genomes (strains).
Chen Cao, Matthew Greenberg, Q. Long
semanticscholar +1 more source
Rapid whole genome sequencing methods for RNA viruses
Frontiers in Microbiology, 2023 RNA viruses are the etiological agents of many infectious diseases. Since RNA viruses are error-prone during genome replication, rapid, accurate and economical whole RNA viral genome sequence determination is highly demanded.
Masayasu Misu +10 more
doaj +1 more source
Sustainable cities and society, 2020 Highlights • BioAider is an efficient tool for high-throughput analysis of viral genomes.• BioAider monitors viral variation that facilitates epidemic control of COVID-19.• 14 substitution hotspots in SARS-CoV-2 genome indicates viral polymorphism ...
Z. Zhou +4 more
semanticscholar +1 more source
Parvovirus b19 DNA CpG dinucleotide methylation and epigenetic regulation of viral expression. [PDF]
PLoS ONE, 2012 CpG DNA methylation is one of the main epigenetic modifications playing a role in the control of gene expression. For DNA viruses whose genome has the ability to integrate in the host genome or to maintain as a latent episome, a correlation has been ...
Francesca Bonvicini +4 more
doaj +1 more source
CRISPR/Cas9 editing of endogenous banana streak virus in the B genome of Musa spp. overcomes a major challenge in banana breeding [PDF]
, 2020 Open Access Journal; Published online: 31 Jan 2019Presence of the integrated endogenous banana streak virus (eBSV) in the B genome of plantain (AAB) is a major challenge for breeding and dissemination of hybrids.
Britt, A. +5 more
core +1 more source