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
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
Packing nanomechanics of viral genomes [PDF]
The European Physical Journal E, 2008 We investigate the osmotic equilibrium between a bulk polyethylene glycol (PEG) solution and DNA tightly packed in a spherical capsid. We base our analysis on the equations of thermodynamic equilibrium in terms of osmotic pressure. The equality between external osmotic pressure of PEG and osmotic pressure of tightly packed DNA gives us the DNA ...
Šiber, Antonio +3 more
openaire +2 more sources
Epigenetic control of Epstein–Barr virus transcription – relevance to viral life cycle? [PDF]
, 2013 DNA methylation normally leads to silencing of gene expression but Epstein–Barr virus (EBV) provides an exception to the epigenetic paradigm. DNA methylation is absolutely required for the expression of many viral genes.
Sinclair, Alison J
core +7 more sources
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
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
Development of a minigenome cassette for Lettuce necrotic yellows virus: A first step in rescuing a plant cytorhabdovirus [PDF]
, 2020 Rhabdoviruses are enveloped negative-sense RNA viruses that have numerous biotechnological applications. However, recovering plant rhabdoviruses from cDNA remains difficult due to technical difficulties such as the need for concurrent in planta ...
Drake, P +3 more
core +1 more source