BHap: a novel approach for bacterial haplotype reconstruction
Motivation The bacterial haplotype reconstruction is critical for selecting proper treatments
for diseases caused by unknown haplotypes. Existing methods and tools do not work well …
for diseases caused by unknown haplotypes. Existing methods and tools do not work well …
Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y
ABSTRACT RNA viruses are one of the fastest-evolving biological entities. Within their
hosts, they exist as genetically diverse populations (ie, viral mutant swarms), which are …
hosts, they exist as genetically diverse populations (ie, viral mutant swarms), which are …
The population structure of Rose rosette virus in the USA
Rose rosette virus (RRV)(genus Emaravirus) is the causal agent of the homonymous
disease, the most destructive malady of roses in the USA. Although the importance of the …
disease, the most destructive malady of roses in the USA. Although the importance of the …
Characterization of the dynamics of human cytomegalovirus resistance to antiviral drugs by ultra-deep sequencing
H Guermouche, S Burrel, M Mercier-Darty, T Kofman… - Antiviral Research, 2020 - Elsevier
Prophylactic or preemptive treatment strategies are required to prevent human
cytomegalovirus (CMV) infections in transplant recipients. However, treatment failure occurs …
cytomegalovirus (CMV) infections in transplant recipients. However, treatment failure occurs …
Cliquesnv: Scalable reconstruction of intra-host viral populations from ngs reads
Highly mutable RNA viruses such as influenza A virus, human immunodeficiency virus and
hepatitis C virus exist in infected hosts as highly heterogeneous populations of closely …
hepatitis C virus exist in infected hosts as highly heterogeneous populations of closely …
A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection
S Leviyang, I Griva, S Ita, WE Johnson - Bioinformatics, 2017 - academic.oup.com
Motivation Next generation sequencing (NGS) has been increasingly applied to characterize
viral evolution during HIV and SIV infections. In particular, NGS datasets sampled during the …
viral evolution during HIV and SIV infections. In particular, NGS datasets sampled during the …
Reconstruction of microbial haplotypes by integration of statistical and physical linkage in scaffolding
DNA sequencing technologies provide unprecedented opportunities to analyze within-host
evolution of microorganism populations. Often, within-host populations are analyzed via …
evolution of microorganism populations. Often, within-host populations are analyzed via …
Inference of viral quasispecies with a paired de Bruijn graph
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 …
population of closely related strains called viral quasispecies. The viral quasispecies …
Bioinformatics tools for analysing viral genomic data
The field of viral genomics and bioinformatics is experiencing a strong resurgence due to
high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective …
high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective …
Epstein-Barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids
N Renzette, M Somasundaran, F Brewster… - Journal of …, 2014 - Am Soc Microbiol
We report the diversity of latent membrane protein 1 (LMP1) gene founder sequences and
the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic …
the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic …