ArticlePLoS computational biology2008
Viral population estimation using pyrosequencing.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed, 223 citations in OpenAlex.
- Article
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- Haploflow: strain-resolved de novo assembly of viral genomes.Genome biology · 2021Article
- Haploflow: Strain-resolvedbioRxiv : the preprint server for biology · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing.Computational and structural biotechnology journal · 2021Review
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.Frontiers in microbiology · 2021Article
- Using earth mover's distance for viral outbreak investigations.BMC genomics · 2020Article
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- Evaluation of haplotype callers for next-generation sequencing of viruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Genomic characterization of hepatitis C virus transmitted founder variants with deep sequencing.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2019Article
- Viral quasispecies reconstruction via tensor factorization with successive read removal.Bioinformatics (Oxford, England) · 2018Article
- HIV evolution and diversity in ART-treated patients.Retrovirology · 2018Review
- Quasispecies variant of pre-S/S gene in HBV-related hepatocellular carcinoma with HBs antigen positive and occult infection.Infectious agents and cancer · 2018Article
- Inference of genetic relatedness between viral quasispecies from sequencing data.BMC genomics · 2017Article
- Separation and assembly of deep sequencing data into discrete sub-population genomes.Nucleic acids research · 2017Article
- A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection.Bioinformatics (Oxford, England) · 2017Article
- Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host.Virus evolution · 2017Article
- Generic Amplicon Deep Sequencing to DetermineFrontiers in microbiology · 2017Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
Abstract
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate-based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug-resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an expectation-maximization (EM) algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.