ArticleJournal of computational biology : a journal of computational molecular cell biology2013
Probabilistic inference of viral quasispecies subject to recombination.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 156 citations in OpenAlex.
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- Algorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2025Review
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- T-Cell Exhaustion in HIV-1/Hepatitis C Virus Coinfection Is Reduced After Successful Treatment of Chronic Hepatitis C.Open forum infectious diseases · 2023Article
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- Efficient Minimum Flow Decomposition via Integer Linear Programming.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Foot-and-Mouth Disease Virus Interserotypic Recombination in Superinfected Carrier Cattle.Pathogens (Basel, Switzerland) · 2022Article
- Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa.Nucleic acids research · 2022Article
- Impact of Intrahost NS5 Nucleotide Variations on Dengue Virus Replication.Frontiers in microbiology · 2022Article
- CD8Frontiers in immunology · 2022Article
- Dose-Dependent Response to Infection with Ebola Virus in the Ferret Model and Evidence of Viral Evolution in the Eye.Journal of virology · 2021Article
- Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.Nucleic acids research · 2021Article
- Prolonged norovirus infections correlate to quasispecies evolution resulting in structural changes of surface-exposed epitopes.iScience · 2021Article
12 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
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination of genetic change and natural selection. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of viral quasispecies and a method to infer its parameters from next-generation sequencing data. The model introduces position-specific probability tables over the sequence alphabet to explain the diversity that can be found in the population at each site. Recombination events are indicated by a change of state, allowing a single observed read to originate from multiple sequences. We present a specific implementation of the expectation maximization (EM) algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and applied to reads obtained from a clinical HIV sample.
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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.