ArticleBMC bioinformatics2010
vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Review
- Premature Stop Codon at Residue 101 within HIV-1 Rev Does Not Influence Viral Replication of Clade BC but Severely Reduces Viral Fitness of Clade B.Virologica Sinica · 2020Article
- Inference of clonal selection in cancer populations using single-cell sequencing data.Bioinformatics (Oxford, England) · 2019Article
- Unraveling the web of viroinformatics: computational tools and databases in virus research.Journal of virology · 2015Review
- A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory.Genetics · 2015Article
- Article
- Basis for early and preferential selection of the E138K mutation in HIV-1 reverse transcriptase.Antimicrobial agents and chemotherapy · 2013Article
- HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity.Journal of virology · 2013Article
- A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture.Journal of virological methods · 2013Article
- Article
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe replication rate (or fitness) between viral variants has been investigated in vivo and in vitro for human immunodeficiency virus (HIV). HIV fitness plays an important role in the development and persistence of drug resistance. The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness.
resultsBased on a mathematical model and several statistical methods (least-squares approach and measurement error models), a Web-based computing tool has been developed for improving estimation of virus fitness in growth competition assays of human immunodeficiency virus type 1 (HIV-1).
conclusionsUnlike the two-point calculation used in previous studies, the estimation here uses linear regression methods with all observed data in the competition experiment to more accurately estimate relative viral fitness parameters. The dilution factor is introduced for making the computational tool more flexible to accommodate various experimental conditions. This Web-based tool is implemented in C# language with Microsoft ASP.NET, and is publicly available on the Web at http://bis.urmc.rochester.edu/vFitness/.
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Registered trials
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.