ArticleBioinformatics (Oxford, England)2016
SAMFIRE: multi-locus variant calling for time-resolved sequence data.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Clinical effectiveness, safety, and viral mutagenicity of oral favipiravir for COVID-19: results from a community-based, open-label, randomized Phase III trial.Antimicrobial agents and chemotherapy · 2025Trial
- Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection.Virus evolution · 2024Article
- Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children.eLife · 2021Article
- Article
- Drivers of within-host genetic diversity in acute infections of viruses.PLoS pathogens · 2020Article
- A large effective population size for established within-host influenza virus infection.eLife · 2020Article
- Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method.Journal of virology · 2020Article
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- Measurements of intrahost viral diversity require an unbiased diversity metric.Virus evolution · 2019Article
- A novel framework for inferring parameters of transmission from viral sequence data.PLoS genetics · 2018Article
- Within-Host Evolution of Human Influenza Virus.Trends in microbiology · 2018Review
- On the effective depth of viral sequence data.Virus evolution · 2017Article
- The effective rate of influenza reassortment is limited during human infection.PLoS pathogens · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
unlabelledAn increasingly common method for studying evolution is the collection of time-resolved short-read sequence data. Such datasets allow for the direct observation of rapid evolutionary processes, as might occur in natural microbial populations and in evolutionary experiments. In many circumstances, evolutionary pressure acting upon single variants can cause genomic changes at multiple nearby loci. SAMFIRE is an open-access software package for processing and analyzing sequence reads from time-resolved data, calling important single- and multi-locus variants over time, identifying alleles potentially affected by selection, calculating linkage disequilibrium statistics, performing haplotype reconstruction and exploiting time-resolved information to estimate the extent of uncertainty in reported genomic data. AVAILABILITY AND IMPLEMENTATION: C ++ code may be found at https://github.com/cjri/samfire/ CONTACT: chris.illingworth@gen.cam.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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What OpenQuestion holds
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.