ArticleNucleic acids research2014
Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 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.
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Who cites it
87 citing papers in PubMed, 119 citations in OpenAlex.
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- Copy-back RNA synthesis by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir.Science advances · 2026Article
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- A respiratory syncytial virus trailer sequence modulates viral replication and the generation and propagation kinetics of copy-back defective viral genomes.Journal of virology · 2026Article
- Reovirus recombination is highly selective, and its profiles are primarily dictated by viral gene segment identity.Journal of virology · 2026Article
- Evidence for Powassan virus deletions and defective RNA in field-collected ticks.Journal of virology · 2026Article
- Molecular characterization of arenavirus defective viral genomes reveals sequence features associated with their formation.Journal of virology · 2026Article
- Bioinformatics identification of copyback and multihost-adapted defective viral genomes in dengue virus.Frontiers in cellular and infection microbiology · 2026Article
- Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives.Virus evolution · 2026Article
- Classification, functions, evolution, and applications of defective viral genomes.Frontiers in microbiology · 2026Review
- Host PI3K inhibition via anti-cancer drug alpelisib influences Influenza A non-infectious particles and deletion-containing viral genomes.Cell communication and signaling : CCS · 2025Article
- SARS-CoV-2 EndoU-ribonuclease regulates RNA recombination and impacts viral fitness.Nature communications · 2025Article
- Review
- Defective but promising: evaluating the utility of currently available bioinformatic pipelines for detecting defective viral genomes in RNA-Seq data.The Journal of general virology · 2025Article
- Reovirus recombination is highly selective, and its profiles are primarily dictated by viral gene segment identity.bioRxiv : the preprint server for biology · 2025Article
- Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus.Genome medicine · 2025Article
- Next-Generation Sequencing Reveals Field Strain Dynamics and PRRSV-2 Clearance in Gilts When Using Tylvalosin During MLV Vaccination.Vaccines · 2025Article
- A Respiratory Syncytial Virus trailer sequence modulates viral replication and copy-back defective viral genome generation and propagation kinetics.bioRxiv : the preprint server for biology · 2025Article
- Validation of diverse and previously untraceable Sendai virus copyback viral genomes by direct RNA sequencing.Journal of virology · 2025Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5' end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3' end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
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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.