ArticleNature communications2020
Integrative functional genomics decodes herpes simplex virus 1.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 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.
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Who cites it
69 citing papers in PubMed, 100 citations in OpenAlex.
- Current advances in psittacine beak and feather disease: From molecular pathogenesis to integrated surveillance and global control strategies.Veterinary world · 2026Review
- Viral microRNA inhibition enhances antiviral immunity by modulating corneal inflammatory and resolution pathways in HSV-1 induced keratitis.Experimental eye research · 2026Article
- A murine cytomegalovirus cell cycle regulator (m54.5p) evolved within the conserved viral DNA polymerase gene.PLoS pathogens · 2026Article
- Herpes simplex virus type 1 R-loops are targets for APOBEC-mediated mutagenesis.Genome biology · 2026Article
- Herpesvirus-encoded lncRNA targets host splicing by interacting with splicing factors.PLoS pathogens · 2026Article
- Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing.Nature communications · 2026Article
- Article
- Structural basis of herpesvirus helicase-primase inhibition by pritelivir and amenamevir.Science advances · 2025Article
- Structural host-virus interactome profiling of intact infected cells.Nature communications · 2025Article
- Global cis-regulatory landscape of double-stranded DNA viruses.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive resolution and classification of the Epstein Barr virus transcriptome.Nature communications · 2025Article
- Direct relationship between protein expression and progeny yield of herpes simplex virus 1.mBio · 2025Article
- HSV-1 infection induces a downstream shift of the +1 nucleosome.Journal of virology · 2025Article
- Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling.Nature communications · 2025Article
- Identification of Viral Variants from Functional Genomics Data.F1000Research · 2025Article
- Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.PloS one · 2025Article
- Viral Genomic Variation and the Severity of Genital Herpes Simplex Virus-2 Infection as Quantified by Shedding Rate: A Viral Genome-Wide Association Study.The Journal of infectious diseases · 2024Article
- A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses.Nature communications · 2024Article
- Herpes simplex virus 1 inhibits phosphorylation of RNA polymerase II CTD serine-7.Journal of virology · 2024Article
- Viral cis-regulatory elements as sensors of cellular states and environmental cues.Trends in genetics : TIG · 2024Review
9 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
26 authors at 5 institutions in 2 countries.
Funding
Abstract
The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution.
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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.