ArticleNature communications2023
A deep learning approach reveals unexplored landscape of viral expression in cancer.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
21 citing papers in PubMed, 28 citations in OpenAlex.
- A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease.bioRxiv : the preprint server for biology · 2026Article
- VISDB 2.0: A manually curated resource of viral integration sites and their regulatory maps in human diseases.Scientific data · 2026Article
- ViTrace detects viral signatures in tumor transcriptomes using a hybrid language model.Communications biology · 2025Article
- kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.PLoS computational biology · 2025Article
- NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.PLoS computational biology · 2025Article
- Convergent Mechanisms in Virus-Induced Cancers: A Perspective on Classical Viruses, SARS-CoV-2, and AI-Driven Solutions.Infectious disease reports · 2025Article
- HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma.Cancer research · 2025Article
- Defective but tumorigenic: the evolutionary and functional roles of mutated oncoviruses.FEMS microbiology reviews · 2025Review
- A Metagenomic Survey of Virological Hazards in Market-Ready Oysters.Food and environmental virology · 2025Article
- Enhanced deep Convolutional Neural Network for SARS-CoV-2 variants classification.Frontiers in artificial intelligence · 2025Article
- Adaptive natural killer cell expression in response to cytomegalovirus infection in blood and solid cancer.Heliyon · 2024Review
- VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.Bioinformatics (Oxford, England) · 2024Article
- Widespread Horizontal Gene Transfer Among Animal Viruses.bioRxiv : the preprint server for biology · 2024Article
- Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer.Nature communications · 2024Article
- The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses.Journal of microbiology (Seoul, Korea) · 2024Review
- Leveraging a KRAS-based signature to predict the prognosis and drug sensitivity of colon cancer and identifying SPINK4 as a new biomarker.Scientific reports · 2023Article
- Microbial gene expression analysis of healthy and cancerous esophagus uncovers bacterial biomarkers of clinical outcomes.ISME communications · 2023Article
- Overexpression of the mitochondrial anti-viral signaling protein, MAVS, in cancers is associated with cell survival and inflammation.Molecular therapy. Nucleic acids · 2023Article
- Gastric Cancer: The Microbiome Beyond Helicobacter pylori.Current topics in microbiology and immunology · 2023Article
- Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing.International journal of chronic obstructive pulmonary disease · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
Indexed as
Identifiers
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.