NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.

Journal: PLoS computational biology
Published Date: Aug 21, 2025

Abstract

MOTIVATION: Oncoviruses, pathogens known to cause or increase the risk of cancer, include both common viruses such as human papillomaviruses and rarer pathogens such as human T-lymphotropic viruses. Computational methods for detecting viral DNA from data acquired by modern DNA sequencing technologies have enabled studies of the association between oncoviruses and cancers. Those studies are rendered particularly challenging when multiple species of oncovirus are present in a tumor sample. In such scenarios, merely detecting the presence of a sequencing read of viral origin is insufficiently informative-instead, a more precise characterization of the viral content in the sample is required.

Authors

  • John Robertson
    Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas, USA.
  • Shorya Consul
    Chandra Family Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas, USA.
  • Haris Vikalo

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