{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T17:14:24Z","timestamp":1765214064569,"version":"3.46.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T00:00:00Z","timestamp":1762905600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute at the National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000016","name":"U.S. Department of Health and Human Services","doi-asserted-by":"publisher","award":["UG1CA233333","U24CA264021","R01CA211939","R01DE025712","F30CA265224"],"award-info":[{"award-number":["UG1CA233333","U24CA264021","R01CA211939","R01DE025712","F30CA265224"]}],"id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Tumor viruses account for \u223c10% of cancer diagnoses. Virally induced tumorigenesis is understood as direct signaling through oncogenes such as E6 and E7 genes in the case of human papillomavirus. Furthermore, pathogen characteristics such as viral oncogene dose may impact the disease course. To our knowledge, no tool has been proposed to assess the intra-viral copy number alterations that define the gene dose of viral oncogenes and associated suppressive pathways native to the pathogen\u2019s normal life cycle.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose an R package, \u201cELViS,\u201d that analyzes viral copy number changes from DNA sequencing of whole viral genomes. The method adjusts for viral load with 2D transformation and segmentation to offer the relative viral gene doses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The ELViS R package is available from https:\/\/bioconductor.org\/packages\/ELViS. This article used controlled access data from dbGaP (phs001713.v1.p1).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf622","type":"journal-article","created":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T13:03:49Z","timestamp":1762952629000},"source":"Crossref","is-referenced-by-count":0,"title":["ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5366-7488","authenticated-orcid":false,"given":"Jin Young","family":"Lee","sequence":"first","affiliation":[{"name":"UTHSC Center for Cancer Research, University of Tennessee Health Science Center , Memphis, TN, 38163,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeremiah R","family":"Holt","sequence":"additional","affiliation":[{"name":"UTHSC Center for Cancer Research, University of Tennessee Health Science Center , Memphis, TN, 38163,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaobei","family":"Zhao","sequence":"additional","affiliation":[{"name":"UTHSC Center for Cancer Research, University of Tennessee Health Science Center , Memphis, TN, 38163,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1216-477X","authenticated-orcid":false,"given":"Katherine A","family":"Hoadley","sequence":"additional","affiliation":[{"name":"Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina , Chapel Hill, NC, 27599,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D Neil","family":"Hayes","sequence":"additional","affiliation":[{"name":"UTHSC Center for Cancer Research, University of Tennessee Health Science Center , Memphis, TN, 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