{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T23:27:28Z","timestamp":1773790048324,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2021,1,16]],"date-time":"2021-01-16T00:00:00Z","timestamp":1610755200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["31900479"],"award-info":[{"award-number":["31900479"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Huazhong Agricultural University Scientific & Technological Self-innovation Foundation","award":["2662019QD019"],"award-info":[{"award-number":["2662019QD019"]}]},{"name":"Shanghai rising star program","award":["20QA1412000"],"award-info":[{"award-number":["20QA1412000"]}]},{"name":"Shanghai rising star program","award":["NSFC"],"award-info":[{"award-number":["NSFC"]}]},{"name":"Shanghai rising star program","award":["81702734"],"award-info":[{"award-number":["81702734"]}]},{"name":"Natural science foundation of Shanghai Municipal Commission of Health and Family Planning","award":["20174Y0109"],"award-info":[{"award-number":["20174Y0109"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Virus integration in the host genome is frequently reported to be closely associated with many human diseases, and the detection of virus integration is a critically challenging task. However, most existing tools show limited specificity and sensitivity. Therefore, the objective of this study is to develop a method for accurate detection of virus integration into host genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Herein, we report a novel method termed HIVID2 that is a significant upgrade of HIVID. HIVID2 performs a paired-end combination (PE-combination) for potentially integrated reads. The resulting sequences are then remapped onto the reference genomes, and both split and discordant chimeric reads are used to identify accurate integration breakpoints with high confidence. HIVID2 represents a great improvement in specificity and sensitivity, and predicts breakpoints closer to the real integrations, compared with existing methods. The advantage of our method was demonstrated using both simulated and real datasets. HIVID2 uncovered novel integration breakpoints in well-known cervical cancer-related genes, including FHIT and LRP1B, which was verified using protein expression data. In addition, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations. By analyzing the simulated data and real data tests, we demonstrated that HIVID2 is not only more accurate than HIVID but also better than other existing programs with respect to both sensitivity and specificity. We believe that HIVID2 will help in enhancing future research associated with virus integration.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>HIVID2 can be accessed at https:\/\/github.com\/zengxi-hada\/HIVID2\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab031","type":"journal-article","created":{"date-parts":[[2021,1,13]],"date-time":"2021-01-13T18:07:39Z","timestamp":1610561259000},"page":"1821-1827","source":"Crossref","is-referenced-by-count":11,"title":["HIVID2: an accurate tool to detect virus integrations in the host genome"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5355-0773","authenticated-orcid":false,"given":"Xi","family":"Zeng","sequence":"first","affiliation":[{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linghao","family":"Zhao","sequence":"additional","affiliation":[{"name":"Eastern Hepatobiliary Surgery Hospital, Second Military Medical University , Shanghai 200438, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenhang","family":"Shen","sequence":"additional","affiliation":[{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wing-Kin","family":"Sung","sequence":"additional","affiliation":[{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Department of Computer Science, National University of Singapore , Singapore 117417, Singapore"},{"name":"Department of Computational and Systems Biology, Genome Institute of Singapore , Singapore 138672, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,1,16]]},"reference":[{"key":"2023051611462292900_btab031-B1","doi-asserted-by":"crossref","first-page":"8041","DOI":"10.7314\/APJCP.2015.16.18.8041","article-title":"Identification of HPV integration and genomic patterns delineating the clinical landscape of cervical cancer","volume":"16","author":"Akeel","year":"2016","journal-title":"Asian Pac. 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