{"id":"https://openalex.org/W3126121283","doi":"https://doi.org/10.1093/bioinformatics/btab031","title":"HIVID2: an accurate tool to detect virus integrations in the host genome","display_name":"HIVID2: an accurate tool to detect virus integrations in the host genome","publication_year":2021,"publication_date":"2021-01-13","ids":{"openalex":"https://openalex.org/W3126121283","doi":"https://doi.org/10.1093/bioinformatics/btab031","mag":"3126121283","pmid":"https://pubmed.ncbi.nlm.nih.gov/33453108"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab031","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab031","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087485700","display_name":"Xi Zeng","orcid":"https://orcid.org/0000-0002-5355-0773"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xi Zeng","raw_affiliation_strings":["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"],"raw_orcid":"https://orcid.org/0000-0002-5355-0773","affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054532295","display_name":"Linghao Zhao","orcid":"https://orcid.org/0000-0001-7467-0566"},"institutions":[{"id":"https://openalex.org/I177933477","display_name":"Second Military Medical University","ror":"https://ror.org/04tavpn47","country_code":"CN","type":"education","lineage":["https://openalex.org/I177933477"]},{"id":"https://openalex.org/I4210137389","display_name":"Eastern Hepatobiliary Surgery Hospital","ror":"https://ror.org/043sbvg03","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210137389"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Linghao Zhao","raw_affiliation_strings":["Eastern Hepatobiliary Surgery Hospital, Second Military Medical University , Shanghai 200438, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Eastern Hepatobiliary Surgery Hospital, Second Military Medical University , Shanghai 200438, China","institution_ids":["https://openalex.org/I4210137389","https://openalex.org/I177933477"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027973576","display_name":"Chenhang Shen","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenhang Shen","raw_affiliation_strings":["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"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100753051","display_name":"Yi Zhou","orcid":"https://orcid.org/0000-0001-5195-5294"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhou","raw_affiliation_strings":["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"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100404163","display_name":"Guoliang Li","orcid":"https://orcid.org/0000-0003-1601-6640"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoliang Li","raw_affiliation_strings":["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"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012563463","display_name":"Wing\u2010Kin Sung","orcid":"https://orcid.org/0000-0001-7806-7086"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["CN","SG"],"is_corresponding":false,"raw_author_name":"Wing-Kin Sung","raw_affiliation_strings":["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","Department of Computational and Systems Biology, Genome Institute of Singapore , Singapore 138672, Singapore","Department of Computer Science, National University of Singapore , Singapore 117417, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"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","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Department of Computational and Systems Biology, Genome Institute of Singapore , Singapore 138672, Singapore","institution_ids":["https://openalex.org/I66068411"]},{"raw_affiliation_string":"Department of Computer Science, National University of Singapore , Singapore 117417, Singapore","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5054532295","https://openalex.org/A5087485700"],"corresponding_institution_ids":["https://openalex.org/I177933477","https://openalex.org/I204823248","https://openalex.org/I4210137389"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8633,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.67037552,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"13","first_page":"1821","last_page":"1827"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.37400001287460327,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.37400001287460327,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.26170000433921814,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10685","display_name":"Viral-associated cancers and disorders","score":0.07199999690055847,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6802765727043152},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6158971786499023},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.493294894695282},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4892852008342743},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.468219518661499},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4498797357082367},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44772815704345703},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2616574466228485},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22634410858154297},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17396169900894165}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6802765727043152},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6158971786499023},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.493294894695282},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4892852008342743},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.468219518661499},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4498797357082367},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44772815704345703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2616574466228485},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22634410858154297},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17396169900894165},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab031","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab031","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33453108","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33453108","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G3370421853","display_name":null,"funder_award_id":"31900479","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1038682962","https://openalex.org/W1588320408","https://openalex.org/W1978429201","https://openalex.org/W1979266859","https://openalex.org/W1983616044","https://openalex.org/W2007218683","https://openalex.org/W2017474562","https://openalex.org/W2035322315","https://openalex.org/W2076038974","https://openalex.org/W2082481679","https://openalex.org/W2092987969","https://openalex.org/W2095680943","https://openalex.org/W2131255017","https://openalex.org/W2131271579","https://openalex.org/W2139760555","https://openalex.org/W2145513855","https://openalex.org/W2158274053","https://openalex.org/W2223500847","https://openalex.org/W2267624095","https://openalex.org/W2275576232","https://openalex.org/W2344220109","https://openalex.org/W2439563586","https://openalex.org/W2529771496","https://openalex.org/W2561550127","https://openalex.org/W2562928006","https://openalex.org/W2567934328","https://openalex.org/W2598769113","https://openalex.org/W2606276381","https://openalex.org/W2741211555","https://openalex.org/W2755864984","https://openalex.org/W2766477897","https://openalex.org/W2771219703","https://openalex.org/W2787575626","https://openalex.org/W2789624890","https://openalex.org/W2790404504","https://openalex.org/W2795138264","https://openalex.org/W2809210462","https://openalex.org/W2883260610","https://openalex.org/W2887748806","https://openalex.org/W2888554793","https://openalex.org/W2891836094","https://openalex.org/W2904394579","https://openalex.org/W2908170302","https://openalex.org/W2913426519","https://openalex.org/W2914479866","https://openalex.org/W2922069583","https://openalex.org/W2922223444","https://openalex.org/W2941618015","https://openalex.org/W2944938627","https://openalex.org/W2985532529","https://openalex.org/W3002972711","https://openalex.org/W3005400930","https://openalex.org/W3033831314","https://openalex.org/W3036157276","https://openalex.org/W3092159191","https://openalex.org/W3106922462","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6748763185","https://openalex.org/W6784482913"],"related_works":["https://openalex.org/W2117112636","https://openalex.org/W2086525401","https://openalex.org/W2001981265","https://openalex.org/W2079327011","https://openalex.org/W2317560666","https://openalex.org/W2006735166","https://openalex.org/W2053325634","https://openalex.org/W193851735","https://openalex.org/W3178279768","https://openalex.org/W2014134454"],"abstract_inverted_index":{"MOTIVATION:":[0],"Virus":[1],"integration":[2,23,54,106,148],"in":[3,116,150,225],"the":[4,19,39,91,125,170,181,187],"host":[5,56],"genome":[6],"is":[7,24,44,68,198],"frequently":[8],"reported":[9],"to":[10,45,103,124,172,175,214],"be":[11,237],"closely":[12],"associated":[13,229],"with":[14,108,129,212,230],"many":[15],"human":[16],"diseases,":[17],"and":[18,36,94,97,118,120,142,157,190,217],"detection":[20,51],"of":[21,41,52,72,134],"virus":[22,53,183,231],"a":[25,47,62,69,76,113],"critically":[26],"challenging":[27],"task.":[28],"However,":[29],"most":[30],"existing":[31,130,210],"tools":[32],"show":[33],"limited":[34],"specificity":[35,117],"sensitivity.":[37],"Therefore,":[38],"objective":[40],"this":[42],"study":[43],"develop":[46],"method":[48,64,136],"for":[49,80],"accurate":[50,105,202],"into":[55],"genomes.":[57],"RESULTS:":[58],"Herein,":[59],"we":[60,194],"report":[61],"novel":[63,147],"termed":[65],"HIVID2":[66,74,111,145,168,197,222,235],"that":[67,196,221],"significant":[70],"upgrade":[71],"HIVID.":[73],"performs":[75],"paired-end":[77],"combination":[78],"(PE-combination)":[79],"potentially":[81],"integrated":[82],"reads.":[83],"The":[84,132],"resulting":[85],"sequences":[86],"are":[87,101,245],"then":[88],"remapped":[89],"onto":[90],"reference":[92],"genomes,":[93],"both":[95,140,215],"split":[96],"discordant":[98],"chimeric":[99],"reads":[100],"used":[102],"identify":[104],"breakpoints":[107,122,149],"high":[109],"confidence.":[110],"represents":[112],"great":[114],"improvement":[115],"sensitivity,":[119],"predicts":[121],"closer":[123],"real":[126,143,191],"integrations,":[127],"compared":[128],"methods.":[131],"advantage":[133],"our":[135],"was":[137,160],"demonstrated":[138,195],"using":[139,162,180],"simulated":[141,188],"datasets.":[144],"uncovered":[146],"well-known":[151],"cervical":[152],"cancer-related":[153],"genes,":[154],"including":[155],"FHIT":[156],"LRP1B,":[158],"which":[159],"verified":[161],"protein":[163],"expression":[164],"data.":[165],"In":[166],"addition,":[167],"allows":[169],"user":[171],"decide":[173],"whether":[174],"automatically":[176],"perform":[177],"advanced":[178],"analysis":[179],"identified":[182],"integrations.":[184],"By":[185],"analyzing":[186],"data":[189,192,244],"tests,":[193],"not":[199],"only":[200],"more":[201],"than":[203,208],"HIVID":[204],"but":[205],"also":[206],"better":[207],"other":[209],"programs":[211],"respect":[213],"sensitivity":[216],"specificity.":[218],"We":[219],"believe":[220],"will":[223],"help":[224],"enhancing":[226],"future":[227],"research":[228],"integration.":[232],"AVAILABILITYAND":[233],"IMPLEMENTATION:":[234],"can":[236],"accessed":[238],"at":[239,247],"https://github.com/zengxi-hada/HIVID2/.":[240],"SUPPLEMENTARY":[241],"INFORMATION:":[242],"Supplementary":[243],"available":[246],"Bioinformatics":[248],"online.":[249]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
