{"id":"https://openalex.org/W2092987969","doi":"https://doi.org/10.1186/s13073-015-0126-6","title":"VERSE: a novel approach to detect virus integration in host genomes through reference genome customization","display_name":"VERSE: a novel approach to detect virus integration in host genomes through reference genome customization","publication_year":2015,"publication_date":"2015-01-19","ids":{"openalex":"https://openalex.org/W2092987969","doi":"https://doi.org/10.1186/s13073-015-0126-6","mag":"2092987969","pmid":"https://pubmed.ncbi.nlm.nih.gov/25699093","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4333248"},"language":"en","primary_location":{"id":"doi:10.1186/s13073-015-0126-6","doi":"https://doi.org/10.1186/s13073-015-0126-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13073-015-0126-6","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13073-015-0126-6.pdf","source":{"id":"https://openalex.org/S149201819","display_name":"Genome Medicine","issn_l":"1756-994X","issn":["1756-994X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Medicine","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s13073-015-0126-6.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100682410","display_name":"Qingguo Wang","orcid":"https://orcid.org/0000-0002-5125-3724","observed_orcids":["https://orcid.org/0000-0002-5125-3724"]},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qingguo Wang","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056121087","display_name":"Peilin Jia","orcid":"https://orcid.org/0000-0003-4523-4153","observed_orcids":["https://orcid.org/0000-0003-4523-4153"]},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peilin Jia","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA","Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA","institution_ids":["https://openalex.org/I200719446","https://openalex.org/I901861585"]},{"raw_affiliation_string":"Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, USA","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006688612","display_name":"Zhongming Zhao","orcid":"https://orcid.org/0000-0002-3477-0914","observed_orcids":["https://orcid.org/0000-0002-3477-0914"]},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhongming Zhao","raw_affiliation_strings":["Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA","Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA","institution_ids":["https://openalex.org/I200719446","https://openalex.org/I901861585"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, USA","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006688612"],"corresponding_institution_ids":["https://openalex.org/I200719446","https://openalex.org/I901861585"],"apc_list":{"value":5290,"currency":"USD","value_usd":5290},"apc_paid":{"value":5290,"currency":"USD","value_usd":5290},"fwci":2.005,"has_fulltext":true,"cited_by_count":92,"citation_normalized_percentile":{"value":0.87174815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9179999828338623,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9179999828338623,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.013100000098347664,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10685","display_name":"Viral-associated cancers and disorders","score":0.012199999764561653,"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/viral-evolution","display_name":"viral evolution","score":0.39500001072883606},{"id":"https://openalex.org/keywords/cancer-cell-lines","display_name":"cancer cell lines","score":0.871999979019165},{"id":"https://openalex.org/keywords/viral-carcinogenesis","display_name":"viral oncogenesis","score":0.5590000152587891}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.76658695936203},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.5811229348182678},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5273438692092896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5163282752037048},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4814293086528778},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.43137413263320923},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4311119019985199},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3486308455467224},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34273117780685425},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2044019103050232}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13073-015-0126-6","doi":"https://doi.org/10.1186/s13073-015-0126-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13073-015-0126-6","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13073-015-0126-6.pdf","source":{"id":"https://openalex.org/S149201819","display_name":"Genome Medicine","issn_l":"1756-994X","issn":["1756-994X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Medicine","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4333248","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4333248","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Med","raw_type":"Text"},{"id":"pmid:25699093","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25699093","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,"listed_in":[],"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":"Genome medicine","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/s13073-015-0126-6","doi":"https://doi.org/10.1186/s13073-015-0126-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13073-015-0126-6","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13073-015-0126-6.pdf","source":{"id":"https://openalex.org/S149201819","display_name":"Genome Medicine","issn_l":"1756-994X","issn":["1756-994X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-1","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genome Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.504800021648407,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3402196040","display_name":"Mapping the Genetic Architecture of Complex Disease via RNA-seq and GWAS","funder_award_id":"R01LM011177","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G4841106333","display_name":"SPORE in GI Cancer","funder_award_id":"P50CA095103","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7248731751","display_name":"SPORE in Breast Cancer","funder_award_id":"P50CA098131","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000880732","display_name":"Cancer Center Support Grant","funder_award_id":"P30CA068485","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2092987969.pdf","grobid_xml":"https://content.openalex.org/works/W2092987969.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1987816906","https://openalex.org/W1988460088","https://openalex.org/W1995462034","https://openalex.org/W2018274843","https://openalex.org/W2019849264","https://openalex.org/W2035322315","https://openalex.org/W2054524196","https://openalex.org/W2056086199","https://openalex.org/W2064930197","https://openalex.org/W2065817684","https://openalex.org/W2066447073","https://openalex.org/W2070181423","https://openalex.org/W2070791418","https://openalex.org/W2076038974","https://openalex.org/W2081116295","https://openalex.org/W2098172031","https://openalex.org/W2098521327","https://openalex.org/W2099333915","https://openalex.org/W2103441770","https://openalex.org/W2103962160","https://openalex.org/W2105164094","https://openalex.org/W2105611306","https://openalex.org/W2111664429","https://openalex.org/W2122855404","https://openalex.org/W2130734615","https://openalex.org/W2137662380","https://openalex.org/W2140481064","https://openalex.org/W2141860194","https://openalex.org/W2142926640","https://openalex.org/W2145605402","https://openalex.org/W2145767845","https://openalex.org/W2146397496","https://openalex.org/W2158274053","https://openalex.org/W2162116127","https://openalex.org/W2163314170","https://openalex.org/W2164710273","https://openalex.org/W2169145121","https://openalex.org/W2170551349","https://openalex.org/W2170855681","https://openalex.org/W4247053599","https://openalex.org/W7097581469"],"related_works":["https://openalex.org/W7097716745","https://openalex.org/W2035322315","https://openalex.org/W7098619221","https://openalex.org/W2158274053","https://openalex.org/W1588320408","https://openalex.org/W2747360283","https://openalex.org/W2598769113","https://openalex.org/W2887748806","https://openalex.org/W3118380717","https://openalex.org/W3126121283"],"abstract_inverted_index":{"Fueled":[0],"by":[1],"widespread":[2],"applications":[3],"of":[4,17,89,124,158],"high-throughput":[5],"next":[6],"generation":[7],"sequencing":[8],"(NGS)":[9],"technologies":[10],"and":[11,55,96,143],"urgent":[12],"need":[13],"to":[14,25,64,77,100,132],"counter":[15],"threats":[16],"pathogenic":[18],"viruses,":[19],"large-scale":[20],"studies":[21],"were":[22],"conducted":[23],"recently":[24],"investigate":[26],"virus":[27,53,67,73,90,159],"integration":[28,74,160],"in":[29,47,166],"host":[30,83],"genomes":[31],"(for":[32],"example,":[33],"human":[34,141],"tumor":[35],"genomes)":[36],"that":[37,110,152,173],"may":[38],"cause":[39],"carcinogenesis":[40],"or":[41],"other":[42],"diseases.":[43],"A":[44],"limiting":[45],"factor":[46,81],"these":[48,94],"studies,":[49],"however,":[50],"is":[51,82,128,164,174],"rapid":[52],"evolution":[54],"resulting":[56],"polymorphisms,":[57],"which":[58],"prevent":[59],"reads":[60],"from":[61],"aligning":[62],"readily":[63],"commonly":[65],"used":[66],"reference":[68,137],"genomes,":[69],"and,":[70],"accordingly,":[71],"make":[72],"sites":[75,114],"difficult":[76],"detect.":[78],"Another":[79],"confounding":[80],"genomic":[84],"instability":[85],"as":[86,147],"a":[87,107],"result":[88],"insertions.":[91],"To":[92,121],"tackle":[93],"challenges":[95],"improve":[97,133],"our":[98,125],"capability":[99],"identify":[101],"cryptic":[102],"virus-host":[103],"fusions,":[104],"we":[105,150],"present":[106],"new":[108],"approach":[109,131],"detects":[111],"Virus":[112],"intEgration":[113],"through":[115,135],"iterative":[116],"Reference":[117],"SEquence":[118],"customization":[119],"(VERSE).":[120],"the":[122,129,156,167],"best":[123],"knowledge,":[126],"VERSE":[127,153,163],"first":[130],"detection":[134],"customizing":[136],"genomes.":[138],"Using":[139],"19":[140],"tumors":[142],"cancer":[144],"cell":[145],"lines":[146],"test":[148],"data,":[149],"demonstrated":[151],"substantially":[154],"enhanced":[155],"sensitivity":[157],"site":[161],"detection.":[162],"implemented":[165],"open":[168],"source":[169],"package":[170],"VirusFinder":[171],"2":[172],"available":[175],"at":[176],"http://bioinfo.mc.vanderbilt.edu/VirusFinder/.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":32},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}