{"id":"https://openalex.org/W4396653382","doi":"https://doi.org/10.1186/s12859-024-05763-0","title":"ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding","display_name":"ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding","publication_year":2024,"publication_date":"2024-05-04","ids":{"openalex":"https://openalex.org/W4396653382","doi":"https://doi.org/10.1186/s12859-024-05763-0"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05763-0","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/s12859-024-05763-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05763-0.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05763-0.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101348521","display_name":"Lei Qiao","orcid":null},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lei Qiao","raw_affiliation_strings":["College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007581833","display_name":"Chang Li","orcid":"https://orcid.org/0000-0002-3267-1859"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chang Li","raw_affiliation_strings":["College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006470567","display_name":"Lin Wei","orcid":"https://orcid.org/0000-0001-7146-891X"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Lin","raw_affiliation_strings":["College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047025946","display_name":"Xiangrong He","orcid":"https://orcid.org/0000-0003-4820-0346"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqi He","raw_affiliation_strings":["College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013404991","display_name":"Jia Mi","orcid":"https://orcid.org/0000-0001-5723-4252"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia Mi","raw_affiliation_strings":["College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045599780","display_name":"Yigang Tong","orcid":"https://orcid.org/0000-0002-8503-8045"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yigang Tong","raw_affiliation_strings":["College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China. tongyigang@mail.buct.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]},{"raw_affiliation_string":"College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China. tongyigang@mail.buct.edu.cn","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078894109","display_name":"Jingyang Gao","orcid":"https://orcid.org/0000-0003-1270-6257"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingyang Gao","raw_affiliation_strings":["College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China. gaojy@mail.buct.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China","institution_ids":["https://openalex.org/I75390827"]},{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China. gaojy@mail.buct.edu.cn","institution_ids":["https://openalex.org/I75390827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5101348521"],"corresponding_institution_ids":["https://openalex.org/I75390827"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3521,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.60626259,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10340","display_name":"Hepatitis B Virus Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10340","display_name":"Hepatitis B Virus Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10151","display_name":"Hepatitis C virus research","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11364","display_name":"Cholangiocarcinoma and Gallbladder Cancer Studies","score":0.9927999973297119,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"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/hepatitis-b-virus","display_name":"Hepatitis B virus","score":0.6564034223556519},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4829367995262146},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.479845255613327},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4772063195705414},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.46521735191345215},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42901045083999634},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4208090305328369},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.31290203332901},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.27111130952835083},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.22002246975898743}],"concepts":[{"id":"https://openalex.org/C2780593183","wikidata":"https://www.wikidata.org/wiki/Q6844","display_name":"Hepatitis B virus","level":3,"score":0.6564034223556519},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4829367995262146},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.479845255613327},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4772063195705414},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.46521735191345215},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42901045083999634},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4208090305328369},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.31290203332901},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.27111130952835083},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.22002246975898743},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-024-05763-0","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/s12859-024-05763-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05763-0.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11070082","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11070082","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11070082/pdf/12859_2024_Article_5763.pdf","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:485521c703d74116a8a07062ee2ab51b","is_oa":false,"landing_page_url":"https://doaj.org/article/485521c703d74116a8a07062ee2ab51b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05763-0","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/s12859-024-05763-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-024-05763-0.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4396653382.pdf","grobid_xml":"https://content.openalex.org/works/W4396653382.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1630717967","https://openalex.org/W2042753075","https://openalex.org/W2076038974","https://openalex.org/W2086887894","https://openalex.org/W2094599288","https://openalex.org/W2111350087","https://openalex.org/W2117990720","https://openalex.org/W2129501325","https://openalex.org/W2141860194","https://openalex.org/W2154397429","https://openalex.org/W2518983308","https://openalex.org/W2529646902","https://openalex.org/W2529771496","https://openalex.org/W2736293969","https://openalex.org/W2791839818","https://openalex.org/W2804015468","https://openalex.org/W2885369705","https://openalex.org/W2893897533","https://openalex.org/W2896457183","https://openalex.org/W2912917671","https://openalex.org/W3000362554","https://openalex.org/W3007847150","https://openalex.org/W3118380717","https://openalex.org/W3118986139","https://openalex.org/W3128646645","https://openalex.org/W3190730109","https://openalex.org/W4210712554","https://openalex.org/W4317607162","https://openalex.org/W4328007445","https://openalex.org/W4375955768","https://openalex.org/W4385330534"],"related_works":["https://openalex.org/W3147584709","https://openalex.org/W2977677679","https://openalex.org/W1992327129","https://openalex.org/W2381986121","https://openalex.org/W2370918718","https://openalex.org/W2256933480","https://openalex.org/W2027854990","https://openalex.org/W2370081953","https://openalex.org/W2364428742","https://openalex.org/W2378290951"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Hepatitis":[2],"B":[3],"virus":[4],"(HBV)":[5],"integrates":[6],"into":[7,121],"human":[8,181],"chromosomes":[9],"and":[10,16,27,48,66,73,80,88,103,117,134,146,162,190],"can":[11],"lead":[12],"to":[13,56,77,119,141,169],"genomic":[14],"instability":[15],"hepatocarcinogenesis.":[17],"Current":[18],"tools":[19],"for":[20,39,186],"HBV":[21,111,125,177],"integration":[22,41,58,81,101,112,126,136],"site":[23],"detection":[24],"lack":[25],"accuracy":[26],"stability.":[28],"Results":[29],"This":[30],"study":[31],"proposes":[32],"a":[33],"deep":[34],"learning-based":[35],"method,":[36],"named":[37],"ViroISDC,":[38],"detecting":[40],"sites.":[42],"ViroISDC":[43,68,98,156],"generates":[44],"corresponding":[45],"grammar":[46],"rules":[47],"encodes":[49],"the":[50,53,100,150,153,180,187],"characteristics":[51],"of":[52,93,105,152,193],"language":[54],"data":[55],"predict":[57],"sites":[59,95,137],"accurately.":[60],"Compared":[61],"with":[62],"Lumpy,":[63],"Pindel,":[64],"Seeksv,":[65],"SurVirus,":[67],"exhibits":[69,113,158],"better":[70],"overall":[71],"performance":[72],"is":[74,108,173],"less":[75],"sensitive":[76],"sequencing":[78],"depth":[79],"sequence":[82],"length,":[83],"displaying":[84],"good":[85],"reliability,":[86],"stability,":[87,161],"generality.":[89],"Further":[90],"downstream":[91],"analysis":[92],"integrated":[94],"detected":[96],"by":[97],"reveals":[99],"patterns":[102],"features":[104],"HBV.":[106],"It":[107,172],"observed":[109],"that":[110],"specific":[114],"chromosomal":[115],"preferences":[116],"tends":[118],"integrate":[120],"cancerous":[122],"tissue.":[123],"Moreover,":[124],"frequency":[127],"was":[128],"higher":[129],"in":[130,175,179],"males":[131],"than":[132],"females,":[133],"high-frequency":[135],"were":[138],"more":[139],"likely":[140],"be":[142],"present":[143],"on":[144],"hepatocarcinogenesis-":[145],"anti-cancer-related":[147],"genes,":[148],"validating":[149],"reliability":[151,163],"ViroISDC.":[154],"Conclusions":[155],"pipeline":[157],"superior":[159],"precision,":[160],"across":[164],"various":[165],"datasets":[166],"when":[167],"compared":[168],"similar":[170],"software.":[171],"invaluable":[174],"exploring":[176],"infection":[178],"body,":[182],"holding":[183],"significant":[184],"implications":[185],"diagnosis,":[188],"treatment,":[189],"prognosis":[191],"assessment":[192],"HCC.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2024-05-05T00:00:00"}