{"id":"https://openalex.org/W4220828441","doi":"https://doi.org/10.1109/tcbb.2022.3161135","title":"Virsearcher: Identifying Bacteriophages from Metagenomes by Combining Convolutional Neural Network and Gene Information","display_name":"Virsearcher: Identifying Bacteriophages from Metagenomes by Combining Convolutional Neural Network and Gene Information","publication_year":2022,"publication_date":"2022-03-22","ids":{"openalex":"https://openalex.org/W4220828441","doi":"https://doi.org/10.1109/tcbb.2022.3161135","pmid":"https://pubmed.ncbi.nlm.nih.gov/35316191"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3161135","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3161135","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Qiaoliang Liu","orcid":"https://orcid.org/0000-0002-6832-3223"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiaoliang Liu","raw_affiliation_strings":["College of Communication Engineering, Jilin University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0002-6832-3223","affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fu Liu","orcid":"https://orcid.org/0000-0003-4378-3140"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fu Liu","raw_affiliation_strings":["College of Communication Engineering, Jilin University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0003-4378-3140","affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yan Miao","orcid":"https://orcid.org/0000-0001-7719-426X"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Miao","raw_affiliation_strings":["College of Communication Engineering, Jilin University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0001-7719-426X","affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jiaxue He","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210125137","display_name":"First Hospital of Jilin University","ror":"https://ror.org/034haf133","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210125137"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxue He","raw_affiliation_strings":["Genetic Diagnosis Center, First Hospital of Jilin University, Changchun, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genetic Diagnosis Center, First Hospital of Jilin University, Changchun, China","institution_ids":["https://openalex.org/I4210125137","https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tian Dong","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tian Dong","raw_affiliation_strings":["College of Communication Engineering, Jilin University, Changchun, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tao Hou","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Hou","raw_affiliation_strings":["College of Communication Engineering, Jilin University, Changchun, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":null,"display_name":"Yun Liu","orcid":"https://orcid.org/0000-0003-0883-2453"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Liu","raw_affiliation_strings":["College of Communication Engineering, Jilin University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0003-0883-2453","affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.186,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.77717213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"20","issue":"1","first_page":"763","last_page":"774"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.988099992275238,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.004999999888241291,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0019000000320374966,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.6751000285148621},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6534000039100647},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5902000069618225},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5437999963760376},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5138000249862671},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.46459999680519104},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.42329999804496765},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.41290000081062317}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.6751000285148621},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6534000039100647},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5902000069618225},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5437999963760376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5333999991416931},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5138000249862671},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5127000212669373},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.46459999680519104},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.42329999804496765},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.41290000081062317},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40560001134872437},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.40389999747276306},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.38749998807907104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38600000739097595},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3303999900817871},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.32010000944137573},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.3188999891281128},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.30660000443458557},{"id":"https://openalex.org/C2779227376","wikidata":"https://www.wikidata.org/wiki/Q6505497","display_name":"Layer (electronics)","level":2,"score":0.2924000024795532},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28700000047683716},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.2768000066280365},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.26660001277923584}],"mesh":[{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3161135","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3161135","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35316191","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35316191","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6551191678","display_name":null,"funder_award_id":"2019M651204","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1832693441","https://openalex.org/W1966912927","https://openalex.org/W1974758710","https://openalex.org/W1982887640","https://openalex.org/W2008733625","https://openalex.org/W2016944307","https://openalex.org/W2029926937","https://openalex.org/W2035793410","https://openalex.org/W2038120770","https://openalex.org/W2069689025","https://openalex.org/W2081319466","https://openalex.org/W2097146199","https://openalex.org/W2114104680","https://openalex.org/W2119859604","https://openalex.org/W2145537580","https://openalex.org/W2171939812","https://openalex.org/W2260966294","https://openalex.org/W2345791363","https://openalex.org/W2514983714","https://openalex.org/W2562468253","https://openalex.org/W2603415762","https://openalex.org/W2732139758","https://openalex.org/W2781754262","https://openalex.org/W2797126254","https://openalex.org/W2803013275","https://openalex.org/W2886112809","https://openalex.org/W2934099045","https://openalex.org/W2949831026","https://openalex.org/W2992091846","https://openalex.org/W3003110834","https://openalex.org/W3033129278","https://openalex.org/W3091956242","https://openalex.org/W3112703609","https://openalex.org/W3127656915","https://openalex.org/W6756444276"],"related_works":[],"abstract_inverted_index":{"Metagenome":[0],"sequencing":[1],"provides":[2],"an":[3,95],"unprecedented":[4],"opportunity":[5],"for":[6,181,191],"the":[7,28,57,63,82,88,103,110,131,135,141,144,149,152,179,182,189],"discovery":[8],"of":[9,17,30,39,56,59,66,91,106,134,143,151,160,184,197],"unknown":[10],"microbes":[11],"and":[12,19,35,62,87,109,113,162],"viruses.":[13],"A":[14],"large":[15],"number":[16],"phages":[18,31,44,54,77],"prokaryotes":[20],"are":[21],"mixed":[22],"together":[23],"in":[24,69,100],"metagenomes.":[25,46,70],"To":[26],"study":[27],"influence":[29],"on":[32,166],"human":[33],"bodies":[34],"environments,":[36],"it":[37,48],"is":[38,49,73,98,115,138,199],"great":[40],"significance":[41],"to":[42,51,75,146],"isolate":[43],"from":[45,78,202],"However,":[47],"difficult":[50],"identify":[52,76],"novel":[53],"because":[55],"diversity":[58],"their":[60],"sequences":[61],"frequent":[64],"presence":[65],"short":[67,185],"contigs":[68],"Here,":[71],"virSearcher":[72,158,175,198],"developed":[74],"metagenomes":[79,168],"by":[80,157],"combining":[81],"convolutional":[83,128],"neural":[84],"network":[85],"(CNN)":[86],"gene":[89],"information":[90],"input":[92,96],"sequences.":[93],"Firstly,":[94],"sequence":[97],"encoded":[99],"accordance":[101],"with":[102,140,173],"different":[104],"functions":[105],"its":[107],"coding":[108],"non-coding":[111],"regions":[112],"then":[114],"converted":[116],"into":[117],"word":[118,123],"embedding":[119,124],"code":[120,196],"through":[121],"a":[122,127],"layer":[125],"before":[126],"layer.":[129],"Meanwhile,":[130],"hit":[132],"ratio":[133],"virus":[136],"genes":[137,155],"combined":[139],"output":[142],"CNN":[145],"further":[147],"improve":[148,178],"performance":[150,180,190],"network.":[153],"The":[154,194],"used":[156],"consist":[159],"complete":[161],"incomplete":[163],"genes.":[164],"Experiments":[165],"several":[167],"have":[169],"showed":[170],"that,":[171],"compared":[172],"others,":[174],"can":[176],"significantly":[177],"identification":[183],"sequences,":[186],"while":[187],"maintaining":[188],"long":[192],"ones.":[193],"source":[195],"freely":[200],"available":[201],"http://github.com/DrJackson18/virSearcher.":[203]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2022-04-03T00:00:00"}
