{"id":"https://openalex.org/W4391757842","doi":"https://doi.org/10.1093/bib/bbae036","title":"VirGrapher: a graph-based viral identifier for long sequences from metagenomes","display_name":"VirGrapher: a graph-based viral identifier for long sequences from metagenomes","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4391757842","doi":"https://doi.org/10.1093/bib/bbae036","pmid":"https://pubmed.ncbi.nlm.nih.gov/38343326"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae036","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae036","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae036/56659752/bbae036.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae036/56659752/bbae036.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004933429","display_name":"Yan Miao","orcid":"https://orcid.org/0000-0001-7719-426X"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Miao","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China"],"raw_orcid":"https://orcid.org/0000-0001-7719-426X","affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028798748","display_name":"Zhenyuan Sun","orcid":"https://orcid.org/0009-0004-7993-0194"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenyuan Sun","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China"],"raw_orcid":"https://orcid.org/0009-0004-7993-0194","affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101304015","display_name":"Chenjing Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenjing Ma","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100707569","display_name":"Chen Lin","orcid":"https://orcid.org/0000-0002-2275-997X"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Lin","raw_affiliation_strings":["National Institute for Data Science in Health and Medicine, Xiamen University , Xiangannan Road, 361104, Fujian Province , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiangannan Road, 361104, Fujian Province , China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100649978","display_name":"Guohua Wang","orcid":"https://orcid.org/0000-0001-7381-2374"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guohua Wang","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China"],"raw_orcid":"https://orcid.org/0000-0001-7381-2374","affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016980537","display_name":"Chunxue Yang","orcid":"https://orcid.org/0000-0003-4842-9044"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chunxue Yang","raw_affiliation_strings":["College of Landscape Architecture, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Landscape Architecture, Northeast Forestry University , Hexing Road, 150040, Heilongjiang Province , China","institution_ids":["https://openalex.org/I47689461"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5016980537","https://openalex.org/A5100649978"],"corresponding_institution_ids":["https://openalex.org/I47689461"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.1243,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.85555101,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9973999857902527,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9851999878883362,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7697417736053467},{"id":"https://openalex.org/keywords/human-virome","display_name":"Human virome","score":0.6439992785453796},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6159229278564453},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5657692551612854},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.556002676486969},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.538449764251709},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.47488564252853394},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46719738841056824},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4199443459510803},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.31385380029678345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2996406853199005},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1315363347530365},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10584902763366699},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.07283061742782593}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7697417736053467},{"id":"https://openalex.org/C190743605","wikidata":"https://www.wikidata.org/wiki/Q17027885","display_name":"Human virome","level":4,"score":0.6439992785453796},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6159229278564453},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5657692551612854},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.556002676486969},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.538449764251709},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.47488564252853394},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46719738841056824},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4199443459510803},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.31385380029678345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2996406853199005},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1315363347530365},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10584902763366699},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07283061742782593},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae036","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae036","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae036/56659752/bbae036.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38343326","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38343326","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10859693","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10859693","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10859693/pdf/bbae036.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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae036","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae036","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae036/56659752/bbae036.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.41999998688697815,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G4239478081","display_name":null,"funder_award_id":"62301139","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G78605367","display_name":null,"funder_award_id":"62301139","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G870551797","display_name":null,"funder_award_id":"62225109","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"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391757842.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W2055043387","https://openalex.org/W2072833821","https://openalex.org/W2130725058","https://openalex.org/W2145537580","https://openalex.org/W2342508939","https://openalex.org/W2504173038","https://openalex.org/W2519887557","https://openalex.org/W2732139758","https://openalex.org/W2887749901","https://openalex.org/W2949831026","https://openalex.org/W2961387603","https://openalex.org/W2963925437","https://openalex.org/W2964015378","https://openalex.org/W2964051675","https://openalex.org/W2966145290","https://openalex.org/W2984864519","https://openalex.org/W3003110834","https://openalex.org/W3027189436","https://openalex.org/W3112703609","https://openalex.org/W3136232709","https://openalex.org/W3145834862","https://openalex.org/W3159489040","https://openalex.org/W3170522411","https://openalex.org/W3202160788","https://openalex.org/W4200505767","https://openalex.org/W4205203149","https://openalex.org/W4206958745","https://openalex.org/W4282936970","https://openalex.org/W4297146276","https://openalex.org/W4298395933","https://openalex.org/W4318612108","https://openalex.org/W4366742305","https://openalex.org/W4380986103","https://openalex.org/W4390492887","https://openalex.org/W6631190155","https://openalex.org/W6740871601","https://openalex.org/W6769823692","https://openalex.org/W6787108163","https://openalex.org/W6842937476"],"related_works":["https://openalex.org/W2519363532","https://openalex.org/W3182597671","https://openalex.org/W4391986707","https://openalex.org/W4220807255","https://openalex.org/W4313305812","https://openalex.org/W3216950677","https://openalex.org/W4293040420","https://openalex.org/W2254157384","https://openalex.org/W2289294330","https://openalex.org/W3133222449"],"abstract_inverted_index":{"Viruses":[0],"are":[1,10],"the":[2,73,96],"most":[3],"abundant":[4],"biological":[5],"entities":[6],"on":[7,83,150],"earth":[8],"and":[9,54,67,120,148],"important":[11],"components":[12],"of":[13,52,99],"microbial":[14],"communities.":[15],"A":[16],"metagenome":[17],"contains":[18],"all":[19],"microorganisms":[20],"from":[21,28,109,134],"an":[22],"environmental":[23],"sample.":[24],"Correctly":[25],"identifying":[26,84],"viruses":[27],"these":[29,61],"mixed":[30],"sequences":[31,63,102,135],"is":[32,38,92,154],"critical":[33],"in":[34],"viral":[35,43,86,101],"analyses.":[36],"It":[37],"common":[39],"to":[40,80,94,128],"identify":[41,68],"long":[42,62,85,100,110,115],"sequences,":[44],"which":[45,153],"has":[46],"already":[47],"been":[48],"passed":[49],"thought":[50],"pipelines":[51],"assembly":[53],"binning.":[55],"Existing":[56],"deep":[57],"learning-based":[58],"methods":[59],"divide":[60],"into":[64],"short":[65,107],"subsequences":[66,108],"them":[69,76],"separately.":[70],"This":[71],"makes":[72],"relationships":[74,105],"between":[75,132],"be":[77],"omitted,":[78],"leading":[79],"poor":[81],"performance":[82,98],"sequences.":[87],"In":[88],"this":[89],"paper,":[90],"VirGrapher":[91,112,142],"proposed":[93],"improve":[95],"identification":[97],"by":[103],"constructing":[104],"among":[106],"ones.":[111],"see":[113],"a":[114,118,122,137,144],"sequence":[116],"as":[117],"graph":[119],"uses":[121],"Graph":[123],"Convolutional":[124],"Network":[125],"(GCN)":[126],"model":[127],"learn":[129],"multilayer":[130],"connections":[131],"nodes":[133],"after":[136],"GCN-based":[138],"node":[139],"embedding":[140],"model.":[141],"achieves":[143],"better":[145,155],"AUC":[146],"value":[147],"accuracy":[149],"validation":[151],"set,":[152],"than":[156],"three":[157],"benchmark":[158],"methods.":[159]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
