{"id":"https://openalex.org/W4313598112","doi":"https://doi.org/10.1089/cmb.2022.0397","title":"FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data","display_name":"FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data","publication_year":2023,"publication_date":"2023-01-06","ids":{"openalex":"https://openalex.org/W4313598112","doi":"https://doi.org/10.1089/cmb.2022.0397","pmid":"https://pubmed.ncbi.nlm.nih.gov/36607772"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2022.0397","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2022.0397","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","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":"https://openalex.org/A5063912603","display_name":"Saima Sultana Tithi","orcid":"https://orcid.org/0000-0001-5087-0125"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saima Sultana Tithi","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064545135","display_name":"Frank O. Aylward","orcid":"https://orcid.org/0000-0002-1279-4050"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Frank O. Aylward","raw_affiliation_strings":["Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015683073","display_name":"Roderick V. Jensen","orcid":"https://orcid.org/0000-0002-3055-4296"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roderick V. Jensen","raw_affiliation_strings":["Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061868278","display_name":"Liqing Zhang","orcid":"https://orcid.org/0000-0003-4660-9199"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Liqing Zhang","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061868278"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":1.0182,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.75670464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"30","issue":"4","first_page":"391","last_page":"408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9984999895095825,"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":0.9909999966621399,"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":0.9395172595977783},{"id":"https://openalex.org/keywords/contig","display_name":"Contig","score":0.8565487861633301},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8155738115310669},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.735789954662323},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6748932600021362},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6319716572761536},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32410526275634766},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22546479105949402}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9395172595977783},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.8565487861633301},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8155738115310669},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.735789954662323},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6748932600021362},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6319716572761536},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32410526275634766},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22546479105949402},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"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":"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":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","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},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1089/cmb.2022.0397","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2022.0397","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:36607772","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36607772","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8500000238418579,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1552724685","https://openalex.org/W1684151570","https://openalex.org/W1930975169","https://openalex.org/W1996821789","https://openalex.org/W2029551594","https://openalex.org/W2068687524","https://openalex.org/W2084814249","https://openalex.org/W2100896078","https://openalex.org/W2102619694","https://openalex.org/W2107282968","https://openalex.org/W2108234281","https://openalex.org/W2109848222","https://openalex.org/W2118001436","https://openalex.org/W2120902911","https://openalex.org/W2128880918","https://openalex.org/W2143485490","https://openalex.org/W2147378425","https://openalex.org/W2149981091","https://openalex.org/W2150491437","https://openalex.org/W2158714788","https://openalex.org/W2160174935","https://openalex.org/W2168749192","https://openalex.org/W2169899471","https://openalex.org/W2170551349","https://openalex.org/W2170747616","https://openalex.org/W2279910557","https://openalex.org/W2408892709","https://openalex.org/W2470063865","https://openalex.org/W2514983714","https://openalex.org/W2521169042","https://openalex.org/W2592811885","https://openalex.org/W2599417231","https://openalex.org/W2602855059","https://openalex.org/W2763878612","https://openalex.org/W2764019192","https://openalex.org/W2808035849","https://openalex.org/W2892786048","https://openalex.org/W2904384071","https://openalex.org/W2940459311","https://openalex.org/W2949841808","https://openalex.org/W3007490551"],"related_works":["https://openalex.org/W2950447380","https://openalex.org/W2345730070","https://openalex.org/W2107854630","https://openalex.org/W4319294554","https://openalex.org/W2089480001","https://openalex.org/W2055448750","https://openalex.org/W1986608492","https://openalex.org/W1992950355","https://openalex.org/W4381279187","https://openalex.org/W3134563641"],"abstract_inverted_index":{"Despite":[0],"the":[1,79,87,122,142,146],"recent":[2],"surge":[3],"of":[4,78,121],"viral":[5,21,55,71,95,108,131,173],"metagenomic":[6,13,59,68,103,176],"studies,":[7],"recovering":[8],"complete":[9,52,130],"virus/phage":[10],"genomes":[11,57,174],"from":[12,24,58,113],"data":[14],"is":[15],"still":[16],"extremely":[17],"difficult":[18],"and":[19,38,85,105,119,145,157],"most":[20],"contigs":[22,88],"generated":[23],"de":[25,75,158],"novo":[26,76,159],"assembly":[27,77,91,160],"programs":[28],"are":[29,134,149],"highly":[30],"fragmented,":[31],"posing":[32],"serious":[33],"challenges":[34],"to":[35,65,70,82,92,100,151],"downstream":[36],"analysis":[37],"inference.":[39],"In":[40],"this":[41],"study,":[42],"we":[43,126],"develop":[44],"FastViromeExplorer":[45],"(FVE)-novel,":[46],"a":[47,166],"computational":[48],"pipeline":[49],"for":[50,170],"reconstructing":[51],"or":[53],"near-complete":[54,172],"draft":[56],"data.":[60,177],"The":[61],"FVE-novel":[62,99,164],"deploys":[63],"FVE":[64],"efficiently":[66],"map":[67],"reads":[69,81],"reference":[72],"genomes,":[73,132],"performs":[74],"mapped":[80],"generate":[83],"contigs,":[84],"extends":[86],"through":[89],"iterative":[90],"produce":[93],"final":[94],"scaffolds.":[96],"We":[97],"applied":[98],"an":[101],"ocean":[102],"sample":[104],"obtained":[106],"268":[107],"scaffolds":[109],"that":[110],"potentially":[111],"come":[112],"novel":[114,135],"viruses.":[115],"Through":[116],"manual":[117],"examination":[118],"validation":[120],"10":[123],"longest":[124],"scaffolds,":[125],"successfully":[127],"recovered":[128],"4":[129],"2":[133,148],"as":[136],"they":[137],"cannot":[138],"be":[139],"found":[140],"in":[141,175],"existing":[143],"databases":[144],"other":[147],"related":[150],"known":[152],"phages.":[153],"This":[154],"hybrid":[155],"reference-based":[156],"approach":[161,169],"used":[162],"by":[163],"represents":[165],"powerful":[167],"new":[168],"uncovering":[171]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-13T14:20:09.374765","created_date":"2025-10-10T00:00:00"}