{"id":"https://openalex.org/W4296776309","doi":"https://doi.org/10.1093/bib/bbac413","title":"Critical assessment of pan-genomic analysis of metagenome-assembled genomes","display_name":"Critical assessment of pan-genomic analysis of metagenome-assembled genomes","publication_year":2022,"publication_date":"2022-08-29","ids":{"openalex":"https://openalex.org/W4296776309","doi":"https://doi.org/10.1093/bib/bbac413","pmid":"https://pubmed.ncbi.nlm.nih.gov/36124775"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac413","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac413","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac413/45892398/bbac413.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac413/45892398/bbac413.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100329329","display_name":"Tang Li","orcid":"https://orcid.org/0000-0001-6622-9471"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tang Li","raw_affiliation_strings":["Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln , Lincoln, NE, 68508, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln , Lincoln, NE, 68508, USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090843422","display_name":"Yanbin Yin","orcid":"https://orcid.org/0000-0001-7667-881X"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yanbin Yin","raw_affiliation_strings":["Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln , Lincoln, NE, 68508, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln , Lincoln, NE, 68508, USA","institution_ids":["https://openalex.org/I114395901"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090843422"],"corresponding_institution_ids":["https://openalex.org/I114395901"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.7773,"has_fulltext":false,"cited_by_count":46,"citation_normalized_percentile":{"value":0.94834756,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"23","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11470","display_name":"Legume Nitrogen Fixing Symbiosis","score":0.9830999970436096,"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"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9678000211715698,"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/genome","display_name":"Genome","score":0.9159210920333862},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8140273094177246},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.651053786277771},{"id":"https://openalex.org/keywords/genome-size","display_name":"Genome size","score":0.54941326379776},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5230104327201843},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4891405403614044},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.48655906319618225},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.4726024270057678},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44243112206459045},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43143588304519653}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.9159210920333862},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8140273094177246},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.651053786277771},{"id":"https://openalex.org/C61271108","wikidata":"https://www.wikidata.org/wiki/Q3180866","display_name":"Genome size","level":4,"score":0.54941326379776},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5230104327201843},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4891405403614044},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.48655906319618225},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.4726024270057678},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44243112206459045},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43143588304519653}],"mesh":[{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac413","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac413","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac413/45892398/bbac413.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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:36124775","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36124775","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:9677465","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9677465","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,"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/bbac413","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac413","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac413/45892398/bbac413.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":[],"awards":[{"id":"https://openalex.org/G1801283323","display_name":null,"funder_award_id":"R01 GM140370","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2200030120","display_name":null,"funder_award_id":"R21 AI171952","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3581011668","display_name":null,"funder_award_id":"R01GM140370","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5055379714","display_name":null,"funder_award_id":"DBI-1933521","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6805077450","display_name":null,"funder_award_id":"58-8042-7-089","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G7595864537","display_name":null,"funder_award_id":"R21AI171952","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W1528357204","https://openalex.org/W1958058086","https://openalex.org/W2020324273","https://openalex.org/W2031611770","https://openalex.org/W2060425093","https://openalex.org/W2096093282","https://openalex.org/W2112364185","https://openalex.org/W2117207428","https://openalex.org/W2121960929","https://openalex.org/W2122673596","https://openalex.org/W2124351063","https://openalex.org/W2141052558","https://openalex.org/W2143485490","https://openalex.org/W2150550043","https://openalex.org/W2155090350","https://openalex.org/W2173732482","https://openalex.org/W2277953252","https://openalex.org/W2325111931","https://openalex.org/W2340958225","https://openalex.org/W2730206157","https://openalex.org/W2735611463","https://openalex.org/W2739666533","https://openalex.org/W2745006471","https://openalex.org/W2754579667","https://openalex.org/W2766794435","https://openalex.org/W2804476733","https://openalex.org/W2821958851","https://openalex.org/W2889762847","https://openalex.org/W2900715153","https://openalex.org/W2904603519","https://openalex.org/W2910615673","https://openalex.org/W2911471536","https://openalex.org/W2913003031","https://openalex.org/W2913972921","https://openalex.org/W2921815890","https://openalex.org/W2948263509","https://openalex.org/W2949102320","https://openalex.org/W2952366981","https://openalex.org/W2952673498","https://openalex.org/W2980278484","https://openalex.org/W2991012415","https://openalex.org/W2997125367","https://openalex.org/W2997518568","https://openalex.org/W3005228641","https://openalex.org/W3007303376","https://openalex.org/W3011678041","https://openalex.org/W3015708529","https://openalex.org/W3036189339","https://openalex.org/W3038369633","https://openalex.org/W3042305844","https://openalex.org/W3042744518","https://openalex.org/W3043408355","https://openalex.org/W3045244624","https://openalex.org/W3084380827","https://openalex.org/W3090089243","https://openalex.org/W3092713351","https://openalex.org/W3112234114","https://openalex.org/W3119314116","https://openalex.org/W3125972683","https://openalex.org/W3128002411","https://openalex.org/W3129341958","https://openalex.org/W3141597806","https://openalex.org/W4284990104","https://openalex.org/W6729335427","https://openalex.org/W6757077846"],"related_works":["https://openalex.org/W2318953980","https://openalex.org/W1565527690","https://openalex.org/W1493660383","https://openalex.org/W2759519215","https://openalex.org/W2353729507","https://openalex.org/W4318240630","https://openalex.org/W2350466590","https://openalex.org/W1542620732","https://openalex.org/W3031625301","https://openalex.org/W4386771068"],"abstract_inverted_index":{"Pan-genome":[0],"analyses":[1],"of":[2,24,26,33,69,153,180,183],"metagenome-assembled":[3],"genomes":[4,36],"(MAGs)":[5],"may":[6],"suffer":[7],"from":[8],"the":[9,100,108],"known":[10],"issues":[11],"with":[12,173],"MAGs:":[13],"fragmentation,":[14],"incompleteness":[15,43,126],"and":[16,37,64,71,111,141,164],"contamination.":[17],"Here,":[18],"we":[19],"conducted":[20],"a":[21,67,122,151],"critical":[22],"assessment":[23],"pan-genomics":[25],"MAGs,":[27],"by":[28,106,150],"comparing":[29],"pan-genome":[30,58,138,178,185],"analysis":[31,59,179,186],"results":[32],"complete":[34,72],"bacterial":[35],"simulated":[38],"MAGs.":[39,181],"We":[40,158],"found":[41],"that":[42,116,160],"led":[44,135],"to":[45,86,121,136],"significant":[46],"core":[47,79],"gene":[48,89,113],"(CG)":[49],"loss.":[50],"The":[51,131],"CG":[52,101,109,132,162],"loss":[53,102,133],"remained":[54],"when":[55,65,125],"using":[56,66,112],"different":[57],"tools":[60,187],"(Roary,":[61],"BPGA,":[62],"Anvi'o)":[63],"mixture":[68],"MAGs":[70,190],"genomes.":[73,98],"Contamination":[74],"had":[75,93],"little":[76],"effect":[77],"on":[78,96],"genome":[80,156],"size":[81],"(except":[82],"for":[83,189],"Roary":[84],"due":[85],"in":[87,167,177,193],"its":[88],"clustering":[90],"issue)":[91],"but":[92,120],"major":[94],"influence":[95],"accessory":[97],"Importantly,":[99],"was":[103,127],"partially":[104],"alleviated":[105],"lowering":[107,161],"threshold":[110,163],"prediction":[114],"algorithms":[115],"consider":[117],"fragmented":[118],"genes,":[119],"less":[123],"degree":[124],"higher":[128],"than":[129],"5%.":[130],"also":[134],"incorrect":[137],"functional":[139],"predictions":[140],"inaccurate":[142],"phylogenetic":[143],"trees.":[144],"Our":[145],"main":[146],"findings":[147],"were":[148],"supported":[149],"study":[152],"real":[154],"MAG-isolate":[155],"data.":[157],"conclude":[159],"predicting":[165],"genes":[166],"metagenome":[168],"mode":[169],"(as":[170],"Anvi'o":[171],"does":[172],"Prodigal)":[174],"are":[175,191],"necessary":[176],"Development":[182],"new":[184],"specifically":[188],"needed":[192],"future":[194],"studies.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
