{"id":"https://openalex.org/W4403635236","doi":"https://doi.org/10.1371/journal.pcbi.1012530","title":"Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery","display_name":"Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery","publication_year":2024,"publication_date":"2024-10-22","ids":{"openalex":"https://openalex.org/W4403635236","doi":"https://doi.org/10.1371/journal.pcbi.1012530","pmid":"https://pubmed.ncbi.nlm.nih.gov/39436938"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012530","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012530","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1012530","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024421285","display_name":"Ulisses Nunes da Rocha","orcid":"https://orcid.org/0000-0001-6972-6692"},"institutions":[{"id":"https://openalex.org/I137479271","display_name":"Helmholtz Centre for Environmental Research","ror":"https://ror.org/000h6jb29","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I137479271"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ulisses Rocha","raw_affiliation_strings":["Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0001-6972-6692","affiliations":[{"raw_affiliation_string":"Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany","institution_ids":["https://openalex.org/I137479271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081448047","display_name":"Jonas Coelho Kasmanas","orcid":"https://orcid.org/0000-0001-6513-5350"},"institutions":[{"id":"https://openalex.org/I137479271","display_name":"Helmholtz Centre for Environmental Research","ror":"https://ror.org/000h6jb29","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I137479271"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jonas Coelho Kasmanas","raw_affiliation_strings":["Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany","institution_ids":["https://openalex.org/I137479271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086658226","display_name":"Rodolfo Brizola Toscan","orcid":"https://orcid.org/0000-0002-5652-3666"},"institutions":[{"id":"https://openalex.org/I137479271","display_name":"Helmholtz Centre for Environmental Research","ror":"https://ror.org/000h6jb29","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I137479271"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Rodolfo Toscan","raw_affiliation_strings":["Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany","institution_ids":["https://openalex.org/I137479271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088676977","display_name":"Danilo Sipoli Sanches","orcid":"https://orcid.org/0000-0002-8972-5221"},"institutions":[{"id":"https://openalex.org/I1283613182","display_name":"Universidade Tecnol\u00f3gica Federal do Paran\u00e1","ror":"https://ror.org/002v2kq79","country_code":"BR","type":"education","lineage":["https://openalex.org/I1283613182"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Danilo S. Sanches","raw_affiliation_strings":["Department of Computer Science, Federal University of Technology-Paran\u00e1, UTFPR, Corn\u00e9lio Proc\u00f3pio, Brazil","Department of Computer Science, Federal University of Technology\u2014Paran\u00e1, UTFPR, Corn\u00e9lio Proc\u00f3pio, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Federal University of Technology-Paran\u00e1, UTFPR, Corn\u00e9lio Proc\u00f3pio, Brazil","institution_ids":["https://openalex.org/I1283613182"]},{"raw_affiliation_string":"Department of Computer Science, Federal University of Technology\u2014Paran\u00e1, UTFPR, Corn\u00e9lio Proc\u00f3pio, Brazil","institution_ids":["https://openalex.org/I1283613182"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052638885","display_name":"Stefan\u00eda Magn\u00fasd\u00f3ttir","orcid":"https://orcid.org/0000-0001-6506-8696"},"institutions":[{"id":"https://openalex.org/I137479271","display_name":"Helmholtz Centre for Environmental Research","ror":"https://ror.org/000h6jb29","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I137479271"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Stefania Magnusdottir","raw_affiliation_strings":["Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany","institution_ids":["https://openalex.org/I137479271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091156613","display_name":"J. Saraiva","orcid":"https://orcid.org/0000-0001-8251-1960"},"institutions":[{"id":"https://openalex.org/I137479271","display_name":"Helmholtz Centre for Environmental Research","ror":"https://ror.org/000h6jb29","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I137479271"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Joao Pedro Saraiva","raw_affiliation_strings":["Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8251-1960","affiliations":[{"raw_affiliation_string":"Department of Applied Microbial Ecology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany","institution_ids":["https://openalex.org/I137479271"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5024421285","https://openalex.org/A5052638885","https://openalex.org/A5081448047","https://openalex.org/A5086658226","https://openalex.org/A5088676977","https://openalex.org/A5091156613"],"corresponding_institution_ids":["https://openalex.org/I1283613182","https://openalex.org/I137479271"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.8992,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.86154842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"20","issue":"10","first_page":"e1012530","last_page":"e1012530"},"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9876000285148621,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.987500011920929,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.9010648727416992},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.7731921076774597},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6251617074012756},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5846472978591919},{"id":"https://openalex.org/keywords/abundance","display_name":"Abundance (ecology)","score":0.5707720518112183},{"id":"https://openalex.org/keywords/species-richness","display_name":"Species richness","score":0.5587460398674011},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49638158082962036},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.4789845943450928},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.47394469380378723},{"id":"https://openalex.org/keywords/relative-species-abundance","display_name":"Relative species abundance","score":0.4636361002922058},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4394146800041199},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.4267585277557373},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4208185374736786},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26292315125465393},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.21384450793266296},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12484928965568542},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12130141258239746}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9010648727416992},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7731921076774597},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6251617074012756},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5846472978591919},{"id":"https://openalex.org/C77077793","wikidata":"https://www.wikidata.org/wiki/Q336019","display_name":"Abundance (ecology)","level":2,"score":0.5707720518112183},{"id":"https://openalex.org/C53565203","wikidata":"https://www.wikidata.org/wiki/Q17146659","display_name":"Species richness","level":2,"score":0.5587460398674011},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49638158082962036},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4789845943450928},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.47394469380378723},{"id":"https://openalex.org/C122325731","wikidata":"https://www.wikidata.org/wiki/Q3738459","display_name":"Relative species abundance","level":3,"score":0.4636361002922058},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4394146800041199},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.4267585277557373},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4208185374736786},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26292315125465393},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.21384450793266296},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12484928965568542},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12130141258239746},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1012530","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012530","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:39436938","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39436938","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11530072","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11530072","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11530072/pdf/pcbi.1012530.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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012530","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012530","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.7599999904632568}],"awards":[{"id":"https://openalex.org/G295657101","display_name":null,"funder_award_id":"2019/","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G3618239412","display_name":null,"funder_award_id":"460129525","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3717254026","display_name":null,"funder_award_id":"VH-NG-1248 Micro\u2019 Big Data\u2019","funder_id":"https://openalex.org/F4320320876","funder_display_name":"Helmholtz-Gemeinschaft"},{"id":"https://openalex.org/G4153853600","display_name":null,"funder_award_id":"2022/03534-5","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G5938443454","display_name":null,"funder_award_id":"2019/03396-9","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320876","display_name":"Helmholtz-Gemeinschaft","ror":"https://ror.org/0281dp749"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1584790813","https://openalex.org/W1974195423","https://openalex.org/W1990692999","https://openalex.org/W2048818637","https://openalex.org/W2089859322","https://openalex.org/W2112364185","https://openalex.org/W2119859604","https://openalex.org/W2141920662","https://openalex.org/W2753961085","https://openalex.org/W2771008898","https://openalex.org/W2790453837","https://openalex.org/W2799868407","https://openalex.org/W2901390366","https://openalex.org/W2920716817","https://openalex.org/W2950310673","https://openalex.org/W2950785362","https://openalex.org/W2957295726","https://openalex.org/W2970842946","https://openalex.org/W2973585389","https://openalex.org/W2977723904","https://openalex.org/W2980110280","https://openalex.org/W2986925300","https://openalex.org/W2988411281","https://openalex.org/W2991113705","https://openalex.org/W2996335903","https://openalex.org/W3000916974","https://openalex.org/W3033129278","https://openalex.org/W3079060667","https://openalex.org/W3080559248","https://openalex.org/W3090089243","https://openalex.org/W3108980681","https://openalex.org/W3109640704","https://openalex.org/W3117318244","https://openalex.org/W3119717076","https://openalex.org/W3125972683","https://openalex.org/W3137955457","https://openalex.org/W3141597806","https://openalex.org/W3179854101","https://openalex.org/W4224806117","https://openalex.org/W4225258284","https://openalex.org/W4235413534","https://openalex.org/W4281713953","https://openalex.org/W4293233235","https://openalex.org/W4309326290","https://openalex.org/W4383868362","https://openalex.org/W4388952156","https://openalex.org/W4391349283"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W3111832393","https://openalex.org/W2806408903","https://openalex.org/W3043668926","https://openalex.org/W4281387755","https://openalex.org/W4313305812","https://openalex.org/W3003110834","https://openalex.org/W2826508195","https://openalex.org/W3098103638"],"abstract_inverted_index":{"We":[0],"hypothesize":[1],"that":[2,185,197,224],"sample":[3,42],"species":[4,35,43,164,173,239],"abundance,":[5,44],"sequencing":[6,45,139,198],"depth,":[7,46],"and":[8,47,63,72,86,99,106,120,196,206],"taxonomic":[9,48],"relatedness":[10],"influence":[11],"the":[12,37,67,73,90,97,111,118,126,134,147,162,167,192,225],"recovery":[13,25,113,165,177,205,213],"of":[14,33,70,76,114],"metagenome-assembled":[15],"genomes":[16,115],"(MAGs).":[17],"To":[18],"test":[19],"this":[20],"hypothesis,":[21],"we":[22],"assessed":[23],"MAG":[24,56,204,212,233],"in":[26,28,133,153,179,203],"three":[27,52],"silico":[29],"microbial":[30],"communities":[31,136,154],"composed":[32],"42":[34],"with":[36,123],"same":[38,168],"richness":[39],"but":[40],"different":[41,53],"distribution":[49],"profiles":[50],"using":[51,117],"pipelines":[54],"for":[55],"recovery.":[57],"The":[58,82],"pipeline":[59,83,101,128],"developed":[60,103],"by":[61,84,104],"Parks":[62],"colleagues":[64,87],"(8K)":[65],"generated":[66],"highest":[68],"number":[69,75],"MAGs":[71,131],"lowest":[74],"true":[77,151],"positives":[78,152],"per":[79],"community":[80,194,208,227],"profile.":[81],"Karst":[85],"(DT)":[88],"showed":[89,161],"most":[91],"accurate":[92,112],"results":[93,183],"(~":[94],"92%),":[95],"outperforming":[96],"8K":[98,119,148],"Multi-Metagenome":[100],"(MM)":[102],"Albertsen":[105],"collaborators.":[107],"Sequencing":[108],"depth":[109,199],"influenced":[110],"when":[116,137,236],"MM,":[121],"even":[122,170],"contrasting":[124],"patterns:":[125],"MM":[127],"recovered":[129,149],"more":[130,150,186],"found":[132],"original":[135],"employing":[138],"depths":[140],"up":[141],"to":[142,191],"60":[143,157],"million":[144,158],"reads,":[145],"while":[146],"sequenced":[155],"above":[156],"reads.":[159],"DT":[160],"best":[163],"from":[166,232],"genus,":[169],"though":[171],"close-related":[172],"have":[174],"a":[175,201],"low":[176,211],"rate":[178],"all":[180],"pipelines.":[181],"Our":[182,221],"highlight":[184],"bins":[187],"do":[188],"not":[189],"translate":[190],"actual":[193],"composition":[195],"plays":[200],"role":[202],"increased":[207],"resolution.":[209],"Even":[210],"error":[214],"rates":[215],"can":[216],"significantly":[217],"impact":[218],"biological":[219],"inferences.":[220],"data":[222],"indicates":[223],"scientific":[226],"should":[228],"curate":[229],"their":[230],"findings":[231],"recovery,":[234],"especially":[235],"asserting":[237],"novel":[238],"or":[240],"metabolic":[241],"traits.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
