{"id":"https://openalex.org/W3155261003","doi":"https://doi.org/10.1371/journal.pcbi.1008972","title":"A method for achieving complete microbial genomes and improving bins from metagenomics data","display_name":"A method for achieving complete microbial genomes and improving bins from metagenomics data","publication_year":2021,"publication_date":"2021-05-07","ids":{"openalex":"https://openalex.org/W3155261003","doi":"https://doi.org/10.1371/journal.pcbi.1008972","mag":"3155261003","pmid":"https://pubmed.ncbi.nlm.nih.gov/33961626"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008972","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008972","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008972&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008972&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082136215","display_name":"Lauren Michelle Lui","orcid":"https://orcid.org/0000-0001-8720-5268"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lauren M. Lui","raw_affiliation_strings":["Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072764375","display_name":"Torben Nielsen","orcid":"https://orcid.org/0000-0002-0987-7189"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Torben N. Nielsen","raw_affiliation_strings":["Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066623854","display_name":"Adam P. Arkin","orcid":"https://orcid.org/0000-0002-4999-2931"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I4210109258","display_name":"Innovative Genomics Institute","ror":"https://ror.org/01r4tcq81","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210109258","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam P. Arkin","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, California, United States of America","Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America","Innovative Genomics Institute, Berkeley, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Innovative Genomics Institute, Berkeley, CA, United States of America","institution_ids":["https://openalex.org/I4210109258"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066623854"],"corresponding_institution_ids":["https://openalex.org/I148283060","https://openalex.org/I4210109258","https://openalex.org/I95457486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.5213,"has_fulltext":true,"cited_by_count":39,"citation_normalized_percentile":{"value":0.90471983,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"17","issue":"5","first_page":"e1008972","last_page":"e1008972"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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":0.9968000054359436,"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":0.9957000017166138,"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/genome","display_name":"Genome","score":0.8497320413589478},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8112368583679199},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7416301369667053},{"id":"https://openalex.org/keywords/synteny","display_name":"Synteny","score":0.6742507219314575},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.5773545503616333},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.573872447013855},{"id":"https://openalex.org/keywords/ribosomal-rna","display_name":"Ribosomal RNA","score":0.5346198678016663},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4970124065876007},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4219765365123749},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.42118608951568604},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3907920718193054}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8497320413589478},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8112368583679199},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7416301369667053},{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.6742507219314575},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.5773545503616333},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.573872447013855},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.5346198678016663},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4970124065876007},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4219765365123749},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.42118608951568604},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3907920718193054}],"mesh":[{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","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":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1008972","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008972","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008972&type=printable","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:33961626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33961626","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:osti.gov:1788019","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1788019","pdf_url":"https://www.osti.gov/servlets/purl/1788019","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:ark:/13030/qt2676p9qk","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:8f3e01c998e5490b89abc144b33cd7e7","is_oa":true,"landing_page_url":"https://doaj.org/article/8f3e01c998e5490b89abc144b33cd7e7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 5, p e1008972 (2021)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt2676p9qk","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/2676p9qk","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt3hf1j1tc","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/3hf1j1tc","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 17, iss 5","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8172020","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8172020","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1008972","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008972","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008972&type=printable","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":[],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1337544421","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1581387393","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1677143136","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G2503023272","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2857863752","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3432487278","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G425189044","display_name":null,"funder_award_id":"DE-AC02-05CH","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4369507515","display_name":null,"funder_award_id":"NERSC","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4392917094","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4610648879","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G4841871747","display_name":null,"funder_award_id":"DE_AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4979187122","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5076365615","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5296923526","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5315912995","display_name":null,"funder_award_id":"11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G542631466","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5602503670","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G5802748842","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5854489635","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231.","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6330738325","display_name":null,"funder_award_id":"DE_AC02_05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6429026066","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G654302390","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7205239661","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G7340683655","display_name":null,"funder_award_id":"E-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7354628648","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G7406122311","display_name":null,"funder_award_id":"AC02-05CH1123","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7629237052","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7664691372","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7672463193","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7787287669","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7825954517","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7861570460","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G8039660707","display_name":null,"funder_award_id":"DE-AC02-05CH11231.","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G805243471","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G8306346728","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G8413608756","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G8414908677","display_name":null,"funder_award_id":"DE-AC0","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8745373411","display_name":null,"funder_award_id":"DE-AC02-05CH11231.","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G8903227471","display_name":null,"funder_award_id":"DE-AC02-05CH11231.","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G897164627","display_name":null,"funder_award_id":"DE-AC02_05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320317220","display_name":"National Energy Research Scientific Computing Center","ror":"https://ror.org/05v3mvq14"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320338292","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3155261003.pdf","grobid_xml":"https://content.openalex.org/works/W3155261003.grobid-xml"},"referenced_works_count":95,"referenced_works":["https://openalex.org/W1513623536","https://openalex.org/W1528357204","https://openalex.org/W1596049933","https://openalex.org/W1635391495","https://openalex.org/W1704078308","https://openalex.org/W1750017366","https://openalex.org/W1930561965","https://openalex.org/W1964499343","https://openalex.org/W1964554231","https://openalex.org/W1976611794","https://openalex.org/W1982855075","https://openalex.org/W1987386760","https://openalex.org/W1987639630","https://openalex.org/W1998330439","https://openalex.org/W2017003789","https://openalex.org/W2026181790","https://openalex.org/W2048124712","https://openalex.org/W2080347313","https://openalex.org/W2081676964","https://openalex.org/W2085675199","https://openalex.org/W2087487397","https://openalex.org/W2089859322","https://openalex.org/W2090401806","https://openalex.org/W2103441770","https://openalex.org/W2107772251","https://openalex.org/W2111211467","https://openalex.org/W2112364185","https://openalex.org/W2115501618","https://openalex.org/W2119556995","https://openalex.org/W2120457919","https://openalex.org/W2120902911","https://openalex.org/W2123939922","https://openalex.org/W2125609055","https://openalex.org/W2130682154","https://openalex.org/W2136812605","https://openalex.org/W2137756176","https://openalex.org/W2141137078","https://openalex.org/W2141152740","https://openalex.org/W2143407915","https://openalex.org/W2143485490","https://openalex.org/W2153325555","https://openalex.org/W2165446840","https://openalex.org/W2167877584","https://openalex.org/W2175526948","https://openalex.org/W2292044244","https://openalex.org/W2336400828","https://openalex.org/W2468861611","https://openalex.org/W2533015169","https://openalex.org/W2565628225","https://openalex.org/W2572263783","https://openalex.org/W2586343403","https://openalex.org/W2586579175","https://openalex.org/W2599417231","https://openalex.org/W2603061425","https://openalex.org/W2679694071","https://openalex.org/W2753961085","https://openalex.org/W2761898164","https://openalex.org/W2768548400","https://openalex.org/W2771499133","https://openalex.org/W2773939681","https://openalex.org/W2793856982","https://openalex.org/W2799437413","https://openalex.org/W2859249641","https://openalex.org/W2883564985","https://openalex.org/W2908989331","https://openalex.org/W2918965813","https://openalex.org/W2938868597","https://openalex.org/W2942757983","https://openalex.org/W2948263509","https://openalex.org/W2949511453","https://openalex.org/W2950671516","https://openalex.org/W2950785362","https://openalex.org/W2952167528","https://openalex.org/W2952525214","https://openalex.org/W2971262600","https://openalex.org/W2975619549","https://openalex.org/W2976969251","https://openalex.org/W2986925300","https://openalex.org/W2987266449","https://openalex.org/W2991113705","https://openalex.org/W2999493833","https://openalex.org/W3003385798","https://openalex.org/W3005528502","https://openalex.org/W3006022816","https://openalex.org/W3007588112","https://openalex.org/W3011678041","https://openalex.org/W3033129278","https://openalex.org/W3112039908","https://openalex.org/W3168040031","https://openalex.org/W3173711206","https://openalex.org/W4231821896","https://openalex.org/W4237162866","https://openalex.org/W6719946149","https://openalex.org/W6735437158","https://openalex.org/W7074110266"],"related_works":["https://openalex.org/W2626545547","https://openalex.org/W4375955900","https://openalex.org/W2952105401","https://openalex.org/W2566862871","https://openalex.org/W4254915624","https://openalex.org/W2097001759","https://openalex.org/W2088015737","https://openalex.org/W4243833328","https://openalex.org/W4382394703","https://openalex.org/W2332110477"],"abstract_inverted_index":{"Metagenomics":[0],"facilitates":[1],"the":[2,5,79,120,185,258,288],"study":[3],"of":[4,81,106,115,125,184,260,269],"genetic":[6],"information":[7],"from":[8,18,75,177,232],"uncultured":[9],"microbes":[10],"and":[11,30,42,45,67,73,123,127,160,167,200,227,235,262,274,284],"complex":[12],"microbial":[13],"communities.":[14],"Assembling":[15],"complete":[16,39,103],"genomes":[17,44,52,69,87,162,199,231],"metagenomics":[19,76],"data":[20,77],"is":[21,280,285],"difficult":[22,245],"because":[23,195],"most":[24],"samples":[25],"have":[26,35,70,197,205],"high":[27],"organismal":[28],"complexity":[29],"strain":[31],"diversity.":[32],"Some":[33],"studies":[34],"attempted":[36],"to":[37,133,137,154,190,204,212],"extract":[38],"bacterial,":[40,158],"archaeal,":[41,159],"viral":[43,161],"often":[46],"focus":[47,191],"on":[48,287],"species":[49,183],"with":[50,59],"circular":[51,214,220,224,229],"so":[53],"they":[54,196],"can":[55],"help":[56,155],"confirm":[57],"completeness":[58],"circularity.":[60],"However,":[61],"less":[62],"than":[63],"100":[64],"circularized":[65],"bacterial":[66],"archaeal":[68],"been":[71],"assembled":[72],"published":[74,236],"despite":[78],"thousands":[80],"datasets":[82],"that":[83,241,250,263],"are":[84,88,201,253],"available.":[85],"Circularized":[86],"important":[89],"for":[90,98,277],"(1)":[91],"building":[92],"a":[93,107,116,149,275,294],"reference":[94],"collection":[95],"as":[96,293],"scaffolds":[97],"future":[99],"assemblies,":[100],"(2)":[101],"providing":[102],"gene":[104,144],"content":[105],"genome,":[108,117,222,226],"(3)":[109],"confirming":[110],"little":[111],"or":[112],"no":[113],"contamination":[114],"(4)":[118],"studying":[119],"genomic":[121],"context":[122],"synteny":[124],"genes,":[126],"(5)":[128],"linking":[129],"protein":[130],"coding":[131],"genes":[132,136,252],"ribosomal":[134,207,251],"RNA":[135,208],"aid":[138],"metabolic":[139],"inference":[140],"in":[141,257],"16S":[142],"rRNA":[143],"sequencing":[145],"studies.":[146],"We":[147,181,238],"developed":[148],"semi-automated":[150],"method":[151,173,279],"called":[152],"Jorg":[153],"circularize":[156],"small":[157,198],"using":[163],"iterative":[164],"assembly,":[165],"binning,":[166],"read":[168],"mapping.":[169],"In":[170,210],"addition,":[171],"this":[172,278],"exposes":[174],"potential":[175],"misassemblies":[176],"k-mer":[178],"based":[179],"assemblies.":[180],"chose":[182],"Candidate":[186],"Phyla":[187],"Radiation":[188],"(CPR)":[189],"our":[192],"initial":[193],"efforts":[194],"only":[202],"known":[203],"one":[206,219,223],"operon.":[209],"addition":[211],"34":[213],"CPR":[215,265],"genomes,":[216,248],"we":[217],"present":[218],"Margulisbacteria":[221],"Chloroflexi":[225],"two":[228],"megaphage":[230],"19":[233],"public":[234],"datasets.":[237],"demonstrate":[239],"findings":[240],"would":[242],"likely":[243,254],"be":[244],"without":[246],"circularizing":[247],"including":[249],"not":[255],"operonic":[256],"majority":[259],"CPR,":[261],"some":[264],"harbor":[266],"diverged":[267],"forms":[268],"RNase":[270],"P":[271],"RNA.":[272],"Code":[273],"tutorial":[276],"available":[281,286],"at":[282],"https://github.com/lmlui/Jorg":[283],"DOE":[289],"Systems":[290],"Biology":[291],"KnowledgeBase":[292],"beta":[295],"app.":[296]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":5}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}