{"id":"https://openalex.org/W2995409652","doi":"https://doi.org/10.1101/2019.12.20.885269","title":"Identifying Core Operons in Metagenomic Data","display_name":"Identifying Core Operons in Metagenomic Data","publication_year":2019,"publication_date":"2019-12-21","ids":{"openalex":"https://openalex.org/W2995409652","doi":"https://doi.org/10.1101/2019.12.20.885269","mag":"2995409652"},"language":"en","primary_location":{"id":"doi:10.1101/2019.12.20.885269","doi":"https://doi.org/10.1101/2019.12.20.885269","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2019.12.20.885269","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/28/2019.12.20.885269.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/28/2019.12.20.885269.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057994049","display_name":"Xiao Hu","orcid":"https://orcid.org/0000-0002-3309-9575","observed_orcids":["https://orcid.org/0000-0002-3309-9575"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Hu","raw_affiliation_strings":["Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA","Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 500, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 500, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041597050","display_name":"Iddo Friedberg","orcid":"https://orcid.org/0000-0002-1789-8000","observed_orcids":["https://orcid.org/0000-0002-1789-8000"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Iddo Friedberg","raw_affiliation_strings":["Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA","Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50010 USA","Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 500, USA"],"raw_orcid":"https://orcid.org/0000-0002-1789-8000","affiliations":[{"raw_affiliation_string":"Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50010 USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 500, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5041597050"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9922000169754028,"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":0.9922000169754028,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.0038999998942017555,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.0005000000237487257,"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/operon","display_name":"operon","score":0.7940000295639038},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.8450000286102295},{"id":"https://openalex.org/keywords/polycistronic-transcription","display_name":"polycistronic transcription","score":0.7580000162124634},{"id":"https://openalex.org/keywords/gene-co-regulation","display_name":"gene co-regulation","score":0.7139999866485596},{"id":"https://openalex.org/keywords/human-gut-metagenome","display_name":"human gut metagenome","score":0.7910000085830688},{"id":"https://openalex.org/keywords/neofunctionalization","display_name":"neofunctionalization","score":0.8690000176429749},{"id":"https://openalex.org/keywords/bacterial-gene-regulation","display_name":"bacterial gene regulation","score":0.42899999022483826}],"concepts":[{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.8783639073371887},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8235616087913513},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5790047645568848},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.574815034866333},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5502833724021912},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4482755661010742},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0844988226890564}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2019.12.20.885269","doi":"https://doi.org/10.1101/2019.12.20.885269","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2019.12.20.885269","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/28/2019.12.20.885269.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2019.12.20.885269","doi":"https://doi.org/10.1101/2019.12.20.885269","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2019.12.20.885269","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/28/2019.12.20.885269.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2995409652.pdf","grobid_xml":"https://content.openalex.org/works/W2995409652.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W192889406","https://openalex.org/W1496933752","https://openalex.org/W1514308025","https://openalex.org/W1995117714","https://openalex.org/W1997246534","https://openalex.org/W2006465310","https://openalex.org/W2033984457","https://openalex.org/W2045204781","https://openalex.org/W2045967366","https://openalex.org/W2048673910","https://openalex.org/W2055109879","https://openalex.org/W2061732951","https://openalex.org/W2073128992","https://openalex.org/W2096093282","https://openalex.org/W2099006507","https://openalex.org/W2100332892","https://openalex.org/W2102199998","https://openalex.org/W2102498314","https://openalex.org/W2105792118","https://openalex.org/W2109848222","https://openalex.org/W2113679889","https://openalex.org/W2114956488","https://openalex.org/W2115413658","https://openalex.org/W2117486996","https://openalex.org/W2118576272","https://openalex.org/W2120267228","https://openalex.org/W2120358246","https://openalex.org/W2127596034","https://openalex.org/W2129149283","https://openalex.org/W2141920662","https://openalex.org/W2142967149","https://openalex.org/W2143485490","https://openalex.org/W2144795887","https://openalex.org/W2146436858","https://openalex.org/W2156125289","https://openalex.org/W2156701707","https://openalex.org/W2157539385","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2160794724","https://openalex.org/W2160969485","https://openalex.org/W2166406784","https://openalex.org/W2167583584","https://openalex.org/W2168330474","https://openalex.org/W2170747616","https://openalex.org/W2232370058","https://openalex.org/W2522874168","https://openalex.org/W4235121031","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W4234966234","https://openalex.org/W3121184687","https://openalex.org/W4404234641","https://openalex.org/W2927873716","https://openalex.org/W2809500310","https://openalex.org/W2144795887","https://openalex.org/W2522874168","https://openalex.org/W1529742738","https://openalex.org/W4405427406","https://openalex.org/W2531227267"],"abstract_inverted_index":{"Abstract":[0],"An":[1],"operon":[2,74],"is":[3,104],"a":[4,17,22,46,64,67,72,76,79,95,105],"functional":[5,27,68],"unit":[6,69],"of":[7,25,34,58,63,81,88],"DNA":[8],"whose":[9],"genes":[10],"are":[11,21,32],"co-transcribed":[12],"on":[13,94],"polycistronic":[14],"mRNA,":[15],"in":[16,29,36,51,75,123],"co-regulated":[18],"fashion.":[19],"Operons":[20],"powerful":[23],"mechanism":[24],"introducing":[26],"complexity":[28],"bacteria,":[30],"and":[31,41,90,115,120],"therefore":[33],"interest":[35],"microbial":[37],"genetics,":[38],"physiology,":[39],"biochemistry,":[40],"evolution.":[42],"Here":[43],"we":[44,83],"present":[45],"Pipeline":[47],"for":[48,108,116],"Operon":[49],"Exploration":[50],"Metagenomes":[52],"or":[53],"POEM.":[54],"At":[55],"the":[56,61,85,112],"heart":[57],"POEM":[59,103],"lies":[60],"concept":[62],"core":[65],"operon,":[66],"enabled":[70],"by":[71],"predicted":[73],"metagenome.":[77],"Using":[78],"series":[80],"benchmarks,":[82],"show":[84],"high":[86],"accuracy":[87],"POEM,":[89],"demonstrate":[91],"its":[92],"use":[93],"human":[96],"gut":[97],"metagenome":[98],"sample.":[99],"We":[100],"conclude":[101],"that":[102],"useful":[106],"tool":[107],"analyzing":[109],"metagenomes":[110],"beyond":[111],"genomic":[113],"level,":[114],"identifying":[117],"multi-gene":[118],"functionalities":[119],"possible":[121],"neofunctionalization":[122],"metagenomes.":[124],"Availability:":[125],"https://github.com/Rinoahu/POEM_py3k":[126]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-09-08T07:41:39.490200","created_date":"2019-12-26T00:00:00"}