{"id":"https://openalex.org/W3202547677","doi":"https://doi.org/10.1093/bioinformatics/btab672","title":"Tiara: deep learning-based classification system for eukaryotic sequences","display_name":"Tiara: deep learning-based classification system for eukaryotic sequences","publication_year":2021,"publication_date":"2021-09-21","ids":{"openalex":"https://openalex.org/W3202547677","doi":"https://doi.org/10.1093/bioinformatics/btab672","mag":"3202547677","pmid":"https://pubmed.ncbi.nlm.nih.gov/34570171"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab672","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab672","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/344/42040094/btab672.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/bioinformatics/article-pdf/38/2/344/42040094/btab672.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008520391","display_name":"Micha\u0142 Karlicki","orcid":"https://orcid.org/0000-0002-7952-6288"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Micha\u0142 Karlicki","raw_affiliation_strings":["Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018091933","display_name":"Stanis\u0142aw Antonowicz","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Stanis\u0142aw Antonowicz","raw_affiliation_strings":["Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010077821","display_name":"Anna Karnkowska","orcid":"https://orcid.org/0000-0003-3709-7873"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Anna Karnkowska","raw_affiliation_strings":["Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland"],"raw_orcid":"https://orcid.org/0000-0003-3709-7873","affiliations":[{"raw_affiliation_string":"Institute of Evolutionary Biology, Faculty of Biology & Biological and Chemical Research Centre, University of Warsaw, Warszawa 02-089, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5010077821"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.0266,"has_fulltext":true,"cited_by_count":142,"citation_normalized_percentile":{"value":0.96860297,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"38","issue":"2","first_page":"344","last_page":"350"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11879","display_name":"Protist diversity and phylogeny","score":0.9017000198364258,"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/T11879","display_name":"Protist diversity and phylogeny","score":0.9017000198364258,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.050700001418590546,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.02239999920129776,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6966050863265991},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5397525429725647},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5248441696166992},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5171972513198853},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49720457196235657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49060335755348206},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4190983176231384},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38498643040657043},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.331464558839798},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3278294801712036},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2095683515071869},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12821334600448608},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08655804395675659}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6966050863265991},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5397525429725647},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5248441696166992},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5171972513198853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49720457196235657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49060335755348206},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4190983176231384},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38498643040657043},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.331464558839798},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3278294801712036},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2095683515071869},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12821334600448608},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08655804395675659},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","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":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab672","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab672","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/344/42040094/btab672.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8722755","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8722755","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:34570171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34570171","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab672","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab672","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/344/42040094/btab672.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","display_name":"Life below water","score":0.8600000143051147}],"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/G1414775356","display_name":null,"funder_award_id":"No. DE-AC02- 05-CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1816284028","display_name":null,"funder_award_id":"Contract No. DE-AC02-05-CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"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/G365575497","display_name":null,"funder_award_id":"No. DE-AC02-05-CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G419881185","display_name":null,"funder_award_id":"DEAC02\u201305CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G42916606","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/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/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/G6652958823","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"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/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/G834277795","display_name":null,"funder_award_id":"DE\u2013AC02\u201305CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"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/F4320307844","display_name":"European Molecular Biology Organization","ror":"https://ror.org/04wfr2810"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3202547677.pdf","grobid_xml":"https://content.openalex.org/works/W3202547677.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1680797894","https://openalex.org/W1724257157","https://openalex.org/W1881066983","https://openalex.org/W1958058086","https://openalex.org/W1984156791","https://openalex.org/W1989142927","https://openalex.org/W2009320543","https://openalex.org/W2035181544","https://openalex.org/W2055043387","https://openalex.org/W2087064593","https://openalex.org/W2092491668","https://openalex.org/W2096525273","https://openalex.org/W2100561213","https://openalex.org/W2114850508","https://openalex.org/W2118020653","https://openalex.org/W2127175247","https://openalex.org/W2136145671","https://openalex.org/W2146906779","https://openalex.org/W2147790590","https://openalex.org/W2169583837","https://openalex.org/W2170990028","https://openalex.org/W2171450710","https://openalex.org/W2255506873","https://openalex.org/W2311039602","https://openalex.org/W2502949459","https://openalex.org/W2624474137","https://openalex.org/W2735611463","https://openalex.org/W2761759859","https://openalex.org/W2782623083","https://openalex.org/W2891674727","https://openalex.org/W2913972921","https://openalex.org/W2922146544","https://openalex.org/W2922484653","https://openalex.org/W2950310673","https://openalex.org/W2950509696","https://openalex.org/W2963607348","https://openalex.org/W2963740900","https://openalex.org/W2979715961","https://openalex.org/W2981778858","https://openalex.org/W2983947643","https://openalex.org/W2990356758","https://openalex.org/W2990618091","https://openalex.org/W2992541521","https://openalex.org/W2999926571","https://openalex.org/W3006363311","https://openalex.org/W3008594856","https://openalex.org/W3024872414","https://openalex.org/W3034596566","https://openalex.org/W3082966508","https://openalex.org/W3093460524","https://openalex.org/W3097237112","https://openalex.org/W3171987770","https://openalex.org/W4239634997","https://openalex.org/W4255164308","https://openalex.org/W4287869566","https://openalex.org/W4293196852","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W3198631238","https://openalex.org/W4388282505","https://openalex.org/W2968048207"],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"a":[2,14,31,41],"large":[3,124],"number":[4],"of":[5,20,34,47,61,130,149,197],"metagenomic":[6,52,162],"datasets":[7],"becoming":[8],"available,":[9],"eukaryotic":[10,21,35,48,65,120],"metagenomics":[11],"emerged":[12],"as":[13],"new":[15],"challenge.":[16],"The":[17],"proper":[18],"classification":[19,56,60,91,97],"nuclear":[22,62],"and":[23,63,67,74,92,123,153,160,176,189],"organellar":[24,64,70,141],"genomes":[25,155],"is":[26,133,168,182,191],"an":[27,185],"essential":[28],"step":[29],"toward":[30],"better":[32,111],"understanding":[33],"diversity.":[36],"RESULTS:":[37],"We":[38],"developed":[39],"Tiara,":[40],"deep-learning-based":[42],"approach":[43],"for":[44,89,95,202],"the":[45,51,59,77,103,106,116,127,135,147,157],"identification":[46],"sequences":[49,71],"in":[50,114,170],"datasets.":[53],"Its":[54],"two-step":[55],"process":[57],"enables":[58],"fractions":[66],"subsequently":[68],"divides":[69],"into":[72],"plastidial":[73],"mitochondrial.":[75],"Using":[76],"test":[78,158],"dataset,":[79],"we":[80],"have":[81],"shown":[82],"that":[83],"Tiara":[84,109,132,167,198],"performed":[85,110],"similarly":[86],"to":[87],"EukRep":[88,113],"prokaryotes":[90],"outperformed":[93],"it":[94],"eukaryotes":[96],"with":[98],"lower":[99],"calculation":[100],"time.":[101],"In":[102],"tests":[104],"on":[105,178],"real":[107,161],"data,":[108],"than":[112],"analyzing":[115],"small":[117],"dataset":[118,125],"representing":[119],"cell":[121],"microbiome":[122],"from":[126,156],"pelagic":[128],"zone":[129],"oceans.":[131],"also":[134],"only":[136],"available":[137,173,192,210],"tool":[138],"correctly":[139],"classifying":[140],"sequences,":[142],"which":[143],"was":[144],"confirmed":[145],"by":[146],"recovery":[148],"nearly":[150],"complete":[151],"plastid":[152],"mitochondrial":[154],"data":[159,208],"data.":[163],"AVAILABILITY":[164],"AND":[165],"IMPLEMENTATION:":[166],"implemented":[169],"python":[171],"3.8,":[172],"at":[174,193,211],"https://github.com/ibe-uw/tiara":[175],"tested":[177],"Unix-based":[179],"systems.":[180],"It":[181],"released":[183],"under":[184],"open-source":[186],"MIT":[187],"license":[188],"documentation":[190],"https://ibe-uw.github.io/tiara.":[194],"Version":[195],"1.0.1":[196],"has":[199],"been":[200],"used":[201],"all":[203],"benchmarks.":[204],"SUPPLEMENTARY":[205],"INFORMATION:":[206],"Supplementary":[207],"are":[209],"Bioinformatics":[212],"online.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":29},{"year":2025,"cited_by_count":47},{"year":2024,"cited_by_count":40},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":2}],"updated_date":"2026-08-14T07:06:38.338062","created_date":"2025-10-10T00:00:00"}
