{"id":"https://openalex.org/W2270339418","doi":"https://doi.org/10.1093/bioinformatics/btw040","title":"Optimization of alignment-based methods for taxonomic binning of metagenomics reads","display_name":"Optimization of alignment-based methods for taxonomic binning of metagenomics reads","publication_year":2016,"publication_date":"2016-02-01","ids":{"openalex":"https://openalex.org/W2270339418","doi":"https://doi.org/10.1093/bioinformatics/btw040","mag":"2270339418","pmid":"https://pubmed.ncbi.nlm.nih.gov/26833346"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw040","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw040","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017778397","display_name":"Magali Jaillard","orcid":"https://orcid.org/0000-0001-7010-1921"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210139047","display_name":"bioM\u00e9rieux (France)","ror":"https://ror.org/03hf69k85","country_code":"FR","type":"company","lineage":["https://openalex.org/I1284886586","https://openalex.org/I4210139047"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Magali Jaillard","raw_affiliation_strings":["1 Bioinformatics Research Department, bioMerieux, Marcy L\u2019etoile 69280, France,","2 LBBE, UMR CNRS 5558 University Lyon 1, Villeurbanne F-69622, France"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Research Department, bioMerieux, Marcy L\u2019etoile 69280, France,","institution_ids":["https://openalex.org/I4210139047"]},{"raw_affiliation_string":"2 LBBE, UMR CNRS 5558 University Lyon 1, Villeurbanne F-69622, France","institution_ids":["https://openalex.org/I4210135640","https://openalex.org/I100532134","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077330976","display_name":"Maud Tournoud","orcid":"https://orcid.org/0000-0003-2459-9831"},"institutions":[{"id":"https://openalex.org/I4210139047","display_name":"bioM\u00e9rieux (France)","ror":"https://ror.org/03hf69k85","country_code":"FR","type":"company","lineage":["https://openalex.org/I1284886586","https://openalex.org/I4210139047"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Maud Tournoud","raw_affiliation_strings":["1 Bioinformatics Research Department, bioMerieux, Marcy L\u2019etoile 69280, France,"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Research Department, bioMerieux, Marcy L\u2019etoile 69280, France,","institution_ids":["https://openalex.org/I4210139047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064338560","display_name":"F. Meynier","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139047","display_name":"bioM\u00e9rieux (France)","ror":"https://ror.org/03hf69k85","country_code":"FR","type":"company","lineage":["https://openalex.org/I1284886586","https://openalex.org/I4210139047"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Faustine Meynier","raw_affiliation_strings":["3 Biomathematics System Development, bioMerieux, Marcy L\u2019etoile 69280, France"],"affiliations":[{"raw_affiliation_string":"3 Biomathematics System Development, bioMerieux, Marcy L\u2019etoile 69280, France","institution_ids":["https://openalex.org/I4210139047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046798754","display_name":"Jean\u2010Baptiste Veyrieras","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139047","display_name":"bioM\u00e9rieux (France)","ror":"https://ror.org/03hf69k85","country_code":"FR","type":"company","lineage":["https://openalex.org/I1284886586","https://openalex.org/I4210139047"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jean-Baptiste Veyrieras","raw_affiliation_strings":["1 Bioinformatics Research Department, bioMerieux, Marcy L\u2019etoile 69280, France,"],"affiliations":[{"raw_affiliation_string":"1 Bioinformatics Research Department, bioMerieux, Marcy L\u2019etoile 69280, France,","institution_ids":["https://openalex.org/I4210139047"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017778397"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I4210135640","https://openalex.org/I4210139047"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.00320453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"12","first_page":"1779","last_page":"1787"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9952999949455261,"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/T10066","display_name":"Gut microbiota and health","score":0.9922999739646912,"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":0.7840572595596313},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7789809703826904},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.747519850730896},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6147447824478149},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5248361229896545},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.30233800411224365},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12856712937355042},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1090695858001709}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7840572595596313},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7789809703826904},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.747519850730896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6147447824478149},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5248361229896545},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30233800411224365},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12856712937355042},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1090695858001709},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","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":"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":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":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw040","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw040","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26833346","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26833346","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},{"id":"pmh:oai:HAL:hal-02012378v1","is_oa":false,"landing_page_url":"https://univ-lyon1.hal.science/hal-02012378","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2016, 32, pp.1779-87. &#x27E8;10.1093/bioinformatics/btw040&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/12/1779","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/12/1779","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1528905581","https://openalex.org/W1555265423","https://openalex.org/W1964209583","https://openalex.org/W1969882260","https://openalex.org/W1973530293","https://openalex.org/W2006901874","https://openalex.org/W2035983506","https://openalex.org/W2078689689","https://openalex.org/W2087977557","https://openalex.org/W2091193685","https://openalex.org/W2100561213","https://openalex.org/W2103441770","https://openalex.org/W2105708056","https://openalex.org/W2116895571","https://openalex.org/W2123009189","https://openalex.org/W2124927293","https://openalex.org/W2131026689","https://openalex.org/W2134751812","https://openalex.org/W2141570612","https://openalex.org/W2142915116","https://openalex.org/W2150612144","https://openalex.org/W2151450114","https://openalex.org/W2153805608","https://openalex.org/W2154969423","https://openalex.org/W2156715753","https://openalex.org/W2159682570","https://openalex.org/W2170551349","https://openalex.org/W2794027193","https://openalex.org/W2796700885","https://openalex.org/W4301861531","https://openalex.org/W7075715917"],"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/W3044162010"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
