{"id":"https://openalex.org/W2625565554","doi":"https://doi.org/10.1093/bioinformatics/bty830","title":"MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data","display_name":"MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data","publication_year":2018,"publication_date":"2018-09-24","ids":{"openalex":"https://openalex.org/W2625565554","doi":"https://doi.org/10.1093/bioinformatics/bty830","mag":"2625565554","pmid":"https://pubmed.ncbi.nlm.nih.gov/30252023"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/9/1544/28557416/bty830.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","license_id":"https://openalex.org/licenses/cc-by","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/35/9/1544/28557416/bty830.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090853589","display_name":"Florian Plaza O\u00f1ate","orcid":"https://orcid.org/0000-0001-6036-0989"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210102442","display_name":"Enterome (France)","ror":"https://ror.org/0139s2465","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210102442"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Florian Plaza O\u00f1ate","raw_affiliation_strings":["Enterome, 94-96 Avenue Ledru Rollin, Paris, France","MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","MetaGenoPolis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Enterome, 94-96 Avenue Ledru Rollin, Paris, France","institution_ids":["https://openalex.org/I4210102442"]},{"raw_affiliation_string":"MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MetaGenoPolis","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087410187","display_name":"Emmanuelle Le Chatelier","orcid":"https://orcid.org/0000-0002-2724-0536"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emmanuelle Le Chatelier","raw_affiliation_strings":["MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","MetaGenoPolis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MetaGenoPolis","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067904253","display_name":"Mathieu Almeida","orcid":"https://orcid.org/0000-0003-4971-0049"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Mathieu Almeida","raw_affiliation_strings":["MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","MetaGenoPolis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MetaGenoPolis","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007599741","display_name":"Alessandra Cervino","orcid":null},"institutions":[{"id":"https://openalex.org/I4210102442","display_name":"Enterome (France)","ror":"https://ror.org/0139s2465","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210102442"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Alessandra C L Cervino","raw_affiliation_strings":["Enterome, 94-96 Avenue Ledru Rollin, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Enterome, 94-96 Avenue Ledru Rollin, Paris, France","institution_ids":["https://openalex.org/I4210102442"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054500662","display_name":"Franck Gauthier","orcid":"https://orcid.org/0000-0003-0574-065X"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Franck Gauthier","raw_affiliation_strings":["MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","MetaGenoPolis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MetaGenoPolis","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018228258","display_name":"Fr\u00e9d\u00e9ric Magoul\u00e8s","orcid":"https://orcid.org/0000-0002-1198-7539"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fr\u00e9d\u00e9ric Magoul\u00e8s","raw_affiliation_strings":["CentraleSup\u00e9lec, Universit\u00e9 Paris Saclay, 9 rue Joliot Curie, Gif-sur-Yvette, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CentraleSup\u00e9lec, Universit\u00e9 Paris Saclay, 9 rue Joliot Curie, Gif-sur-Yvette, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078857122","display_name":"S. Dusko Ehrlich","orcid":"https://orcid.org/0000-0002-7563-4046"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"S Dusko Ehrlich","raw_affiliation_strings":["MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","MetaGenoPolis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MGP MetaG\u00e9noPolis, INRA, Universit\u00e9 Paris-Saclay, Jouy en Josas, France","institution_ids":["https://openalex.org/I277688954"]},{"raw_affiliation_string":"MetaGenoPolis","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023185569","display_name":"Matthieu Pichaud","orcid":"https://orcid.org/0000-0002-9089-6693"},"institutions":[{"id":"https://openalex.org/I4210102442","display_name":"Enterome (France)","ror":"https://ror.org/0139s2465","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210102442"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Matthieu Pichaud","raw_affiliation_strings":["Enterome, 94-96 Avenue Ledru Rollin, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Enterome, 94-96 Avenue Ledru Rollin, Paris, France","institution_ids":["https://openalex.org/I4210102442"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5090853589"],"corresponding_institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210102442"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.1876,"has_fulltext":true,"cited_by_count":147,"citation_normalized_percentile":{"value":0.9671991,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"35","issue":"9","first_page":"1544","last_page":"1552"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9998999834060669,"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/T10066","display_name":"Gut microbiota and health","score":0.9998999834060669,"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":0.963100016117096,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9539999961853027,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.956835925579071},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7409889698028564},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6911293864250183},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.649249255657196},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.6108271479606628},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.6015213131904602},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.5210206508636475},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5111237168312073},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.41831234097480774},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3821777105331421}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.956835925579071},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7409889698028564},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6911293864250183},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.649249255657196},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.6108271479606628},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.6015213131904602},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.5210206508636475},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5111237168312073},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.41831234097480774},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3821777105331421}],"mesh":[{"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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","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":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bty830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/9/1544/28557416/bty830.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30252023","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30252023","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:pubmedcentral.nih.gov:6499236","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6499236","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:HAL:hal-02417979v1","is_oa":false,"landing_page_url":"https://centralesupelec.hal.science/hal-02417979","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":"https://watermark.silverchair.com","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/9/1544/28557416/bty830.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","license_id":"https://openalex.org/licenses/cc-by","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/15","display_name":"Life in Land","score":0.6899999976158142}],"awards":[{"id":"https://openalex.org/G6783009387","display_name":"MetaGenoPolis","funder_award_id":"ANR-11-DPBS-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8904009006","display_name":null,"funder_award_id":"CIFRE 2014/0057","funder_id":"https://openalex.org/F4320321663","funder_display_name":"Association Nationale de la Recherche et de la Technologie"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320321663","display_name":"Association Nationale de la Recherche et de la Technologie","ror":"https://ror.org/00ht2ab73"},{"id":"https://openalex.org/F4320323910","display_name":"Institut National de la Recherche Agronomique","ror":"https://ror.org/01x3gbx83"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2625565554.pdf","grobid_xml":"https://content.openalex.org/works/W2625565554.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W55816715","https://openalex.org/W171938871","https://openalex.org/W1433995531","https://openalex.org/W1577826155","https://openalex.org/W1703384511","https://openalex.org/W1895017250","https://openalex.org/W1971738871","https://openalex.org/W2001561488","https://openalex.org/W2004549986","https://openalex.org/W2017002453","https://openalex.org/W2023615726","https://openalex.org/W2040322093","https://openalex.org/W2041561663","https://openalex.org/W2054385769","https://openalex.org/W2055250702","https://openalex.org/W2055615325","https://openalex.org/W2071841602","https://openalex.org/W2093401639","https://openalex.org/W2097124003","https://openalex.org/W2113925621","https://openalex.org/W2124927293","https://openalex.org/W2142402047","https://openalex.org/W2147581876","https://openalex.org/W2151372451","https://openalex.org/W2161762698","https://openalex.org/W2164337734","https://openalex.org/W2165340870","https://openalex.org/W2207819727","https://openalex.org/W2289103733","https://openalex.org/W2307206101","https://openalex.org/W2313339984","https://openalex.org/W2340748026","https://openalex.org/W2345813655","https://openalex.org/W2438307216","https://openalex.org/W2463312000","https://openalex.org/W2464096417","https://openalex.org/W2533132894","https://openalex.org/W2535360044","https://openalex.org/W2549670165","https://openalex.org/W2586360538","https://openalex.org/W2597419428","https://openalex.org/W2624196074","https://openalex.org/W2761865284","https://openalex.org/W2773939681","https://openalex.org/W2796218018","https://openalex.org/W2969027338","https://openalex.org/W3007138124","https://openalex.org/W3012927825","https://openalex.org/W3017216193","https://openalex.org/W3039380610","https://openalex.org/W6606989637"],"related_works":["https://openalex.org/W3043668926","https://openalex.org/W3036436206","https://openalex.org/W4389452281","https://openalex.org/W4238948313","https://openalex.org/W2391004329","https://openalex.org/W3111832393","https://openalex.org/W3000916974","https://openalex.org/W3134948850","https://openalex.org/W2769345399","https://openalex.org/W2926411812"],"abstract_inverted_index":{"MOTIVATION:":[0],"Analysis":[1],"toolkits":[2],"for":[3,209,245],"shotgun":[4],"metagenomic":[5,120,154,218],"data":[6,253],"achieve":[7],"strain-level":[8],"characterization":[9],"of":[10,28,71,129,166,182,194,197],"complex":[11],"microbial":[12,37,72,168],"communities":[13],"by":[14,25,115],"capturing":[15],"intra-species":[16],"gene":[17,69,92,164,227],"content":[18],"variation.":[19],"Yet,":[20],"these":[21],"tools":[22],"are":[23,32,42,254],"hampered":[24],"the":[26,163,192,195,198],"extent":[27],"reference":[29],"genomes":[30],"that":[31,94,109],"far":[33],"from":[34,56,230],"covering":[35],"all":[36],"variability,":[38],"as":[39],"many":[40,84],"species":[41,79,142,169,196],"still":[43],"not":[44,140],"sequenced":[45],"or":[46,87],"have":[47],"only":[48,141],"few":[49,161],"strains":[50],"available.":[51],"Binning":[52],"co-abundant":[53,117],"genes":[54,86,118,144,147],"obtained":[55],"de":[57],"novo":[58],"assembly":[59],"is":[60,242],"a":[61,104,125,151,160],"powerful":[62],"reference-free":[63],"technique":[64],"to":[65,97,136,150,233],"discover":[66],"and":[67,138,173,188,212],"reconstitute":[68],"repertoire":[70],"species.":[73],"While":[74],"current":[75],"methods":[76],"accurately":[77],"identify":[78],"core":[80,98,143],"parts,":[81],"they":[82],"miss":[83],"accessory":[85,146],"split":[88],"them":[89],"into":[90],"small":[91],"groups":[93],"remain":[95],"unassociated":[96],"clusters.":[99],"RESULTS:":[100],"We":[101],"introduce":[102],"MSPminer,":[103],"computationally":[105],"efficient":[106],"software":[107],"tool":[108],"reconstitutes":[110],"Metagenomic":[111],"Species":[112],"Pan-genomes":[113],"(MSPs)":[114],"binning":[116],"across":[119],"samples.":[121,219],"MSPminer":[122,156,222],"relies":[123],"on":[124,226],"new":[126],"robust":[127],"measure":[128],"proportionality":[130],"coupled":[131],"with":[132,170],"an":[133],"empirical":[134],"classifier":[135],"group":[137],"distinguish":[139],"but":[145],"also.":[148],"Applied":[149],"large":[152],"scale":[153],"dataset,":[155],"successfully":[157],"delineates":[158],"in":[159,191,215],"hours":[162],"repertoires":[165],"1661":[167],"similar":[171,235],"specificity":[172],"higher":[174],"sensitivity":[175],"than":[176],"existing":[177],"tools.":[178],"The":[179,202,240],"taxonomic":[180,210],"annotation":[181],"MSPs":[183,204],"reveals":[184],"microorganisms":[185],"hitherto":[186],"unknown":[187],"brings":[189],"coherence":[190],"nomenclature":[193],"human":[199,216],"gut":[200,217],"microbiota.":[201],"provided":[203],"can":[205,223],"be":[206,224],"readily":[207],"used":[208],"profiling":[211],"biomarkers":[213],"discovery":[214],"In":[220],"addition,":[221],"applied":[225],"count":[228],"tables":[229],"other":[231],"ecosystems":[232],"perform":[234],"analyses.":[236],"AVAILABILITY":[237],"AND":[238],"IMPLEMENTATION:":[239],"binary":[241],"freely":[243],"available":[244,255],"non-commercial":[246],"users":[247],"at":[248,256],"www.enterome.com/downloads.":[249],"SUPPLEMENTARY":[250],"INFORMATION:":[251],"Supplementary":[252],"Bioinformatics":[257],"online.":[258]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":22},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2017-06-23T00:00:00"}
