{"id":"https://openalex.org/W3023627704","doi":"https://doi.org/10.1093/bioinformatics/btaa277","title":"SHOGUN: a modular, accurate and scalable framework for microbiome quantification","display_name":"SHOGUN: a modular, accurate and scalable framework for microbiome quantification","publication_year":2020,"publication_date":"2020-04-24","ids":{"openalex":"https://openalex.org/W3023627704","doi":"https://doi.org/10.1093/bioinformatics/btaa277","mag":"3023627704","pmid":"https://pubmed.ncbi.nlm.nih.gov/32365167"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa277","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa277","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7359755","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063135788","display_name":"Benjamin Hillmann","orcid":"https://orcid.org/0000-0003-4276-1329"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Hillmann","raw_affiliation_strings":["Department of Computer Science and Engineering , University of Minnesota, Minneapolis, 55455 Minnesota, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering , University of Minnesota, Minneapolis, 55455 Minnesota, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058766687","display_name":"Gabriel A. Al\u2010Ghalith","orcid":"https://orcid.org/0000-0002-6953-6319"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriel A Al-Ghalith","raw_affiliation_strings":["Bioinformatics and Computational Biology , University of Minnesota, Minneapolis, 55455 Minnesota, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology , University of Minnesota, Minneapolis, 55455 Minnesota, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081505232","display_name":"Robin Shields\u2010Cutler","orcid":"https://orcid.org/0000-0003-4701-9895"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robin R Shields-Cutler","raw_affiliation_strings":["Biotechnology Institute , University of Minnesota, Minneapolis, 55455 Minnesota, USA"],"affiliations":[{"raw_affiliation_string":"Biotechnology Institute , University of Minnesota, Minneapolis, 55455 Minnesota, USA","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064767131","display_name":"Qiyun Zhu","orcid":"https://orcid.org/0000-0002-3568-6271"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiyun Zhu","raw_affiliation_strings":["Department of Pediatrics , University of California San Diego, San Diego, 92161 5 California, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pediatrics , University of California San Diego, San Diego, 92161 5 California, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033881627","display_name":"Rob Knight","orcid":"https://orcid.org/0000-0002-0975-9019"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Knight","raw_affiliation_strings":["Center for Microbiome Innovation , University of California San Diego, San Diego, 92093 California, USA","Department of Computer of Science and Engineering , University of California San Diego, San Diego, 92093 California, USA","Department of Pediatrics , University of California San Diego, San Diego, 92161 5 California, USA"],"affiliations":[{"raw_affiliation_string":"Center for Microbiome Innovation , University of California San Diego, San Diego, 92093 California, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Computer of Science and Engineering , University of California San Diego, San Diego, 92093 California, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics , University of California San Diego, San Diego, 92161 5 California, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082358375","display_name":"Dan Knights","orcid":"https://orcid.org/0000-0002-8205-2511"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dan Knights","raw_affiliation_strings":["Bioinformatics and Computational Biology , University of Minnesota, Minneapolis, 55455 Minnesota, USA","Biotechnology Institute , University of Minnesota, Minneapolis, 55455 Minnesota, USA","Department of Computer Science and Engineering , University of Minnesota, Minneapolis, 55455 Minnesota, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biology , University of Minnesota, Minneapolis, 55455 Minnesota, USA","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Biotechnology Institute , University of Minnesota, Minneapolis, 55455 Minnesota, USA","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Computer Science and Engineering , University of Minnesota, Minneapolis, 55455 Minnesota, USA","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5082358375"],"corresponding_institution_ids":["https://openalex.org/I130238516","https://openalex.org/I1312106833"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.758,"has_fulltext":false,"cited_by_count":64,"citation_normalized_percentile":{"value":0.91315448,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"36","issue":"13","first_page":"4088","last_page":"4090"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9994000196456909,"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":0.9994000196456909,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9976000189781189,"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":0.991599977016449,"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/modular-design","display_name":"Modular design","score":0.8118664622306824},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.710191547870636},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6907892823219299},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.644239068031311},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5796049237251282},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24025458097457886},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23216578364372253},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2238622009754181},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.05541008710861206}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.8118664622306824},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.710191547870636},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6907892823219299},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.644239068031311},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5796049237251282},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24025458097457886},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23216578364372253},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2238622009754181},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.05541008710861206}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"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":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa277","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa277","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:32365167","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32365167","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:escholarship.org:ark:/13030/qt1vr9c7wg","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/1vr9c7wg","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":"Bioinformatics, vol 36, iss 13","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7359755","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7359755","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7359755","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7359755","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6517130499","display_name":null,"funder_award_id":"R01AI121383","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7952497990","display_name":null,"funder_award_id":"P01DK078669","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8424825761","display_name":null,"funder_award_id":"1565057","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1998767819","https://openalex.org/W2064676287","https://openalex.org/W2096093282","https://openalex.org/W2120172561","https://openalex.org/W2131186249","https://openalex.org/W2154139219","https://openalex.org/W2170551349","https://openalex.org/W2345658906","https://openalex.org/W2604622795","https://openalex.org/W2892206041","https://openalex.org/W2951160681","https://openalex.org/W2951176108","https://openalex.org/W4210702584","https://openalex.org/W6674637670"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2604155846","https://openalex.org/W4390658901","https://openalex.org/W3121185202","https://openalex.org/W4393043634","https://openalex.org/W4206185765","https://openalex.org/W2019887508","https://openalex.org/W3020516445"],"abstract_inverted_index":{"https://github.com/knights-lab/SHOGUN.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
