{"id":"https://openalex.org/W2945645154","doi":"https://doi.org/10.1093/bioinformatics/btz414","title":"MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome","display_name":"MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome","publication_year":2019,"publication_date":"2019-05-14","ids":{"openalex":"https://openalex.org/W2945645154","doi":"https://doi.org/10.1093/bioinformatics/btz414","mag":"2945645154","pmid":"https://pubmed.ncbi.nlm.nih.gov/31116375"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz414","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz414","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4474/30330824/btz414.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":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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4474/30330824/btz414.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056199285","display_name":"Anjun Ma","orcid":"https://orcid.org/0000-0001-6269-398X"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anjun Ma","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University , Columbus, OH, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080196498","display_name":"Minxuan Sun","orcid":"https://orcid.org/0000-0003-2033-6268"},"institutions":[{"id":"https://openalex.org/I177156846","display_name":"South Dakota State University","ror":"https://ror.org/015jmes13","country_code":"US","type":"education","lineage":["https://openalex.org/I177156846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Minxuan Sun","raw_affiliation_strings":["Department of Computer Science, South Dakota State University , Brookings, SD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, South Dakota State University , Brookings, SD, USA","institution_ids":["https://openalex.org/I177156846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032867744","display_name":"Adam McDermaid","orcid":"https://orcid.org/0000-0001-8616-1574"},"institutions":[{"id":"https://openalex.org/I177156846","display_name":"South Dakota State University","ror":"https://ror.org/015jmes13","country_code":"US","type":"education","lineage":["https://openalex.org/I177156846"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam McDermaid","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University , Columbus, OH, USA","Department of Mathematics and Statistics, South Dakota State University , Brookings, SD, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, South Dakota State University , Brookings, SD, USA","institution_ids":["https://openalex.org/I177156846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017344694","display_name":"Bingqiang Liu","orcid":"https://orcid.org/0000-0002-5734-1135"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bingqiang Liu","raw_affiliation_strings":["School of Mathematics, Shandong University , Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University , Jinan, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qin Ma","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University , Columbus, OH, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University , Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022408570"],"corresponding_institution_ids":["https://openalex.org/I52357470"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4294,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.61816477,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"35","issue":"21","first_page":"4474","last_page":"4477"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9965000152587891,"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":0.9940000176429749,"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":0.8860664963722229},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6607500314712524},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6580433249473572},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.6227967739105225},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.48434722423553467},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4283723533153534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4083468019962311},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2553578019142151},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12932130694389343}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8860664963722229},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6607500314712524},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6580433249473572},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.6227967739105225},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.48434722423553467},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4283723533153534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4083468019962311},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2553578019142151},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12932130694389343}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005243","descriptor_name":"Feces","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":"D054892","descriptor_name":"Metagenome","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":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btz414","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz414","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4474/30330824/btz414.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31116375","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31116375","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":"pmid:31580397","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31580397","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:europepmc.org:5915391","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6954636","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6821265","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821265","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":"doi:10.1093/bioinformatics/btz414","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz414","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/21/4474/30330824/btz414.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":null,"license_id":null,"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","score":0.5099999904632568,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1348971378","display_name":null,"funder_award_id":"UL1TR00273","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G1433134892","display_name":null,"funder_award_id":"ACI-154856","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1742171491","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2206590661","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3355158854","display_name":null,"funder_award_id":"548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3709464396","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4897854425","display_name":null,"funder_award_id":"grant number ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6011066816","display_name":null,"funder_award_id":"UL1TR002733","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G6967590396","display_name":null,"funder_award_id":"UL1TR002733","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7260934811","display_name":null,"funder_award_id":"CI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8907196067","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322300","display_name":"Jilin University","ror":"https://ror.org/00js3aw79"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2945645154.pdf","grobid_xml":"https://content.openalex.org/works/W2945645154.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1593486402","https://openalex.org/W2008459449","https://openalex.org/W2043701535","https://openalex.org/W2097124003","https://openalex.org/W2102619694","https://openalex.org/W2105883975","https://openalex.org/W2108234281","https://openalex.org/W2128769815","https://openalex.org/W2143274936","https://openalex.org/W2150930396","https://openalex.org/W2170551349","https://openalex.org/W2240470164","https://openalex.org/W2529517309","https://openalex.org/W2612505479","https://openalex.org/W2784053908","https://openalex.org/W2889693843","https://openalex.org/W2897611961","https://openalex.org/W2949680846","https://openalex.org/W4232838911","https://openalex.org/W4285719527","https://openalex.org/W6635743399","https://openalex.org/W6737744342","https://openalex.org/W6754649743"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2487541429","https://openalex.org/W1910109602","https://openalex.org/W2080583581","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W2329606903","https://openalex.org/W3156493549","https://openalex.org/W3195915274","https://openalex.org/W3158976456"],"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":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2019-05-29T00:00:00"}
