{"id":"https://openalex.org/W2152426066","doi":"https://doi.org/10.1093/bioinformatics/btr669","title":"Identification and removal of ribosomal RNA sequences from metatranscriptomes","display_name":"Identification and removal of ribosomal RNA sequences from metatranscriptomes","publication_year":2011,"publication_date":"2011-12-06","ids":{"openalex":"https://openalex.org/W2152426066","doi":"https://doi.org/10.1093/bioinformatics/btr669","mag":"2152426066","pmid":"https://pubmed.ncbi.nlm.nih.gov/22155869"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr669","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr669","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/433/48877981/bioinformatics_28_3_433.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/28/3/433/48877981/bioinformatics_28_3_433.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021759346","display_name":"Robert Schmieder","orcid":null},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]},{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert Schmieder","raw_affiliation_strings":["1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110437758","display_name":"Yan Wei Lim","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yan Wei Lim","raw_affiliation_strings":["1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I26538001"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036802114","display_name":"Robert A. Edwards","orcid":"https://orcid.org/0000-0001-8383-8949"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Edwards","raw_affiliation_strings":["1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science 2Computational Science Research Center 3Department of Biology, San Diego State University, San Diego, CA 92182 and 4Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I26538001"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021759346"],"corresponding_institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I26538001"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8014,"has_fulltext":true,"cited_by_count":225,"citation_normalized_percentile":{"value":0.91166553,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"28","issue":"3","first_page":"433","last_page":"435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9969000220298767,"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/T11482","display_name":"RNA modifications and cancer","score":0.9866999983787537,"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/computer-science","display_name":"Computer science","score":0.684887170791626},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6681460738182068},{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.6556282639503479},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5992320775985718},{"id":"https://openalex.org/keywords/ribosomal-rna","display_name":"Ribosomal RNA","score":0.5615583658218384},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4770999550819397},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4427374303340912},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35112419724464417},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32661890983581543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27469494938850403},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2721446752548218},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11163187026977539},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07908704876899719},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07121765613555908}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.684887170791626},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6681460738182068},{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.6556282639503479},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5992320775985718},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.5615583658218384},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4770999550819397},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4427374303340912},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35112419724464417},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32661890983581543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27469494938850403},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2721446752548218},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11163187026977539},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07908704876899719},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07121765613555908},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr669","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr669","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/433/48877981/bioinformatics_28_3_433.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":"pmid:22155869","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22155869","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:2273115","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3268242","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:osti.gov:1625277","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1625277","pdf_url":"https://www.osti.gov/servlets/purl/1625277","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr669","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr669","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/433/48877981/bioinformatics_28_3_433.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/17","score":0.4000000059604645,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G8278258816","display_name":"Collaborative Research:  PHANTOME:  PHage ANnotation TOols and MEthods","funder_award_id":"0850356","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"}],"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":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152426066.pdf","grobid_xml":"https://content.openalex.org/works/W2152426066.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1988925586","https://openalex.org/W1989348205","https://openalex.org/W2004548026","https://openalex.org/W2022552842","https://openalex.org/W2078361370","https://openalex.org/W2091922579","https://openalex.org/W2096525273","https://openalex.org/W2103441770","https://openalex.org/W2121180999","https://openalex.org/W2122392896","https://openalex.org/W2130682154","https://openalex.org/W2133626798","https://openalex.org/W2137597742","https://openalex.org/W2155066423","https://openalex.org/W2158088701","https://openalex.org/W2171571559","https://openalex.org/W2914037595","https://openalex.org/W4244606935","https://openalex.org/W4247053599","https://openalex.org/W6680215730"],"related_works":["https://openalex.org/W2480056510","https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2417897055","https://openalex.org/W2613359208","https://openalex.org/W2291334382","https://openalex.org/W2624709009"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":21},{"year":2017,"cited_by_count":22},{"year":2016,"cited_by_count":21},{"year":2015,"cited_by_count":19},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}