{"id":"https://openalex.org/W2102624675","doi":"https://doi.org/10.1093/bioinformatics/btt077","title":"Protein signature-based estimation of metagenomic abundances including all domains of life and viruses","display_name":"Protein signature-based estimation of metagenomic abundances including all domains of life and viruses","publication_year":2013,"publication_date":"2013-02-15","ids":{"openalex":"https://openalex.org/W2102624675","doi":"https://doi.org/10.1093/bioinformatics/btt077","mag":"2102624675","pmid":"https://pubmed.ncbi.nlm.nih.gov/23418187"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/973/48899418/bioinformatics_29_8_973.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/29/8/973/48899418/bioinformatics_29_8_973.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016679823","display_name":"Heiner Klingenberg","orcid":null},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Heiner Klingenberg","raw_affiliation_strings":["Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010248276","display_name":"Kathrin Petra A\u00dfhauer","orcid":null},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kathrin Petra A\u00dfhauer","raw_affiliation_strings":["Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076561076","display_name":"Thomas Lingner","orcid":null},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Lingner","raw_affiliation_strings":["Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030195753","display_name":"Peter Meinicke","orcid":"https://orcid.org/0009-0002-2228-3403"},"institutions":[{"id":"https://openalex.org/I74656192","display_name":"University of G\u00f6ttingen","ror":"https://ror.org/01y9bpm73","country_code":"DE","type":"education","lineage":["https://openalex.org/I74656192"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Peter Meinicke","raw_affiliation_strings":["Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute for Microbiology and Genetics, University of G\u00f6ttingen, 37077 G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I74656192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5030195753"],"corresponding_institution_ids":["https://openalex.org/I74656192"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.0756,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.93199812,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"29","issue":"8","first_page":"973","last_page":"980"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.5803999900817871,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.5803999900817871,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.27090001106262207,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.038600001484155655,"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":0.8443790674209595},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.8436546325683594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6007184386253357},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.5637959241867065},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5135853290557861},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5035354495048523},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.4706931412220001},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.4610513746738434},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35160866379737854},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3459808826446533},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2993597984313965},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10962307453155518},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1005888283252716}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8443790674209595},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.8436546325683594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6007184386253357},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.5637959241867065},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5135853290557861},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5035354495048523},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.4706931412220001},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.4610513746738434},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35160866379737854},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3459808826446533},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2993597984313965},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10962307453155518},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1005888283252716},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019641","descriptor_name":"DNA, Archaeal","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D019641","descriptor_name":"DNA, Archaeal","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D019641","descriptor_name":"DNA, Archaeal","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/973/48899418/bioinformatics_29_8_973.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:23418187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23418187","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:2625529","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3624802","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3624802","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3624802","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/8/973/48899418/bioinformatics_29_8_973.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":0.5099999904632568}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2102624675.pdf","grobid_xml":"https://content.openalex.org/works/W2102624675.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1936995073","https://openalex.org/W1989348205","https://openalex.org/W2000589358","https://openalex.org/W2002160484","https://openalex.org/W2013544175","https://openalex.org/W2029437806","https://openalex.org/W2031842324","https://openalex.org/W2040486579","https://openalex.org/W2048818637","https://openalex.org/W2049633694","https://openalex.org/W2052118501","https://openalex.org/W2055043387","https://openalex.org/W2069689025","https://openalex.org/W2116895571","https://openalex.org/W2118129812","https://openalex.org/W2123837003","https://openalex.org/W2128124531","https://openalex.org/W2128769815","https://openalex.org/W2131026689","https://openalex.org/W2135621733","https://openalex.org/W2140604849","https://openalex.org/W2141885858","https://openalex.org/W2147618390","https://openalex.org/W2149205772","https://openalex.org/W2153138305","https://openalex.org/W2153990926","https://openalex.org/W2157380302","https://openalex.org/W2159788862","https://openalex.org/W2166278306","https://openalex.org/W2170196186","https://openalex.org/W2171571559","https://openalex.org/W2914037595","https://openalex.org/W2914081640","https://openalex.org/W4210623056"],"related_works":["https://openalex.org/W2391004329","https://openalex.org/W1968369492","https://openalex.org/W2043102924","https://openalex.org/W2995607319","https://openalex.org/W1222064643","https://openalex.org/W2761818597","https://openalex.org/W2624135745","https://openalex.org/W1543301402","https://openalex.org/W2315403509","https://openalex.org/W3139084279"],"abstract_inverted_index":{"MOTIVATION:":[0],"Metagenome":[1],"analysis":[2,98,142],"requires":[3],"tools":[4],"that":[5,92],"can":[6],"estimate":[7,166],"the":[8,16,30,60,110,113,124,130,146,152,168],"taxonomic":[9,47,88],"abundances":[10,121],"in":[11,46],"anonymous":[12],"sequence":[13],"data":[14,31,108,144],"over":[15],"whole":[17],"range":[18],"of":[19,37,63,90,99,112,129,143,154,167],"biological":[20],"entities.":[21],"Because":[22],"there":[23],"is":[24,54,93,177],"usually":[25],"no":[26],"prior":[27],"knowledge":[28],"about":[29],"composition,":[32],"not":[33,74],"only":[34],"all":[35],"domains":[36],"life":[38],"but":[39],"also":[40],"viruses":[41,71],"have":[42],"to":[43,56,59,87],"be":[44],"included":[45],"profiling.":[48],"Such":[49],"a":[50,84,140,158,164],"full-range":[51],"approach,":[52],"however,":[53],"difficult":[55],"realize":[57],"owing":[58],"limited":[61],"coverage":[62],"available":[64,178],"reference":[65],"data.":[66],"In":[67],"particular,":[68],"archaea":[69],"and":[70,106,122],"are":[72],"generally":[73],"well":[75],"represented":[76],"by":[77],"current":[78],"genome":[79],"databases.":[80],"RESULTS:":[81],"We":[82],"introduce":[83],"novel":[85],"approach":[86],"profiling":[89,127,161],"metagenomes":[91],"based":[94],"on":[95,104],"mixture":[96,132],"model":[97],"protein":[100],"signatures.":[101],"Our":[102],"results":[103],"simulated":[105],"real":[107],"reveal":[109],"difficulties":[111],"existing":[114],"methods":[115],"when":[116],"measuring":[117],"achaeal":[118],"or":[119],"viral":[120],"show":[123],"overall":[125],"good":[126],"performance":[128],"protein-based":[131],"model.":[133],"As":[134],"an":[135],"application":[136],"example,":[137],"we":[138],"provide":[139],"large-scale":[141],"from":[145],"Human":[147],"Microbiome":[148],"Project.":[149],"This":[150],"demonstrates":[151],"utility":[153],"our":[155],"method":[156],"as":[157],"first":[159],"instance":[160],"tool":[162],"for":[163],"fast":[165],"community":[169],"structure.":[170],"AVAILABILITY:":[171],"http://gobics.de/TaxyPro.":[172],"SUPPLEMENTARY":[173],"INFORMATION:":[174],"Supplementary":[175],"Material":[176],"at":[179],"Bioinformatics":[180],"online.":[181]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
