{"id":"https://openalex.org/W2097815349","doi":"https://doi.org/10.1093/bioinformatics/btv340","title":"A note on the false discovery rate of novel peptides in proteogenomics","display_name":"A note on the false discovery rate of novel peptides in proteogenomics","publication_year":2015,"publication_date":"2015-06-14","ids":{"openalex":"https://openalex.org/W2097815349","doi":"https://doi.org/10.1093/bioinformatics/btv340","mag":"2097815349","pmid":"https://pubmed.ncbi.nlm.nih.gov/26076724"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3249/49035577/bioinformatics_31_20_3249.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/31/20/3249/49035577/bioinformatics_31_20_3249.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100342359","display_name":"Kun Zhang","orcid":"https://orcid.org/0000-0002-7596-5224"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kun Zhang","raw_affiliation_strings":["1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","2 University of Chinese Academy of Sciences, Beijing 100049,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"raw_affiliation_string":"2 University of Chinese Academy of Sciences, Beijing 100049,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110082043","display_name":"Yan Fu","orcid":"https://orcid.org/0000-0001-6896-5931"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yan Fu","raw_affiliation_strings":["3 National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 and","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033490134","display_name":"Wenfeng Zeng","orcid":"https://orcid.org/0000-0002-4725-9541"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen-Feng Zeng","raw_affiliation_strings":["1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","2 University of Chinese Academy of Sciences, Beijing 100049,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"raw_affiliation_string":"2 University of Chinese Academy of Sciences, Beijing 100049,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101939666","display_name":"Kun He","orcid":"https://orcid.org/0000-0002-0828-0794"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kun He","raw_affiliation_strings":["1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","2 University of Chinese Academy of Sciences, Beijing 100049,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"raw_affiliation_string":"2 University of Chinese Academy of Sciences, Beijing 100049,","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054261613","display_name":"Hao Chi","orcid":"https://orcid.org/0000-0002-7898-2599"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Chi","raw_affiliation_strings":["1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100728204","display_name":"Chao Liu","orcid":"https://orcid.org/0000-0002-5286-6944"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Liu","raw_affiliation_strings":["1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064351041","display_name":"Yanchang Li","orcid":"https://orcid.org/0000-0002-4177-3726"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan-Chang Li","raw_affiliation_strings":["4 State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040035637","display_name":"Yuan Gao","orcid":"https://orcid.org/0000-0002-9510-6515"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Gao","raw_affiliation_strings":["4 State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089378821","display_name":"Ping Xu","orcid":"https://orcid.org/0000-0002-0628-6981"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ping Xu","raw_affiliation_strings":["4 State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100695089","display_name":"Si\u2010Min He","orcid":"https://orcid.org/0000-0002-2434-7194"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Si-Min He","raw_affiliation_strings":["1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190,","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5089378821","https://openalex.org/A5100695089","https://openalex.org/A5110082043"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176","https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210149540"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.1414,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.86440983,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"20","first_page":"3249","last_page":"3253"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.3433000147342682,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.3433000147342682,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.12939999997615814,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.09179999679327011,"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/proteogenomics","display_name":"Proteogenomics","score":0.95340895652771},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.8434966802597046},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.8107966184616089},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5840510725975037},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5295751094818115},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5024077892303467},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49301788210868835},{"id":"https://openalex.org/keywords/false-positive-rate","display_name":"False positive rate","score":0.4367210566997528},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38658636808395386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2530888319015503},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19691967964172363},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1886885166168213},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.1812014877796173}],"concepts":[{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.95340895652771},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.8434966802597046},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.8107966184616089},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5840510725975037},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5295751094818115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5024077892303467},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49301788210868835},{"id":"https://openalex.org/C95922358","wikidata":"https://www.wikidata.org/wiki/Q5432725","display_name":"False positive rate","level":2,"score":0.4367210566997528},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38658636808395386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2530888319015503},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19691967964172363},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1886885166168213},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.1812014877796173}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3249/49035577/bioinformatics_31_20_3249.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:26076724","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26076724","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:3576051","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4595894","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:open-archive.highwire.org:bioinfo:31/20/3249","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/20/3249","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/20/3249/49035577/bioinformatics_31_20_3249.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":[{"score":0.75,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1997509288","https://openalex.org/W1999647786","https://openalex.org/W2021653707","https://openalex.org/W2026433130","https://openalex.org/W2053943711","https://openalex.org/W2056499061","https://openalex.org/W2079563665","https://openalex.org/W2096057003","https://openalex.org/W2098354599","https://openalex.org/W2113620105","https://openalex.org/W2114882995","https://openalex.org/W2117217503","https://openalex.org/W2131856634","https://openalex.org/W2139578623","https://openalex.org/W2158302225","https://openalex.org/W2162690609","https://openalex.org/W2314880009","https://openalex.org/W4247610414","https://openalex.org/W4365787616"],"related_works":["https://openalex.org/W2020413892","https://openalex.org/W2128909276","https://openalex.org/W2097815349","https://openalex.org/W1991225657","https://openalex.org/W1825621501","https://openalex.org/W101962219","https://openalex.org/W256699647","https://openalex.org/W2389124870","https://openalex.org/W2093463665","https://openalex.org/W2102122784"],"abstract_inverted_index":{"MOTIVATION:":[0],"Proteogenomics":[1],"has":[2,37],"been":[3,38],"well":[4],"accepted":[5],"as":[6],"a":[7,18,89],"tool":[8],"to":[9,25],"discover":[10],"novel":[11,33,48,78,100],"genes.":[12],"In":[13],"most":[14],"conventional":[15],"proteogenomic":[16],"studies,":[17],"global":[19],"false":[20,28,45,72],"discovery":[21,73],"rate":[22],"is":[23,50,91],"used":[24],"filter":[26],"out":[27,52],"positives":[29,46],"for":[30,58],"identifying":[31],"credible":[32],"peptides.":[34,79,101],"However,":[35],"it":[36],"found":[39],"that":[40,83],"the":[41,70,84,92,96],"actual":[42],"level":[43],"of":[44,53,75,88,99,108],"in":[47],"peptides":[49],"often":[51],"control":[54],"and":[55,77,111],"behaves":[56],"differently":[57],"different":[59],"genomes.":[60],"RESULTS:":[61],"To":[62],"quantitatively":[63],"model":[64],"this":[65],"problem,":[66],"we":[67],"theoretically":[68],"analyze":[69],"subgroup":[71,97],"rates":[74],"annotated":[76],"Our":[80],"analysis":[81],"shows":[82],"annotation":[85],"completeness":[86],"ratio":[87],"genome":[90],"dominant":[93],"factor":[94],"influencing":[95],"FDR":[98],"Experimental":[102],"results":[103],"on":[104],"two":[105],"real":[106],"datasets":[107],"Escherichia":[109],"coli":[110],"Mycobacterium":[112],"tuberculosis":[113],"support":[114],"our":[115],"conjecture.":[116],"CONTACT:":[117],"yfu@amss.ac.cn":[118],"or":[119,121],"xupingghy@gmail.com":[120],"smhe@ict.ac.cn":[122],"SUPPLEMENTARY":[123],"INFORMATION:":[124],"Supplementary":[125],"data":[126],"are":[127],"available":[128],"at":[129],"Bioinformatics":[130],"online.":[131]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
