{"id":"https://openalex.org/W3023043090","doi":"https://doi.org/10.1093/bioinformatics/btaa289","title":"pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies","display_name":"pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies","publication_year":2020,"publication_date":"2020-04-27","ids":{"openalex":"https://openalex.org/W3023043090","doi":"https://doi.org/10.1093/bioinformatics/btaa289","mag":"3023043090","pmid":"https://pubmed.ncbi.nlm.nih.gov/32369596"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa289","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa289","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000867120","display_name":"Caitlin M. A. Simopoulos","orcid":"https://orcid.org/0000-0001-9832-7797"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Caitlin M A Simopoulos","raw_affiliation_strings":["Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":"https://orcid.org/0000-0001-9832-7797","affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051417425","display_name":"Zhibin Ning","orcid":"https://orcid.org/0000-0003-2045-7596"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zhibin Ning","raw_affiliation_strings":["Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100437298","display_name":"Xu Zhang","orcid":"https://orcid.org/0000-0003-2406-9478"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Xu Zhang","raw_affiliation_strings":["Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043886470","display_name":"Leyuan Li","orcid":"https://orcid.org/0000-0003-2063-4441"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Leyuan Li","raw_affiliation_strings":["Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051554394","display_name":"Krystal Walker","orcid":"https://orcid.org/0000-0001-6541-9185"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Krystal Walker","raw_affiliation_strings":["Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071097577","display_name":"Mathieu Lavall\u00e9e\u2010Adam","orcid":"https://orcid.org/0000-0003-2124-3872"},"institutions":[{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mathieu Lavall\u00e9e-Adam","raw_affiliation_strings":["Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079780359","display_name":"Daniel Figeys","orcid":"https://orcid.org/0000-0002-5373-7546"},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I153718931","display_name":"University of Ottawa","ror":"https://ror.org/03c4mmv16","country_code":"CA","type":"education","lineage":["https://openalex.org/I153718931"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Daniel Figeys","raw_affiliation_strings":["Canadian Institute for Advanced Research , Toronto, ON M5G 1M1, Canada","Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Canadian Institute for Advanced Research , Toronto, ON M5G 1M1, Canada","institution_ids":["https://openalex.org/I109736498"]},{"raw_affiliation_string":"Department of Biochemistry , Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]},{"raw_affiliation_string":"Faculty of Medicine , SIMM-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada","institution_ids":["https://openalex.org/I153718931"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079780359"],"corresponding_institution_ids":["https://openalex.org/I109736498","https://openalex.org/I153718931"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.7785,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.64587798,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"14","first_page":"4171","last_page":"4179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9110000133514404,"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":0.9110000133514404,"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/T10066","display_name":"Gut microbiota and health","score":0.014800000004470348,"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":0.009800000116229057,"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/workflow","display_name":"Workflow","score":0.770168125629425},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.7166841626167297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5721744894981384},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5568552017211914},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4923824071884155},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4788248836994171},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.45931437611579895},{"id":"https://openalex.org/keywords/metaproteomics","display_name":"Metaproteomics","score":0.4114696979522705},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3046542704105377},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2877785563468933},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17378348112106323},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13471022248268127},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.10975000262260437},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08912292122840881}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.770168125629425},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.7166841626167297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5721744894981384},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5568552017211914},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4923824071884155},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4788248836994171},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.45931437611579895},{"id":"https://openalex.org/C199465337","wikidata":"https://www.wikidata.org/wiki/Q6823168","display_name":"Metaproteomics","level":4,"score":0.4114696979522705},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3046542704105377},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2877785563468933},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17378348112106323},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13471022248268127},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.10975000262260437},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08912292122840881},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"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":"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":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa289","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa289","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32369596","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32369596","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":"Journal Article"},{"id":"pmh:oai:ueaeprints.uea.ac.uk:102615","is_oa":false,"landing_page_url":"https://ueaeprints.uea.ac.uk/id/eprint/102615/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"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":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G4942729553","display_name":null,"funder_award_id":"OGI-156","funder_id":"https://openalex.org/F4320319905","funder_display_name":"Ontario Genomics Institute"}],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320319905","display_name":"Ontario Genomics Institute","ror":"https://ror.org/00c68jz96"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W265464850","https://openalex.org/W1967961065","https://openalex.org/W1984285653","https://openalex.org/W2034157397","https://openalex.org/W2045204781","https://openalex.org/W2096501714","https://openalex.org/W2097124003","https://openalex.org/W2100768052","https://openalex.org/W2102461176","https://openalex.org/W2110065044","https://openalex.org/W2110768797","https://openalex.org/W2120592477","https://openalex.org/W2128599926","https://openalex.org/W2137111266","https://openalex.org/W2140628770","https://openalex.org/W2143777796","https://openalex.org/W2146512944","https://openalex.org/W2152839556","https://openalex.org/W2155443196","https://openalex.org/W2159556209","https://openalex.org/W2159707944","https://openalex.org/W2162088497","https://openalex.org/W2179438025","https://openalex.org/W2239108612","https://openalex.org/W2286981208","https://openalex.org/W2288929640","https://openalex.org/W2315519665","https://openalex.org/W2318081520","https://openalex.org/W2415885702","https://openalex.org/W2461853012","https://openalex.org/W2465534016","https://openalex.org/W2510387023","https://openalex.org/W2526956161","https://openalex.org/W2537132940","https://openalex.org/W2553515186","https://openalex.org/W2582743722","https://openalex.org/W2588997555","https://openalex.org/W2600254651","https://openalex.org/W2734871402","https://openalex.org/W2773610445","https://openalex.org/W2780760144","https://openalex.org/W2805748438","https://openalex.org/W2808973977","https://openalex.org/W2883427056","https://openalex.org/W2889185930","https://openalex.org/W2890512197","https://openalex.org/W2899760200","https://openalex.org/W2901096493","https://openalex.org/W2901903498","https://openalex.org/W2912939143","https://openalex.org/W2952859665","https://openalex.org/W2972185270","https://openalex.org/W2972940198","https://openalex.org/W3099018540","https://openalex.org/W6725311943"],"related_works":["https://openalex.org/W4211121339","https://openalex.org/W2171309014","https://openalex.org/W1493461584","https://openalex.org/W3033457987","https://openalex.org/W1577826155","https://openalex.org/W3149998985","https://openalex.org/W125827869","https://openalex.org/W3201900227","https://openalex.org/W1983206417","https://openalex.org/W2119925477"],"abstract_inverted_index":{"MOTIVATION:":[0],"Enzymatic":[1],"digestion":[2,49],"of":[3,47,87,103],"proteins":[4,58],"before":[5],"mass":[6,28],"spectrometry":[7],"analysis":[8,86,143],"is":[9,126,149,169],"a":[10,31,79,95,110,132,155,173],"key":[11],"process":[12],"in":[13,56],"metaproteomic":[14,17,81],"workflows.":[15],"Canonical":[16],"data":[18,189],"processing":[19],"pipelines":[20],"typically":[21],"involve":[22],"matching":[23,37],"spectra":[24,33],"produced":[25],"by":[26,36],"the":[27,38,45,85],"spectrometer":[29],"to":[30,42,60,131,161],"theoretical":[32],"database,":[34],"followed":[35],"identified":[39],"peptides":[40,51],"back":[41],"parent-proteins.":[43],"However,":[44],"nature":[46],"enzymatic":[48],"produces":[50],"that":[52],"can":[53,136],"be":[54,162],"found":[55],"multiple":[57],"due":[59],"conservation":[61],"or":[62,158],"chance,":[63],"presenting":[64],"difficulties":[65],"with":[66,100,178],"protein":[67],"and":[68,105,109,128,135,152],"functional":[69],"assignment.":[70],"RESULTS:":[71],"To":[72],"combat":[73],"this":[74],"challenge,":[75],"we":[76],"developed":[77],"pepFunk,":[78],"peptide-centric":[80,124],"workflow":[82,93,125,148],"focused":[83],"on":[84],"human":[88],"gut":[89],"microbiome":[90],"samples.":[91],"Our":[92,147],"includes":[94],"curated":[96],"peptide":[97],"database":[98],"annotated":[99],"Kyoto":[101],"Encyclopedia":[102],"Genes":[104],"Genomes":[106],"(KEGG)":[107],"terms":[108],"gene":[111],"set":[112],"variation":[113],"analysis-inspired":[114],"pathway":[115],"enrichment":[116],"adapted":[117],"for":[118],"peptide-level":[119],"data.":[120,146],"Analysis":[121],"using":[122,144],"our":[123],"fast":[127],"highly":[129],"correlated":[130],"protein-centric":[133],"analysis,":[134],"identify":[137],"more":[138],"enriched":[139],"KEGG":[140],"pathways":[141],"than":[142],"protein-level":[145],"open":[150],"source":[151,159],"available":[153,170,181,191],"as":[154,172],"web":[156,174],"application":[157,175],"code":[160,180],"run":[163],"locally.":[164],"AVAILABILITY":[165],"AND":[166],"IMPLEMENTATION:":[167],"pepFunk":[168],"online":[171],"at":[176,192],"https://shiny.imetalab.ca/pepFunk/":[177],"open-source":[179],"from":[182],"https://github.com/northomics/pepFunk.":[183],"CONTACT:":[184],"dfigeys@uottawa.ca.":[185],"SUPPLEMENTARY":[186],"INFORMATION:":[187],"Supplementary":[188],"are":[190],"Bioinformatics":[193],"online.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}