{"id":"https://openalex.org/W4413803451","doi":"https://doi.org/10.1007/s13755-025-00369-z","title":"Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence","display_name":"Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence","publication_year":2025,"publication_date":"2025-08-29","ids":{"openalex":"https://openalex.org/W4413803451","doi":"https://doi.org/10.1007/s13755-025-00369-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/40893175"},"language":"en","primary_location":{"id":"doi:10.1007/s13755-025-00369-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s13755-025-00369-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s13755-025-00369-z.pdf","source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Health Information Science and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s13755-025-00369-z.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086734911","display_name":"Jamie Canderan","orcid":"https://orcid.org/0000-0002-3079-8856"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jamie Canderan","raw_affiliation_strings":["Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408 USA","Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA"],"raw_orcid":"https://orcid.org/0000-0002-3079-8856","affiliations":[{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408 USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074353601","display_name":"Moses Stamboulian","orcid":"https://orcid.org/0000-0003-4212-0548"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Moses Stamboulian","raw_affiliation_strings":["Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408 USA","Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408 USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082620694","display_name":"Yuzhen Ye","orcid":"https://orcid.org/0000-0003-3707-3185"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuzhen Ye","raw_affiliation_strings":["Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408 USA","Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408 USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082620694"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":2790,"currency":"EUR","value_usd":3590},"apc_paid":{"value":2790,"currency":"EUR","value_usd":3590},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17307429,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":"1","first_page":"54","last_page":"54"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976999759674072,"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":0.9976999759674072,"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":0.9976000189781189,"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":0.9973999857902527,"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/metaproteomics","display_name":"Metaproteomics","score":0.9956202507019043},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6930296421051025},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.5797131657600403},{"id":"https://openalex.org/keywords/human-microbiome","display_name":"Human microbiome","score":0.5467745661735535},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.48332738876342773},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48187097907066345},{"id":"https://openalex.org/keywords/human-disease","display_name":"Human disease","score":0.4548214077949524},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4462793171405792},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.4430623948574066},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.4375772774219513},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3833238482475281},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.34024518728256226},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1541929543018341},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11145031452178955},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10780256986618042}],"concepts":[{"id":"https://openalex.org/C199465337","wikidata":"https://www.wikidata.org/wiki/Q6823168","display_name":"Metaproteomics","level":4,"score":0.9956202507019043},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6930296421051025},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5797131657600403},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.5467745661735535},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.48332738876342773},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48187097907066345},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.4548214077949524},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4462793171405792},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.4430623948574066},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4375772774219513},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3833238482475281},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34024518728256226},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1541929543018341},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11145031452178955},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10780256986618042},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1007/s13755-025-00369-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s13755-025-00369-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s13755-025-00369-z.pdf","source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Health Information Science and Systems","raw_type":"journal-article"},{"id":"pmid:40893175","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40893175","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":"Health information science and systems","raw_type":null},{"id":"pmh:oai:europepmc.org:11205110","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12397042","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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12397042","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12397042/","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":"Health Inf Sci Syst","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s13755-025-00369-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s13755-025-00369-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s13755-025-00369-z.pdf","source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Health Information Science and Systems","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5335497049","display_name":null,"funder_award_id":"2025451","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5851529313","display_name":null,"funder_award_id":"R01AI143254","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G644497182","display_name":null,"funder_award_id":"EF-2025451","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/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413803451.pdf","grobid_xml":"https://content.openalex.org/works/W4413803451.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1903013605","https://openalex.org/W1967320885","https://openalex.org/W1968164444","https://openalex.org/W1973268693","https://openalex.org/W1974062280","https://openalex.org/W2027249101","https://openalex.org/W2028673251","https://openalex.org/W2029849110","https://openalex.org/W2047275456","https://openalex.org/W2055505335","https://openalex.org/W2056499061","https://openalex.org/W2089273345","https://openalex.org/W2094375432","https://openalex.org/W2097804645","https://openalex.org/W2146512944","https://openalex.org/W2154139219","https://openalex.org/W2162088497","https://openalex.org/W2166562121","https://openalex.org/W2418997373","https://openalex.org/W2560295060","https://openalex.org/W2570173529","https://openalex.org/W2588997555","https://openalex.org/W2617316722","https://openalex.org/W2766525247","https://openalex.org/W2790856964","https://openalex.org/W2883427056","https://openalex.org/W2887633388","https://openalex.org/W2896473060","https://openalex.org/W2907574677","https://openalex.org/W2911964244","https://openalex.org/W2921716346","https://openalex.org/W2923008411","https://openalex.org/W2940938526","https://openalex.org/W2947189704","https://openalex.org/W2950438666","https://openalex.org/W2952859665","https://openalex.org/W2977130471","https://openalex.org/W2994932349","https://openalex.org/W3004781275","https://openalex.org/W3012843216","https://openalex.org/W3039863359","https://openalex.org/W3087749616","https://openalex.org/W4239510810","https://openalex.org/W4285727075","https://openalex.org/W4286685204","https://openalex.org/W4317751918","https://openalex.org/W4322739219","https://openalex.org/W4362525665","https://openalex.org/W4378574372"],"related_works":["https://openalex.org/W4211121339","https://openalex.org/W2171309014","https://openalex.org/W1493461584","https://openalex.org/W3033457987","https://openalex.org/W125827869","https://openalex.org/W2595711621","https://openalex.org/W3201900227","https://openalex.org/W1577826155","https://openalex.org/W3149998985","https://openalex.org/W2607484941"],"abstract_inverted_index":{"The":[0],"gut":[1],"microbiome":[2,16],"plays":[3],"a":[4,116],"fundamental":[5],"role":[6],"in":[7,14,194,204],"human":[8,42,51,77,133,165],"health":[9,28,43],"and":[10,17,29,44,78,87,103,115,134,158,181],"disease.":[11,45],"Individual":[12],"variations":[13],"the":[15,18,72,177],"corresponding":[19],"functional":[20],"implications":[21],"are":[22,82],"key":[23],"considerations":[24],"to":[25,130],"enhance":[26],"precision":[27],"medicine.":[30],"Metaproteomics":[31],"has":[32],"recently":[33],"revealed":[34],"protein":[35],"expression":[36],"that":[37,56,81,118,139,182],"might":[38],"be":[39,58,191],"associated":[40],"with":[41],"Existing":[46],"studies":[47],"focused":[48],"on":[49],"either":[50],"proteins":[52,55,80,104,138,159],"or":[53],"bacterial":[54,79,135,199,205],"can":[57,185],"identified":[59,101,156],"from":[60,90],"(meta)proteomics":[61],"data":[62,92,113,124,203],"sets,":[63],"but":[64,201],"not":[65],"both.":[66],"In":[67],"this":[68],"study,":[69],"we":[70,119,127,148],"examined":[71],"feasibility":[73],"of":[74,99,164],"identifying":[75],"both":[76,132],"differentially":[83,136],"expressed":[84,137],"between":[85],"healthy":[86],"diseased":[88],"individuals":[89],"metaproteomics":[91,112,123],"sets.":[93],"We":[94,150],"further":[95,192],"evaluated":[96],"different":[97],"strategies":[98],"using":[100,155],"peptides":[102,157],"for":[105,122,145,162],"building":[106],"predictive":[107,153],"models.":[108],"By":[109],"leveraging":[110],"existing":[111],"sets":[114],"tool":[117],"have":[120],"developed":[121],"analysis":[125],"(MetaProD),":[126],"were":[128],"able":[129],"derive":[131],"could":[140,190],"serve":[141],"as":[142,160],"potential":[143],"biomarkers":[144],"all":[146],"diseases":[147],"studied.":[149],"also":[151],"built":[152],"models":[154,180],"features":[161],"prediction":[163],"diseases.":[166],"Our":[167],"results":[168],"showed":[169],"peptide-based":[170],"identifications":[171,206],"over":[172],"protein-based":[173],"ones":[174],"often":[175],"produce":[176],"most":[178],"accurate":[179],"feature":[183],"selection":[184],"offer":[186],"improvements.":[187],"Prediction":[188],"accuracy":[189],"improved,":[193],"some":[195],"cases,":[196],"by":[197],"including":[198],"identifications,":[200],"missing":[202],"remains":[207],"problematic.":[208]},"counts_by_year":[],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}
