{"id":"https://openalex.org/W4393945009","doi":"https://doi.org/10.3389/fbinf.2024.1329144","title":"BayesAge: A maximum likelihood algorithm to predict epigenetic age","display_name":"BayesAge: A maximum likelihood algorithm to predict epigenetic age","publication_year":2024,"publication_date":"2024-04-04","ids":{"openalex":"https://openalex.org/W4393945009","doi":"https://doi.org/10.3389/fbinf.2024.1329144","pmid":"https://pubmed.ncbi.nlm.nih.gov/38638123"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1329144","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1329144","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1329144/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1329144/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092919253","display_name":"Lajoyce Mboning","orcid":"https://orcid.org/0009-0004-5047-5351"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lajoyce Mboning","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110849356","display_name":"Liudmilla Rubbi","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liudmilla Rubbi","raw_affiliation_strings":["Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA, United States","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076956740","display_name":"Michael J. Thompson","orcid":"https://orcid.org/0000-0002-2914-1080"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Thompson","raw_affiliation_strings":["Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA, United States","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053925403","display_name":"Louis\u2010S. Bouchard","orcid":"https://orcid.org/0000-0003-4151-5628"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Louis-S. Bouchard","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, United States","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011670317","display_name":"Matteo Pellegrini","orcid":"https://orcid.org/0000-0001-9355-9564"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matteo Pellegrini","raw_affiliation_strings":["Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular, Cell and Developmental Biology, University of Los Angeles, Los Angeles, CA, United States","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5092919253"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":{"value":2125,"currency":"USD","value_usd":2125},"apc_paid":{"value":2125,"currency":"USD","value_usd":2125},"fwci":1.0972,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.7504295,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"4","issue":null,"first_page":"1329144","last_page":"1329144"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5917404890060425},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.5710124373435974},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5262945294380188},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.5150134563446045},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.514800488948822},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.5076550245285034},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.4958432614803314},{"id":"https://openalex.org/keywords/covariate","display_name":"Covariate","score":0.4553535282611847},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43495744466781616},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.42547282576560974},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4190123975276947},{"id":"https://openalex.org/keywords/count-data","display_name":"Count data","score":0.41505929827690125},{"id":"https://openalex.org/keywords/regression-analysis","display_name":"Regression analysis","score":0.4143007695674896},{"id":"https://openalex.org/keywords/linear-regression","display_name":"Linear regression","score":0.4139474332332611},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35940849781036377},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3303520083427429},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.324795663356781},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.30352672934532166},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2999267578125},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2083190679550171}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5917404890060425},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5710124373435974},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5262945294380188},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.5150134563446045},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.514800488948822},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.5076550245285034},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.4958432614803314},{"id":"https://openalex.org/C119043178","wikidata":"https://www.wikidata.org/wiki/Q320723","display_name":"Covariate","level":2,"score":0.4553535282611847},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43495744466781616},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.42547282576560974},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4190123975276947},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.41505929827690125},{"id":"https://openalex.org/C152877465","wikidata":"https://www.wikidata.org/wiki/Q208042","display_name":"Regression analysis","level":2,"score":0.4143007695674896},{"id":"https://openalex.org/C48921125","wikidata":"https://www.wikidata.org/wiki/Q10861030","display_name":"Linear regression","level":2,"score":0.4139474332332611},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35940849781036377},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3303520083427429},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.324795663356781},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30352672934532166},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2999267578125},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2083190679550171},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2024.1329144","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1329144","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1329144/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38638123","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38638123","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11024280","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11024280","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11024280/pdf/fbinf-04-1329144.pdf","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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c665913c2e3a4f788a07405cdbdc8d73","is_oa":true,"landing_page_url":"https://doaj.org/article/c665913c2e3a4f788a07405cdbdc8d73","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1329144","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1329144","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2024.1329144/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2355553396","display_name":null,"funder_award_id":"T32\u2010HG002536","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4393945009.pdf","grobid_xml":"https://content.openalex.org/works/W4393945009.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1974047233","https://openalex.org/W2036897871","https://openalex.org/W2108234281","https://openalex.org/W2121091193","https://openalex.org/W2152656267","https://openalex.org/W2158503648","https://openalex.org/W2912654909","https://openalex.org/W2949100461","https://openalex.org/W2952093052","https://openalex.org/W3037895933","https://openalex.org/W3046503173","https://openalex.org/W3105112072","https://openalex.org/W3160819488","https://openalex.org/W3192224792","https://openalex.org/W4206540351","https://openalex.org/W4280632677"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W4312407344","https://openalex.org/W2894289927"],"abstract_inverted_index":{"Introduction:":[0],"DNA":[1,78],"methylation,":[2],"specifically":[3],"the":[4,9,71,144,225],"formation":[5],"of":[6,12,70,135,146,162,227,237],"5-methylcytosine":[7],"at":[8],"C5":[10],"position":[11],"cytosine,":[13],"undergoes":[14],"reproducible":[15],"changes":[16],"as":[17,22],"organisms":[18],"age,":[19,37],"establishing":[20],"it":[21],"a":[23,131,159,179,233],"significant":[24],"biomarker":[25],"in":[26,50,182,210],"aging":[27,239],"studies.":[28],"Epigenetic":[29],"clocks,":[30],"which":[31],"integrate":[32],"methylation":[33,79],"patterns":[34],"to":[35,100,120,154,170,220,232],"predict":[36],"often":[38],"employ":[39],"linear":[40],"models":[41,90],"based":[42],"on":[43,149],"penalized":[44,174],"regression,":[45],"yet":[46],"they":[47],"encounter":[48],"challenges":[49,188],"handling":[51],"missing":[52],"data,":[53,57,156,203],"count-based":[54,202],"bisulfite":[55,111,215],"sequence":[56],"and":[58,96,166,173,198,208],"interpretation.":[59],"Methods:":[60],"To":[61],"address":[62],"these":[63],"limitations,":[64],"we":[65],"introduce":[66],"BayesAge,":[67],"an":[68],"extension":[69],"scAge":[72,172],"methodology":[73],"originally":[74],"designed":[75],"for":[76,87,109,201],"single-cell":[77],"analysis.":[80],"BayesAge":[81,115,142,157,177,204],"employs":[82],"maximum":[83],"likelihood":[84],"estimation":[85,145],"(MLE)":[86],"age":[88,124,128,137,150,184,212,228],"inference,":[89,229],"count":[91],"data":[92],"using":[93],"binomial":[94],"distributions,":[95],"incorporates":[97],"LOWESS":[98],"smoothing":[99],"capture":[101],"non-linear":[102],"methylation-age":[103],"dynamics.":[104],"This":[105],"approach":[106],"is":[107],"tailored":[108,199],"bulk":[110,214],"sequencing":[112,216],"datasets.":[113,217],"Results:":[114],"demonstrates":[116],"superior":[117],"performance":[118],"compared":[119,169],"scAge.":[121],"Notably,":[122],"its":[123],"residuals":[125],"exhibit":[126],"no":[127],"association,":[129],"offering":[130],"less":[132],"biased":[133],"representation":[134],"epigenetic":[136,183,238],"variation":[138],"across":[139],"populations.":[140],"Furthermore,":[141],"facilitates":[143],"error":[147,222],"bounds":[148,223],"inference.":[151],"When":[152],"applied":[153],"down-sampled":[155],"achieves":[158],"higher":[160],"coefficient":[161],"determination":[163],"between":[164],"predicted":[165],"actual":[167],"ages":[168],"both":[171],"regression.":[175],"Discussion:":[176],"presents":[178],"promising":[180],"advancement":[181],"prediction,":[185],"addressing":[186],"key":[187],"encountered":[189],"by":[190],"existing":[191],"models.":[192],"By":[193],"integrating":[194],"robust":[195],"statistical":[196],"techniques":[197],"methodologies":[200],"offers":[205],"improved":[206],"accuracy":[207],"interpretability":[209],"predicting":[211],"from":[213],"Its":[218],"ability":[219],"estimate":[221],"enhances":[224],"reliability":[226],"thereby":[230],"contributing":[231],"more":[234],"comprehensive":[235],"understanding":[236],"processes.":[240]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}