{"id":"https://openalex.org/W4390793968","doi":"https://doi.org/10.1093/bioinformatics/btae001","title":"methyLImp2: faster missing value estimation for DNA methylation data","display_name":"methyLImp2: faster missing value estimation for DNA methylation data","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4390793968","doi":"https://doi.org/10.1093/bioinformatics/btae001","pmid":"https://pubmed.ncbi.nlm.nih.gov/38213002"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae001","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae001/55520221/btae001.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae001/55520221/btae001.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084135552","display_name":"Anna Plaksienko","orcid":"https://orcid.org/0000-0001-9607-057X"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Anna Plaksienko","raw_affiliation_strings":["Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo , Oslo 0317, Norway"],"raw_orcid":"https://orcid.org/0000-0001-9607-057X","affiliations":[{"raw_affiliation_string":"Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo , Oslo 0317, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055593623","display_name":"Pietro Di Lena","orcid":"https://orcid.org/0000-0002-1838-8918"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pietro Di Lena","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Bologna , Bologna 40126, Italy"],"raw_orcid":"https://orcid.org/0000-0002-1838-8918","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Bologna , Bologna 40126, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081542076","display_name":"Christine Nardini","orcid":"https://orcid.org/0000-0001-7601-321X"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Christine Nardini","raw_affiliation_strings":["Institute for Applied Mathematics (IAC) \u201cMauro Picone\u201d, National Research Council (CNR) Rome , Rome 00185, Italy"],"raw_orcid":"https://orcid.org/0000-0001-7601-321X","affiliations":[{"raw_affiliation_string":"Institute for Applied Mathematics (IAC) \u201cMauro Picone\u201d, National Research Council (CNR) Rome , Rome 00185, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001046703","display_name":"Claudia Angelini","orcid":"https://orcid.org/0000-0001-8350-8464"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudia Angelini","raw_affiliation_strings":["Institute for Applied Mathematics (IAC) \u201cMauro Picone\u201d, National Research Council (CNR) Naples , Naples 80131, Italy"],"raw_orcid":"https://orcid.org/0000-0001-8350-8464","affiliations":[{"raw_affiliation_string":"Institute for Applied Mathematics (IAC) \u201cMauro Picone\u201d, National Research Council (CNR) Naples , Naples 80131, Italy","institution_ids":["https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5084135552"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.8682,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.84664764,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"40","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.8529999852180481,"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":0.8529999852180481,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.020600000396370888,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.015300000086426735,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/bioconductor","display_name":"Bioconductor","score":0.8852015733718872},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.8229146003723145},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7884618639945984},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.7778711915016174},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5498573184013367},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5226185917854309},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3147665560245514},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.17333462834358215},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08926579356193542}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8852015733718872},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.8229146003723145},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7884618639945984},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.7778711915016174},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5498573184013367},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5226185917854309},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3147665560245514},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.17333462834358215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08926579356193542},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae001","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae001/55520221/btae001.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38213002","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38213002","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:cris.unibo.it:11585/962579","is_oa":true,"landing_page_url":"https://academic.oup.com/bioinformatics/article/40/1/btae001/7517106","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/1/btae001/56664429/btae001.pdf","source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10826905","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10826905","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10826905/pdf/btae001.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae001","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae001","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae001/55520221/btae001.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G5081903167","display_name":null,"funder_award_id":"216137","funder_id":"https://openalex.org/F4320310758","funder_display_name":"Kreftforeningen"},{"id":"https://openalex.org/G5451116430","display_name":"individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology","funder_award_id":"826121","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320310758","display_name":"Kreftforeningen","ror":"https://ror.org/01925vb10"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390793968.pdf"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1968930562","https://openalex.org/W2101870168","https://openalex.org/W2915194834","https://openalex.org/W3037029383","https://openalex.org/W3123418868"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W2055961818","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549"],"abstract_inverted_index":{"MOTIVATION:":[0],"methyLImp,":[1],"a":[2,79,104,110],"method":[3],"we":[4,77,101],"recently":[5],"introduced":[6,103],"for":[7,115,145],"the":[8,25,68,88,113,116,122],"missing":[9,45],"value":[10],"estimation":[11],"of":[12,40,83,112],"DNA":[13],"methylation":[14],"data,":[15],"has":[16],"demonstrated":[17],"competitive":[18],"performance":[19],"in":[20,38,93,132],"data":[21],"imputation":[22,30],"compared":[23],"to":[24,97,127],"existing,":[26],"general-purpose,":[27],"approaches.":[28],"However,":[29],"running":[31,70,123],"time":[32,71,124],"was":[33],"considerably":[34],"long":[35],"and":[36],"unfeasible":[37],"case":[39],"large":[41,99,133],"datasets":[42],"with":[43],"numerous":[44],"values.":[46],"RESULTS:":[47],"methyLImp2":[48,141],"made":[49],"possible":[50],"computations":[51],"that":[52,64,107],"were":[53],"previously":[54],"unfeasible.":[55],"We":[56],"achieved":[57],"this":[58],"by":[59,90],"introducing":[60],"two":[61],"important":[62],"modifications":[63],"have":[65],"significantly":[66],"reduced":[67,87],"original":[69],"without":[72],"sacrificing":[73],"prediction":[74],"performance.":[75],"First,":[76],"implemented":[78],"chromosome-wise":[80],"parallel":[81],"version":[82],"methyLImp.":[84],"This":[85],"parallelization":[86],"runtime":[89],"several":[91],"10-fold":[92],"our":[94],"experiments.":[95],"Then,":[96],"handle":[98],"datasets,":[100],"also":[102],"mini-batch":[105],"approach":[106],"uses":[108],"only":[109],"subset":[111],"samples":[114],"imputation.":[117],"Thus,":[118],"it":[119],"further":[120],"reduces":[121],"from":[125],"days":[126],"hours":[128],"or":[129],"even":[130],"minutes":[131],"datasets.":[134],"AVAILABILITY":[135],"AND":[136],"IMPLEMENTATION:":[137],"The":[138],"R":[139],"package":[140],"is":[142,148],"under":[143],"review":[144],"Bioconductor.":[146],"It":[147],"currently":[149],"freely":[150],"available":[151],"on":[152],"Github":[153],"https://github.com/annaplaksienko/methyLImp2.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-11T18:08:03.149640","created_date":"2025-10-10T00:00:00"}