{"id":"https://openalex.org/W4410765055","doi":"https://doi.org/10.32614/rj-2024-012","title":"LUCIDus: An R Package For Implementing Latent Unknown Clustering By Integrating Multi-omics Data (LUCID) With Phenotypic Traits","display_name":"LUCIDus: An R Package For Implementing Latent Unknown Clustering By Integrating Multi-omics Data (LUCID) With Phenotypic Traits","publication_year":2025,"publication_date":"2025-03-11","ids":{"openalex":"https://openalex.org/W4410765055","doi":"https://doi.org/10.32614/rj-2024-012"},"language":"en","primary_location":{"id":"doi:10.32614/rj-2024-012","is_oa":true,"landing_page_url":"https://doi.org/10.32614/rj-2024-012","pdf_url":"https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf","source":{"id":"https://openalex.org/S2489169438","display_name":"The R Journal","issn_l":"2073-4859","issn":["2073-4859"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The R Journal","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102172394","display_name":"Yinqi Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinqi Zhao","raw_affiliation_strings":["Division of Biostatistics, Department of Population and Public Health\nSciences, University of Southern California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, Department of Population and Public Health\nSciences, University of Southern California","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113084535","display_name":"Qiran Jia","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiran Jia","raw_affiliation_strings":["Division of Biostatistics, Department of Population and Public Health\nSciences, University of Southern California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, Department of Population and Public Health\nSciences, University of Southern California","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059276203","display_name":"Jesse A. Goodrich","orcid":"https://orcid.org/0000-0001-6615-0472"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jesse A. Goodrich","raw_affiliation_strings":["Division of Environmental Epidemiology, Department of Population and\nPublic Health Sciences, University of Southern California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Environmental Epidemiology, Department of Population and\nPublic Health Sciences, University of Southern California","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114236786","display_name":"David V. Conti","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David V. Conti","raw_affiliation_strings":["Division of Biostatistics, Department of Population and Public Health\nSciences, University of Southern California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, Department of Population and Public Health\nSciences, University of Southern California","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":null,"apc_paid":null,"fwci":0.4868,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.62878569,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"16","issue":"2","first_page":"4","last_page":"27"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9768000245094299,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9768000245094299,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9757000207901001,"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/phenotype","display_name":"Phenotype","score":0.5426064729690552},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5281676650047302},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47482427954673767},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41753771901130676},{"id":"https://openalex.org/keywords/lucid-dream","display_name":"Lucid dream","score":0.4166918694972992},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4107890725135803},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3114360570907593},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16928565502166748},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15634912252426147},{"id":"https://openalex.org/keywords/food-science","display_name":"Food science","score":0.06798982620239258},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.05606117844581604}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5426064729690552},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5281676650047302},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47482427954673767},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41753771901130676},{"id":"https://openalex.org/C139058780","wikidata":"https://www.wikidata.org/wiki/Q181078","display_name":"Lucid dream","level":4,"score":0.4166918694972992},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4107890725135803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3114360570907593},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16928565502166748},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15634912252426147},{"id":"https://openalex.org/C31903555","wikidata":"https://www.wikidata.org/wiki/Q1637030","display_name":"Food science","level":1,"score":0.06798982620239258},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.05606117844581604},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C2992468417","wikidata":"https://www.wikidata.org/wiki/Q271098","display_name":"Ganoderma lucidum","level":2,"score":0.0},{"id":"https://openalex.org/C2776618520","wikidata":"https://www.wikidata.org/wiki/Q1799774","display_name":"Ganoderma","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.32614/rj-2024-012","is_oa":true,"landing_page_url":"https://doi.org/10.32614/rj-2024-012","pdf_url":"https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf","source":{"id":"https://openalex.org/S2489169438","display_name":"The R Journal","issn_l":"2073-4859","issn":["2073-4859"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The R Journal","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.32614/rj-2024-012","is_oa":true,"landing_page_url":"https://doi.org/10.32614/rj-2024-012","pdf_url":"https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf","source":{"id":"https://openalex.org/S2489169438","display_name":"The R Journal","issn_l":"2073-4859","issn":["2073-4859"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The R Journal","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410765055.pdf","grobid_xml":"https://content.openalex.org/works/W4410765055.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1727290854","https://openalex.org/W1975120776","https://openalex.org/W1987219048","https://openalex.org/W2005895632","https://openalex.org/W2023461603","https://openalex.org/W2047708805","https://openalex.org/W2060842569","https://openalex.org/W2065342065","https://openalex.org/W2065760681","https://openalex.org/W2082503527","https://openalex.org/W2097879961","https://openalex.org/W2108435369","https://openalex.org/W2110272025","https://openalex.org/W2116662982","https://openalex.org/W2124061292","https://openalex.org/W2138019504","https://openalex.org/W2138649409","https://openalex.org/W2141599838","https://openalex.org/W2144664383","https://openalex.org/W2147606185","https://openalex.org/W2396849069","https://openalex.org/W2460637143","https://openalex.org/W2474105078","https://openalex.org/W2529746041","https://openalex.org/W2588477357","https://openalex.org/W2726396617","https://openalex.org/W2776619248","https://openalex.org/W2794407793","https://openalex.org/W2884724578","https://openalex.org/W2900760305","https://openalex.org/W2909472027","https://openalex.org/W2920925479","https://openalex.org/W2955363178","https://openalex.org/W2971047517","https://openalex.org/W2985102732","https://openalex.org/W2994283242","https://openalex.org/W3003192283","https://openalex.org/W3046288231","https://openalex.org/W3142716389","https://openalex.org/W3151630303","https://openalex.org/W3207389580","https://openalex.org/W6638995540","https://openalex.org/W6728990032","https://openalex.org/W6869299415"],"related_works":["https://openalex.org/W2996253900","https://openalex.org/W2031063778","https://openalex.org/W2476830224","https://openalex.org/W2003878696","https://openalex.org/W2621024742","https://openalex.org/W2269593430","https://openalex.org/W3012948126","https://openalex.org/W1553123381","https://openalex.org/W4407590498","https://openalex.org/W4396832677"],"abstract_inverted_index":{"Many":[0],"studies":[1,44],"are":[2,17,43,142,156],"leveraging":[3],"current":[4],"technologies":[5],"to":[6,54,61,93,114,131,145,174,222],"obtain":[7],"multiple":[8,120],"omics":[9,121],"measurements":[10,16,53],"on":[11,27,211],"the":[12,49,115,146,176,181,185,189,215,224],"same":[13],"individuals.":[14],"These":[15],"usually":[18],"cross-sectional,":[19],"and":[20,23,37,103,148,187,200],"methods":[21],"developed":[22],"commonly":[24],"used":[25],"focus":[26],"omic":[28,105,129],"integration":[29,126,136,150],"at":[30],"a":[31,38,160,205],"single":[32],"time":[33],"point.":[34],"More":[35],"unique,":[36],"growing":[39],"area":[40],"of":[41,52,97,111,117,124,128,139,153,184,191],"interest,":[42],"that":[45,67,141,155],"leverage":[46],"biology":[47],"or":[48,58,100],"temporal":[50],"sequence":[51],"relate":[55],"long-term":[56],"exposures":[57,99],"germline":[59,101],"genetics":[60,102],"intermediate":[62,135],"measures":[63],"capturing":[64],"transitional":[65],"processes":[66],"ultimately":[68],"result":[69],"in":[70],"an":[71,80,171,212],"outcome.":[72],"In":[73,163],"this":[74,164],"context,":[75],"we":[76,166,203],"have":[77],"previously":[78],"introduced":[79],"integrative":[81],"model":[82,186,194,196],"named":[83],"Latent":[84],"Unknown":[85],"Clustering":[86],"by":[87,159],"Integrating":[88],"multi-omics":[89],"Data":[90],"(LUCID)":[91],"aiming":[92],"distinguish":[94],"unique":[95],"effects":[96,106],"environmental":[98],"informative":[104],"while":[107],"jointly":[108],"estimating":[109],"subgroups":[110,140,154],"individuals":[112],"relevant":[113],"outcome":[116],"interest.":[118],"This":[119],"analysis":[122],"consists":[123],"early":[125],"(concatenation":[127],"layers":[130],"estimate":[132],"common":[133],"subgroups);":[134],"(omic-layer-specific":[137,151],"estimation":[138,152],"all":[143],"related":[144],"outcome);":[147],"late":[149],"then":[157],"interrelated":[158],"priori":[161],"structures).":[162],"article,":[165],"introduce":[167,188],"LUCIDus":[168],"version":[169],"3,":[170],"R":[172],"package":[173],"implement":[175],"LUCID":[177],"model.":[178],"We":[179],"review":[180],"statistical":[182],"background":[183],"workflow":[190],"LUCIDus,":[192],"including":[193],"fitting,":[195],"selection,":[197],"interpretation,":[198],"inference,":[199],"prediction.":[201],"Throughout,":[202],"use":[204],"realistic":[206],"but":[207],"simulated":[208],"dataset":[209],"based":[210],"ongoing":[213],"study,":[214],"Human":[216],"Early":[217],"Life":[218],"Exposome":[219],"Study":[220],"(HELIX),":[221],"illustrate":[223],"workflow.":[225]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}