{"id":"https://openalex.org/W4410227274","doi":"https://doi.org/10.1109/tcbbio.2025.3568376","title":"Autoencoder-Transformed Transcriptome Improves Genotype-Phenotype Association Studies","display_name":"Autoencoder-Transformed Transcriptome Improves Genotype-Phenotype Association Studies","publication_year":2025,"publication_date":"2025-05-09","ids":{"openalex":"https://openalex.org/W4410227274","doi":"https://doi.org/10.1109/tcbbio.2025.3568376","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811310"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3568376","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3568376","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356107/pdf/nihms-2087658.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100404194","display_name":"Qing Li","orcid":"https://orcid.org/0009-0005-1327-4347"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Qing Li","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023142373","display_name":"Jiayi Bian","orcid":"https://orcid.org/0009-0001-8873-4839"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jiayi Bian","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092041251","display_name":"Janith Weeraman","orcid":"https://orcid.org/0000-0002-3016-9582"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Janith Weeraman","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","Department of Biochemistry and Molecular Biology, University of Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353020","display_name":"Zilong Zhang","orcid":"https://orcid.org/0000-0001-9677-4059"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Zilong Zhang","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","Department of Biochemistry and Molecular Biology, University of Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032404525","display_name":"Albert Leung","orcid":"https://orcid.org/0000-0002-1614-5883"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Albert Leung","raw_affiliation_strings":["Data Science and Analytics Program, University of Calgary, Calgary, Canada","Data Science and Analytics program, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Data Science and Analytics Program, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]},{"raw_affiliation_string":"Data Science and Analytics program, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Qi-Xuan Ding","orcid":"https://orcid.org/0009-0007-0083-9921"},"institutions":[{"id":"https://openalex.org/I4210089781","display_name":"Churchill Northern Studies Centre","ror":"https://ror.org/007r8rq24","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210089781"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Qi-Xuan Ding","raw_affiliation_strings":["Sir Winston Churchill High School, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Sir Winston Churchill High School, Calgary, Canada","institution_ids":["https://openalex.org/I4210089781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045541216","display_name":"Thierry Chekouo","orcid":"https://orcid.org/0000-0002-3594-9182"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Thierry Chekouo","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041689190","display_name":"Lang Wu","orcid":"https://orcid.org/0000-0001-9938-3627"},"institutions":[{"id":"https://openalex.org/I117965899","display_name":"University of Hawai\u02bbi at M\u0101noa","ror":"https://ror.org/01wspgy28","country_code":"US","type":"education","lineage":["https://openalex.org/I117965899"]},{"id":"https://openalex.org/I1331384533","display_name":"University of Hawaii System","ror":"https://ror.org/03tzaeb71","country_code":"US","type":"education","lineage":["https://openalex.org/I1331384533"]},{"id":"https://openalex.org/I4210093646","display_name":"Cancer Center of Hawaii","ror":"https://ror.org/0065jhh26","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210093646"]},{"id":"https://openalex.org/I4390039246","display_name":"University of Hawaii Cancer Center","ror":"https://ror.org/00kt3nk56","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4390039246"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lang Wu","raw_affiliation_strings":["University of Hawaii Cancer Center, Honolulu, HI, USA","University of Hawaii Cancer Center, Honolulu, USA"],"affiliations":[{"raw_affiliation_string":"University of Hawaii Cancer Center, Honolulu, HI, USA","institution_ids":["https://openalex.org/I4210093646","https://openalex.org/I117965899","https://openalex.org/I1331384533","https://openalex.org/I4390039246"]},{"raw_affiliation_string":"University of Hawaii Cancer Center, Honolulu, USA","institution_ids":["https://openalex.org/I4210093646","https://openalex.org/I117965899","https://openalex.org/I1331384533","https://openalex.org/I4390039246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103909354","display_name":"Jun Yan","orcid":"https://orcid.org/0000-0002-9786-2170"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jun Yan","raw_affiliation_strings":["Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088751017","display_name":"Jingjing Wu","orcid":"https://orcid.org/0000-0003-4555-1490"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jingjing Wu","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","Department of Mathematics and Statistics, University of Calgary, Calgary, Alberta, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Calgary, Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075141276","display_name":"Quan Long","orcid":"https://orcid.org/0000-0003-3795-1873"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Quan Long","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5100404194"],"corresponding_institution_ids":["https://openalex.org/I168635309"],"apc_list":null,"apc_paid":null,"fwci":0.755,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.70583941,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"22","issue":"4","first_page":"1703","last_page":"1715"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8651999831199646,"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":0.8651999831199646,"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/transcriptome","display_name":"Transcriptome","score":0.7671210765838623},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.7601982355117798},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.7133990526199341},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.6275480389595032},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.5325357913970947},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5066273808479309},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4989023208618164},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41590628027915955},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32825496792793274},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23244556784629822},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.21383100748062134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16807380318641663},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09621936082839966},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.08718764781951904}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7671210765838623},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.7601982355117798},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7133990526199341},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.6275480389595032},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5325357913970947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5066273808479309},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4989023208618164},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41590628027915955},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32825496792793274},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23244556784629822},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.21383100748062134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16807380318641663},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09621936082839966},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.08718764781951904},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbbio.2025.3568376","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3568376","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811310","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12356107","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12356107","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356107/pdf/nihms-2087658.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12356107","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12356107","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12356107/pdf/nihms-2087658.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Zero hunger","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G1304196372","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G5613390209","display_name":null,"funder_award_id":"06154","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6227429296","display_name":null,"funder_award_id":"04679","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G717623787","display_name":null,"funder_award_id":"222300769","funder_id":"https://openalex.org/F4320325651","funder_display_name":"Alberta Innovates"},{"id":"https://openalex.org/G8105784103","display_name":null,"funder_award_id":"RGPIN-202","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320325651","display_name":"Alberta Innovates","ror":null},{"id":"https://openalex.org/F4320333392","display_name":"Cumming School of Medicine, University of Calgary","ror":null},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4410227274.pdf"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1502421007","https://openalex.org/W1533942137","https://openalex.org/W1767978978","https://openalex.org/W1966327575","https://openalex.org/W1970848271","https://openalex.org/W1986911601","https://openalex.org/W1993849755","https://openalex.org/W1998702086","https://openalex.org/W2030701454","https://openalex.org/W2033151532","https://openalex.org/W2068612365","https://openalex.org/W2095234911","https://openalex.org/W2105071916","https://openalex.org/W2134783591","https://openalex.org/W2144086069","https://openalex.org/W2156247618","https://openalex.org/W2264585211","https://openalex.org/W2440748762","https://openalex.org/W2537679995","https://openalex.org/W2591909999","https://openalex.org/W2736837914","https://openalex.org/W2756276968","https://openalex.org/W2761275051","https://openalex.org/W2768612689","https://openalex.org/W2807921964","https://openalex.org/W2808263729","https://openalex.org/W2914762802","https://openalex.org/W2924022225","https://openalex.org/W2950235747","https://openalex.org/W2950772595","https://openalex.org/W2951325776","https://openalex.org/W2962931338","https://openalex.org/W2975208972","https://openalex.org/W2983166786","https://openalex.org/W2997742406","https://openalex.org/W3043243920","https://openalex.org/W3100732120","https://openalex.org/W3113130833","https://openalex.org/W3128602185","https://openalex.org/W3162538759","https://openalex.org/W3173316523","https://openalex.org/W3185492931","https://openalex.org/W3204813719","https://openalex.org/W3215029602","https://openalex.org/W4223932115","https://openalex.org/W4294329053","https://openalex.org/W4310873165","https://openalex.org/W4313278096","https://openalex.org/W4385958045","https://openalex.org/W4389004796","https://openalex.org/W4389955870","https://openalex.org/W6631190155","https://openalex.org/W6757582009","https://openalex.org/W6758622098"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2566616303","https://openalex.org/W2159052453","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W2803255133","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W4386815338","https://openalex.org/W2145836866"],"abstract_inverted_index":{"Transcriptome-wide":[0],"association":[1,14],"study":[2],"(TWAS)":[3],"is":[4,21,40,85],"an":[5],"emerging":[6],"model":[7],"leveraging":[8],"gene":[9,25],"expressions":[10],"to":[11,105,183],"direct":[12],"genotype-phenotype":[13],"mapping.":[15],"A":[16],"key":[17],"component":[18],"in":[19],"TWAS":[20,193],"the":[22,49,64,93,107,121,125,140,148,156,170],"prediction":[23],"of":[24,51,66,87,135,166],"expressions;":[26],"and":[27,100,151,168,190],"many":[28,42],"statistical":[29],"approaches":[30],"have":[31,44],"been":[32],"developed":[33],"along":[34],"this":[35,56],"line.":[36],"However,":[37],"a":[38,76],"problem":[39],"that":[41,59],"genes":[43,175],"low":[45],"expression":[46,67,145],"heritability,":[47],"limiting":[48],"performance":[50,165],"any":[52],"predictive":[53],"model.":[54],"In":[55],"work,":[57],"hypothesizing":[58],"appropriate":[60],"denoising":[61],"may":[62],"improve":[63],"quality":[65],"data":[68,109,142],"(including":[69,117],"heritability),":[70],"we":[71],"propose":[72],"AE-TWAS,":[73],"which":[74],"adds":[75],"transformation":[77,84,114],"step":[78],"before":[79],"conducting":[80],"standard":[81],"TWAS.":[82,129],"The":[83,159],"composed":[86],"two":[88,132],"steps":[89],"by":[90,186],"first":[91],"splitting":[92],"whole":[94],"transcriptome":[95,108,122,141,161],"into":[96],"co-expression":[97],"networks":[98],"(modules)":[99],"then":[101],"using":[102],"autoencoder":[103],"(AE)":[104],"reconstruct":[106],"within":[110,155],"each":[111],"module.":[112],"This":[113],"removes":[115],"noise":[116],"nonlinear":[118],"ones)":[119],"from":[120],"data,":[123],"paving":[124],"path":[126],"for":[127],"downstream":[128],"We":[130],"showed":[131],"inspiring":[133],"properties":[134],"AE-TWAS:":[136],"(1)":[137],"After":[138],"transformation,":[139],"enjoy":[143],"higher":[144,153],"heritability":[146],"at":[147],"low-heritability":[149],"spectrum":[150],"possess":[152],"connectivity":[154],"modules.":[157],"(2)":[158],"transferred":[160],"indeed":[162],"enables":[163],"better":[164],"TWAS;":[167],"moreover,":[169],"newly":[171],"formed":[172],"highly":[173],"connected":[174],"(i.e.,":[176],"hub":[177],"genes)":[178],"are":[179],"more":[180],"functionally":[181],"relevant":[182],"diseases,":[184],"evidenced":[185],"their":[187],"functional":[188],"annotations":[189],"overlap":[191],"with":[192],"hits.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
