{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T02:33:44Z","timestamp":1772159624215,"version":"3.50.1"},"reference-count":54,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"4","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"funder":[{"name":"Alberta Innovates Graduate Student Scholarships"},{"name":"NIH","award":["1R35GM150537-01"],"award-info":[{"award-number":["1R35GM150537-01"]}]},{"name":"NSERC Discovery","award":["RGPIN-2024-06154"],"award-info":[{"award-number":["RGPIN-2024-06154"]}]},{"name":"New Frontiers in Research Fund Exploration","award":["NFRFE-2023-00291"],"award-info":[{"award-number":["NFRFE-2023-00291"]}]},{"name":"Alberta Innovates LevMax-Health Program Bridge Funds","award":["222300769"],"award-info":[{"award-number":["222300769"]}]},{"name":"Canada Foundation","award":["36605"],"award-info":[{"award-number":["36605"]}]},{"name":"NSERC Discovery","award":["RGPIN-2024-04679"],"award-info":[{"award-number":["RGPIN-2024-04679"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Trans. Comput. Biol. Bioinform."],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1109\/tcbbio.2025.3568376","type":"journal-article","created":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T13:59:33Z","timestamp":1746799173000},"page":"1703-1715","source":"Crossref","is-referenced-by-count":1,"title":["Autoencoder-Transformed Transcriptome Improves Genotype-Phenotype Association Studies"],"prefix":"10.1109","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-1327-4347","authenticated-orcid":false,"given":"Qing","family":"Li","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-8873-4839","authenticated-orcid":false,"given":"Jiayi","family":"Bian","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3016-9582","authenticated-orcid":false,"given":"Janith","family":"Weeraman","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada"}]},{"given":"Zilong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada"}]},{"given":"Albert","family":"Leung","sequence":"additional","affiliation":[{"name":"Data Science and Analytics Program, University of Calgary, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0083-9921","authenticated-orcid":false,"given":"Qi-Xuan","family":"Ding","sequence":"additional","affiliation":[{"name":"Sir Winston Churchill High School, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3594-9182","authenticated-orcid":false,"given":"Thierry","family":"Chekouo","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9938-3627","authenticated-orcid":false,"given":"Lang","family":"Wu","sequence":"additional","affiliation":[{"name":"University of Hawaii Cancer Center, Honolulu, HI, USA"}]},{"given":"Jun","family":"Yan","sequence":"additional","affiliation":[{"name":"Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4555-1490","authenticated-orcid":false,"given":"Jingjing","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Calgary, Calgary, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3795-1873","authenticated-orcid":false,"given":"Quan","family":"Long","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada"}]}],"member":"263","reference":[{"key":"ref1","article-title":"Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits","volume-title":"Nature Commun.","volume":"10","author":"Zhang","year":"2019"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003264"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03260-6"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06302-1"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0092-1"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0132-x"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0351-9"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaa270"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2017.07.036"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2023.11.006"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02089-x"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1142\/9789813235533_0041"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0345-7"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3506"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2011.457"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1126\/science.1262110"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1038\/nature24277"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-031-24628-9_16"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2019.02.003"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1109\/metroxraine54828.2022.9967686"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v046.i11"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1038\/nature05911"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1038\/nn.4524"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2303"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bav028"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw943"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz1021"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2021.05.015"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0104s28"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-22"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm563"},{"key":"ref33","article-title":"Adam: A method for stochastic optimization","author":"Kingma","year":"2014"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2105841118"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2010.11.011"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2014.10.001"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.2307\/2533274"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.15302\/J-QB-020-0228"},{"key":"ref39","first-page":"258","article-title":"TIGAR: An improved Bayesian tool for transcriptomic data imputation enhances gene mapping of complex traits","volume-title":"Amer. J. Hum. Genet.","volume":"105","author":"Nagpal","year":"2019"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1016\/j.brainres.2010.11.078"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1097\/YPG.0000000000000100"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1111\/biom.12331"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddz292"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1016\/j.euroneuro.2017.08.174"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.b.32592"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2013.12.007"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.683946"},{"key":"ref48","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-022-08491-y"},{"key":"ref49","doi-asserted-by":"publisher","DOI":"10.1089\/sysm.2019.0003"},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaut.2013.01.013"},{"key":"ref51","doi-asserted-by":"publisher","DOI":"10.1016\/j.crmeth.2021.100050"},{"key":"ref52","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abo2846"},{"key":"ref53","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyab216"},{"key":"ref54","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/iyad204"}],"container-title":["IEEE Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/10723156\/11121392\/10994318.pdf?arnumber=10994318","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,9]],"date-time":"2025-08-09T04:44:04Z","timestamp":1754714644000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/10994318\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":54,"journal-issue":{"issue":"4"},"URL":"https:\/\/doi.org\/10.1109\/tcbbio.2025.3568376","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.07.23.550223","asserted-by":"object"}]},"ISSN":["2998-4165"],"issn-type":[{"value":"2998-4165","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7]]}}}