{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T15:17:16Z","timestamp":1787498236750,"version":"build-2736575974"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,9,6]],"date-time":"2021-09-06T00:00:00Z","timestamp":1630886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CCF-1319981"],"award-info":[{"award-number":["CCF-1319981"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["5R01GM104975"],"award-info":[{"award-number":["5R01GM104975"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Genetic variations of expression quantitative trait loci (eQTLs) play a critical role in influencing complex traits and diseases development. Two main factors that affect the statistical power of detecting eQTLs are: (i) relatively small size of samples available, and (ii) heavy burden of multiple testing due to a very large number of variants to be tested. The later issue is particularly severe when one tries to identify trans-eQTLs that are far away from the genes they influence. If one can exploit co-expressed genes jointly in eQTL-mapping, effective sample size can be increased. Furthermore, using the structure of the gene regulatory network (GRN) may help to identify trans-eQTLs without increasing multiple testing burden.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this article, we use the structure equation model (SEM) to model both GRN and effect of eQTLs on gene expression, and then develop a novel algorithm, named sparse SEM for eQTL mapping (SSEMQ), to conduct joint eQTL mapping and GRN inference. The SEM can exploit co-expressed genes jointly in eQTL mapping and also use GRN to determine trans-eQTLs. Computer simulations demonstrate that our SSEMQ significantly outperforms nine existing eQTL mapping methods. SSEMQ is further used to analyze two real datasets of human breast and whole blood tissues, yielding a number of cis- and trans-eQTLs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>R package ssemQr is available at https:\/\/github.com\/Ivis4ml\/ssemQr.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab609","type":"journal-article","created":{"date-parts":[[2021,9,6]],"date-time":"2021-09-06T13:46:53Z","timestamp":1630936013000},"page":"149-156","source":"Crossref","is-referenced-by-count":10,"title":["Joint eQTL mapping and inference of gene regulatory network improves power of detecting both\n                    <i>cis<\/i>\n                    - and\n                    <i>trans<\/i>\n                    -eQTLs"],"prefix":"10.1093","volume":"38","author":[{"given":"Xin","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of Miami , Coral Gables, FL 33146, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7460-5633","authenticated-orcid":false,"given":"Xiaodong","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, University of Miami , Coral Gables, FL 33146, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,6]]},"reference":[{"key":"2023020201173821300_btab609-B1","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrg3891","article-title":"The role of regulatory variation in complex traits and disease","volume":"16","author":"Albert","year":"2015","journal-title":"Nat. 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