{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T20:55:14Z","timestamp":1791060914993,"version":"4.1.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T00:00:00Z","timestamp":1790985600000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Deciphering the genetic basis of complex traits increasingly leverages intermediate molecular layers (\u201cin-between-omes,\u201d e.g., the transcriptome) in association studies such as transcriptome-wide association studies. Despite many emerging statistical and machine-learning approaches, there is no flexible standard for simulating phenotypes from genotypes while explicitly modeling the role of an in-between-ome, especially under nonlinear architectures (e.g., co-expression networks). This gap hampers fair power estimation and rigorous benchmarking. We present OmeSim, a configurable simulator that jointly generates genotype, an in-between-ome, and phenotype, capturing complex (including nonlinear) relationships. OmeSim outputs the full generative\/causal graph together with data matrices and the induced correlation and association structures, providing gold-standard datasets for developing and evaluating methods that integrate an in-between-ome into genotype\u2013phenotype studies. We validate OmeSim by comparing simulated human transcriptomes to real human transcriptomes and by benchmarking alternative association-mapping tools, demonstrating its utility for reproducible power analyses and method comparison in multi-omics integration. Source code and documentation: https:\/\/github.com\/zhoulongcoding\/OmeSim.<\/jats:p>","DOI":"10.1093\/genetics\/iyag272","type":"journal-article","created":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T20:23:47Z","timestamp":1791059027000},"source":"Crossref","is-referenced-by-count":0,"title":["OmeSim: a genetics-based nonlinear simulator for in-between-ome and phenotype"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9157-367X","authenticated-orcid":false,"given":"Caifeng","family":"Li","sequence":"first","affiliation":[{"name":"Department of Mathematics & Statistics, University of Calgary , Calgary, Alberta T2N 1N4 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhou","family":"Long","sequence":"additional","affiliation":[{"name":"Westmount Charter School , Calgary, Alberta T2N 4Y3 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingrun","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Mathematics & Statistics, University of Calgary , Calgary, Alberta T2N 1N4 ,","place":["Canada"]},{"name":"Department of Biochemistry & Molecular Biology, University of Calgary , Calgary, Alberta T2N 1N4 ,","place":["Canada"]},{"name":"Alberta Children\u2019s Hospital Research Institute, University of Calgary , Calgary, Alberta T2N 1N4 ,","place":["Canada"]},{"name":"Hotchkiss Brain Institute, University of Calgary , Calgary, Alberta T2N 1N4 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,3]]},"container-title":["GENETICS"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/genetics\/advance-article-pdf\/doi\/10.1093\/genetics\/iyag272\/71577492\/iyag272.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/genetics\/advance-article-pdf\/doi\/10.1093\/genetics\/iyag272\/71577492\/iyag272.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T20:23:48Z","timestamp":1791059028000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/genetics\/advance-article\/doi\/10.1093\/genetics\/iyag272\/8860345"}},"subtitle":[],"editor":[{"given":"Yun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,3]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/genetics\/iyag272","relation":{},"ISSN":["1943-2631"],"issn-type":[{"value":"1943-2631","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,3]]},"article-number":"iyag272"}}