{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:21Z","timestamp":1787008461074,"version":"3.56.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T00:00:00Z","timestamp":1632355200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Research and Innovation chair L\u2019Or\u00e9al in Digital Biology"},{"name":"National Health and Medical Research Council (NHMRC) Career Development fellowship","award":["GNT1159458"],"award-info":[{"award-number":["GNT1159458"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Multi-omics data integration enables the global analysis of biological systems and discovery of new biological insights. Multi-omics experimental designs have been further extended with a longitudinal dimension to study dynamic relationships between molecules. However, methods that integrate longitudinal multi-omics data are still in their infancy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce the R package timeOmics, a generic analytical framework for the integration of longitudinal multi-omics data. The framework includes pre-processing, modeling and clustering to identify molecular features strongly associated with time. We illustrate this framework in a case study to detect seasonal patterns of mRNA, metabolites, gut taxa and clinical variables in patients with diabetes mellitus from the integrative Human Microbiome Project.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availabilityand implementation<\/jats:title>\n                    <jats:p>timeOmics is available on Bioconductor and github.com\/abodein\/timeOmics.<\/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\/btab664","type":"journal-article","created":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T15:24:08Z","timestamp":1631719448000},"page":"577-579","source":"Crossref","is-referenced-by-count":41,"title":["timeOmics: an R package for longitudinal multi-omics data integration"],"prefix":"10.1093","volume":"38","author":[{"given":"Antoine","family":"Bodein","sequence":"first","affiliation":[{"name":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie-Pier","family":"Scott-Boyer","sequence":"additional","affiliation":[{"name":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Perin","sequence":"additional","affiliation":[{"name":"Digital Sciences Department, L\u2019Or\u00e9al Advanced Research , Aulnay-sous-bois 93600, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim-Anh","family":"L\u00ea Cao","sequence":"additional","affiliation":[{"name":"Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne , Melbourne, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7922-790X","authenticated-orcid":false,"given":"Arnaud","family":"Droit","sequence":"additional","affiliation":[{"name":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,9,23]]},"reference":[{"key":"2023020108443029100_btab664-B1","doi-asserted-by":"crossref","first-page":"963","DOI":"10.3389\/fgene.2019.00963","article-title":"A generic multivariate framework for the integration of microbiome longitudinal studies with other data types","volume":"10","author":"Bodein","year":"2019","journal-title":"Front. 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