{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T19:11:14Z","timestamp":1763147474775,"version":"3.45.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T00:00:00Z","timestamp":1762646400000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Horizon2020 Project FindingPheno"},{"DOI":"10.13039\/501100002341","name":"Research Council of Finland","doi-asserted-by":"publisher","award":["330887"],"award-info":[{"award-number":["330887"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jane and Aatos Erkko Foundation and the Research Council of Finland","award":["321716","334814"],"award-info":[{"award-number":["321716","334814"]}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF143"],"award-info":[{"award-number":["DNRF143"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10 000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HoloFoodR R\/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https:\/\/doi.org\/10.18129\/B9.bioc.HoloFoodR.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf605","type":"journal-article","created":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T20:35:19Z","timestamp":1762720519000},"source":"Crossref","is-referenced-by-count":0,"title":["HoloFoodR: a statistical programming framework for holo-omics data integration workflows"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8563-8884","authenticated-orcid":false,"given":"Tuomas","family":"Borman","sequence":"first","affiliation":[{"name":"Department of Computing, University of Turku , Turku 20014,","place":["Finland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7765-123X","authenticated-orcid":false,"given":"Artur","family":"Sannikov","sequence":"additional","affiliation":[{"name":"Department of Life Technologies, University of Turku , Turku 20014,","place":["Finland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8626-2148","authenticated-orcid":false,"given":"Robert D","family":"Finn","sequence":"additional","affiliation":[{"name":"Wellcome Genome Campus, EMBL-EBI , Hinxton, Cambridgeshire CB10 1SA,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7718-6531","authenticated-orcid":false,"given":"Morten T\u00f8nsberg","family":"Limborg","sequence":"additional","affiliation":[{"name":"Center 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