Year: 2025
Type: article
Abstract: SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: 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.
Source: Bioinformatics
Authors: Tuomas Borman, Artur Sannikov, Robert D Finn, Morten Tønsberg Limborg, Alexander B Rogers, Varsha Kale, Kati Hanhineva, Leo Lahti
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,989
Awards: G2599391009, Holistic solution to improve animal food production through deconstructing the biomolecular interactions between feed, gut microorganisms and animals in relation to performance parameters, Center For Evolutionary Hologenomics (CEH), G4294000436, Unified computational solutions to disentangle biological interactions in multi-omics data, G6257193852, Eco-evolutionary mechanisms underlying critical transitions in microbial communities, A New Halo-Imidazolums and Halo-Triazoliums Halogen-Bonding Receptors for Anion Recognition and Sensing, G8905364259
OpenAlex ID: W4416222445