{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:29Z","timestamp":1787008469636,"version":"3.56.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T00:00:00Z","timestamp":1759708800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"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>Omics profiling has proven of great use for unbiased and comprehensive identification of key features that define biological phenotypes and underlie medical conditions. While each omics profile assists characterization of specific molecular components relevant for the studied phenotype, their joint evaluation can offer deeper insights into the overall mechanistic functioning of biological systems. Here, we introduce an approach where, starting from representative traits (e.g. differentially expressed elements) obtained for each omics profile, we construct and analyze joint interaction networks. The resulting networks rely on the existing knowledge of confident interactions among biological entities. We use these maps to identify and describe central elements, which connect multiple entities characteristic of the studied phenotypes and we leverage MONET network decomposition tool in order to highlight functionally connected network modules. In order to enable broad usage of this approach, we developed the NOODAI software platform, which enables integrative omics analysis through a user-friendly interface. The analysis outcomes are presented both as raw output tables as well as informative summary plots and written reports. Since the MONET tool enables the use of algorithms with strong performance in identifying disease-relevant modules, NOODAI software platform can be of a high value for analyzing clinical multi-omics datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>NOODAI is freely accessible at https:\/\/omics-oracle.com. Source code is available under GPL3 at: https:\/\/github.com\/TotuTiberiu\/NOODAI with the DOI: 10.5281\/zenodo.17203984.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf553","type":"journal-article","created":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T12:02:35Z","timestamp":1759406555000},"source":"Crossref","is-referenced-by-count":1,"title":["NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline"],"prefix":"10.1093","volume":"41","author":[{"given":"Tiberiu","family":"Totu","sequence":"first","affiliation":[{"name":"Nanomaterials in Health Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa) , 9014 St. Gallen,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , 1015 Lausanne,","place":["Switzerland"]},{"name":"Department of Health Sciences and Technology, Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich (ETH) , 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Riudavets Puig","sequence":"additional","affiliation":[{"name":"Nanomaterials in Health Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa) , 9014 St. Gallen,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , 1015 Lausanne,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukas Jonathan","family":"H\u00e4user","sequence":"additional","affiliation":[{"name":"Nanomaterials in Health Laboratory, Swiss Federal Laboratories for Materials Science and Technology (Empa) , 9014 St. Gallen,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics (SIB) , 1015 Lausanne,","place":["Switzerland"]},{"name":"Department of Health Sciences and Technology, Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich (ETH) , 8092 Zurich,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8775-2384","authenticated-orcid":false,"given":"Mattia","family":"Tomasoni","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, Jules Gonin Eye Hospital , 1004 Lausanne,","place":["Switzerland"]},{"name":"Platform for Research in Ocular Imaging, Fondation Asile des Aveugles, Jules Gonin Eye Hospital , 1004 Lausanne,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hella Anna","family":"Bolck","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich , 8091 Z\u00fcrich,","place":["Switzerland"]},{"name":"Centre for AI, School of Engineering, Zurich University of Applied Sciences (ZHAW) , 8400 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