{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:35Z","timestamp":1772138075557,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T00:00:00Z","timestamp":1754956800000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"GIS Biogenouest","award":["ANR-11-INBS-0013"],"award-info":[{"award-number":["ANR-11-INBS-0013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Transcriptomic analysis is a key tool for exploring gene expression, but the complexity of biological systems often limits its insights. In particular, the lack of intermodal or multi-layered analysis hinders the ability to fully capture key cellular functions such as metabolism from transcriptomic data alone. Here, we introduce a novel approach that informs transcriptomic data analysis with metabolic network modeling to address this. Unlike traditional methods, HUman MEtabolism Specific Signature (HUMESS) uses genome-scale metabolic modeling and flux analysis to highlight reactions and involved genes based on their metabolic significance, offering a deeper understanding of transcriptomic data. Our computational pipeline, supported by a user-friendly Rshiny application, enhances gene expression analysis by uncovering metabolic phenotypic signatures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>HUMESS is open source and available under GitLab https:\/\/gitlab.univ-nantes.fr\/bird_pipeline_registry\/humess with the complete documentation available at https:\/\/gitlab.univ-nantes.fr\/bird_pipeline_registry\/humess\/-\/wikis\/Home. A zenodo archive is also available at the following DOI: https:\/\/doi.org\/10.5281\/zenodo.15487717. An RShiny application has been developed to facilitate the exploration and analysis of HUMESS\u2019s results. The app is available online at the following address: https:\/\/shiny-bird.univ-nantes.fr\/app\/shinymess but can also be installed locally, available under GitLab https:\/\/gitlab.univ-nantes.fr\/pare-l\/shinymess.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf448","type":"journal-article","created":{"date-parts":[[2025,8,11]],"date-time":"2025-08-11T11:24:58Z","timestamp":1754911498000},"source":"Crossref","is-referenced-by-count":0,"title":["HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-4772-8042","authenticated-orcid":false,"given":"Louis","family":"Par\u00e9","sequence":"first","affiliation":[{"name":"Nantes Universit\u00e9, Centrale Nantes, CNRS, LS2N , Nantes 44322,","place":["France"]}]},{"given":"Philippe","family":"Bordron","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Toulouse, INRAE, BioinfOmics, GenoToul Bioinformatics Facility , Castanet-Tolosan 31320,","place":["France"]},{"name":"Universit\u00e9 de Toulouse, INRAE, UR 875 MIAT , Castanet-Tolosan 31320,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3594-0353","authenticated-orcid":false,"given":"Laurent","family":"David","sequence":"additional","affiliation":[{"name":"Nantes Universit\u00e9, Inserm, CR2TI , Nantes F-44000,","place":["France"]},{"name":"Nantes Universit\u00e9, CHU Nantes, CNRS, Inserm, BioCore , Nantes F-44000,","place":["France"]}]},{"given":"Maxime","family":"Mah\u00e9","sequence":"additional","affiliation":[{"name":"Nantes Universit\u00e9, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD , Nantes 44000,","place":["France"]},{"name":"Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati 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