{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T03:13:30Z","timestamp":1775704410306,"version":"3.50.1"},"reference-count":72,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T00:00:00Z","timestamp":1721606400000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Education and Research","award":["031L0212A"],"award-info":[{"award-number":["031L0212A"]}]},{"name":"European Union\u2019s Horizon 2020","award":["860329"],"award-info":[{"award-number":["860329"]}]},{"name":"German Federal Ministry of Education and Research","award":["031L0181B"],"award-info":[{"award-number":["031L0181B"]}]},{"name":"HPC\/Exascale Centre of Excellence for Personalised Medicine in Europe"},{"name":"PerMedCoE"},{"name":"European Union Horizon 2020","award":["951773"],"award-info":[{"award-number":["951773"]}]},{"name":"European Union\u2019s Horizon 2020","award":["965193"],"award-info":[{"award-number":["965193"]}]},{"DOI":"10.13039\/501100001661","name":"Heidelberg University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001661","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>From the catalytic breakdown of nutrients to signaling, interactions between metabolites and proteins play an essential role in cellular function. An important case is cell\u2013cell communication, where metabolites, secreted into the microenvironment, initiate signaling cascades by binding to intra- or extracellular receptors of neighboring cells. Protein\u2013protein cell\u2013cell communication interactions are routinely predicted from transcriptomic data. However, inferring metabolite-mediated intercellular signaling remains challenging, partially due to the limited size of intercellular prior knowledge resources focused on metabolites. Here, we leverage knowledge-graph infrastructure to integrate generalistic metabolite-protein with curated metabolite-receptor resources to create MetalinksDB. MetalinksDB is an order of magnitude larger than existing metabolite-receptor resources and can be tailored to specific biological contexts, such as diseases, pathways, or tissue\/cellular locations. We demonstrate MetalinksDB\u2019s utility in identifying deregulated processes in renal cancer using multi-omics bulk data. Furthermore, we infer metabolite-driven intercellular signaling in acute kidney injury using spatial transcriptomics data. MetalinksDB is a comprehensive and customizable database of intercellular metabolite-protein interactions, accessible via a web interface (https:\/\/metalinks.omnipathdb.org\/) and programmatically as a knowledge graph (https:\/\/github.com\/biocypher\/metalinks). We anticipate that by enabling diverse analyses tailored to specific biological contexts, MetalinksDB will facilitate the discovery of disease-relevant metabolite-mediated intercellular signaling processes.<\/jats:p>","DOI":"10.1093\/bib\/bbae347","type":"journal-article","created":{"date-parts":[[2024,7,8]],"date-time":"2024-07-08T16:25:46Z","timestamp":1720455946000},"source":"Crossref","is-referenced-by-count":21,"title":["MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4441-6513","authenticated-orcid":false,"given":"Elias","family":"Farr","sequence":"first","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"},{"name":"Wellcome Sanger Institute, Wellcome Genome Campus , Cambridge CB10 1SA , United Kingdom"}]},{"given":"Daniel","family":"Dimitrov","sequence":"additional","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"}]},{"given":"Christina","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"}]},{"given":"Denes","family":"Turei","sequence":"additional","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"}]},{"given":"Sebastian","family":"Lobentanzer","sequence":"additional","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"}]},{"given":"Aurelien","family":"Dugourd","sequence":"additional","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"},{"name":"EMBL European Bioinformatics Institute, Wellcome Genome Campus , Cambridge CB10 1SA , United Kingdom"}]},{"given":"Julio","family":"Saez-Rodriguez","sequence":"additional","affiliation":[{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Im Neuenheimer Feld 130.3, 69120, Heidelberg , Germany"},{"name":"EMBL European Bioinformatics Institute, Wellcome Genome Campus , Cambridge CB10 1SA , United Kingdom"}]}],"member":"286","published-online":{"date-parts":[[2024,7,22]]},"reference":[{"key":"2024072223571851300_ref1","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41580-022-00572-w","article-title":"Metabolites as signalling molecules","volume":"24","author":"Baker","year":"2023","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2024072223571851300_ref2","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/j.tibs.2016.02.003","article-title":"Intermediates of metabolism: from bystanders to signalling molecules","volume":"41","author":"Haas","year":"2016","journal-title":"Trends Biochem Sci"},{"key":"2024072223571851300_ref3","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","article-title":"Deciphering cell-cell interactions and communication from gene expression","volume":"22","author":"Armingol","year":"2021","journal-title":"Nat Rev 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