{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:20Z","timestamp":1787008460699,"version":"3.56.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,1,4]],"date-time":"2022-01-04T00:00:00Z","timestamp":1641254400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation program under Grant Agreements","award":["826078"],"award-info":[{"award-number":["826078"]}]},{"name":"European Union\u2019s Horizon 2020 research and innovation program under Grant Agreements","award":["777111"],"award-info":[{"award-number":["777111"]}]},{"name":"German Federal Ministry of Education and Research","award":["01ZX1908A"],"award-info":[{"award-number":["01ZX1908A"]}]},{"name":"German Federal Ministry of Education and Research","award":["01ZX1910D"],"award-info":[{"award-number":["01ZX1910D"]}]},{"name":"German Federal Ministry of Education and Research","award":["031L0214A"],"award-info":[{"award-number":["031L0214A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Disease module mining methods (DMMMs) extract subgraphs that constitute candidate disease mechanisms from molecular interaction networks such as protein\u2013protein interaction (PPI) networks. Irrespective of the employed models, DMMMs typically include non-robust steps in their workflows, i.e. the computed subnetworks vary when running the DMMMs multiple times on equivalent input. This lack of robustness has a negative effect on the trustworthiness of the obtained subnetworks and is hence detrimental for the widespread adoption of DMMMs in the biomedical sciences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To overcome this problem, we present a new DMMM called ROBUST (robust disease module mining via enumeration of diverse prize-collecting Steiner trees). In a large-scale empirical evaluation, we show that ROBUST outperforms competing methods in terms of robustness, scalability and, in most settings, functional relevance of the produced modules, measured via KEGG (Kyoto Encyclopedia of Genes and Genomes) gene set enrichment scores and overlap with DisGeNET disease genes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>A Python 3 implementation and scripts to reproduce the results reported in this article are available on GitHub: https:\/\/github.com\/bionetslab\/robust, https:\/\/github.com\/bionetslab\/robust-eval.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab876","type":"journal-article","created":{"date-parts":[[2021,12,31]],"date-time":"2021-12-31T15:19:20Z","timestamp":1640963960000},"page":"1600-1606","source":"Crossref","is-referenced-by-count":32,"title":["Robust disease module mining via enumeration of diverse prize-collecting Steiner trees"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5812-8013","authenticated-orcid":false,"given":"Judith","family":"Bernett","sequence":"first","affiliation":[{"name":"Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich , 85354 Freising, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominik","family":"Krupke","sequence":"additional","affiliation":[{"name":"Department of Computer Science, TU Braunschweig , 38106 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sepideh","family":"Sadegh","sequence":"additional","affiliation":[{"name":"Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich , 85354 Freising, Germany"},{"name":"Institute for Computational Systems Biology, University of Hamburg , 22607 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Baumbach","sequence":"additional","affiliation":[{"name":"Institute for Computational Systems Biology, University of Hamburg , 22607 Hamburg, Germany"},{"name":"Department of Mathematics and Computer Science, University of Southern Denmark , 5230 Odense, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00e1ndor P","family":"Fekete","sequence":"additional","affiliation":[{"name":"Department of Computer Science, TU Braunschweig , 38106 Braunschweig, Germany"},{"name":"Braunschweig Integrated Centre of Systems Biology (BRICS) , 38106 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5393-2413","authenticated-orcid":false,"given":"Tim","family":"Kacprowski","sequence":"additional","affiliation":[{"name":"Braunschweig Integrated Centre of Systems Biology (BRICS) , 38106 Braunschweig, Germany"},{"name":"Division Data Science in Biomedicine, Peter L. 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