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However, experimental screening of drug combinations is costly and time-consuming. The availability of large-scale transcriptomic datasets (e.g. CMap and LINCS) from in vitro drug treatment experiments makes it possible to computationally predict drug combinations with synergistic effects. Towards this end, we developed a computational approach, termed Identification of Drug Combinations via Multi-Set Operations (iDOMO), to predict drug synergy based on multi-set operations of drug and disease gene signatures. iDOMO quantifies the synergistic effect of a pair of drugs by taking into account the combination\u2019s beneficial and detrimental effects on treating a disease. We evaluated iDOMO, in a DREAM Challenge dataset with the matched, pre- and post-treatment gene expression data and cell viability information. We further evaluated the performance of iDOMO by concordance index and Spearman correlation on predicting the Highest Single Agency (HSA) synergy scores for four most common cancer types in two large-scale drug combination databases, showing that iDOMO\u00a0 significantly outperformed two existing popular drug combination approaches including the Therapeutic Score and the SynergySeq Orthogonality Score. Application of iDOMO to triple-negative breast cancer (TNBC) identified drug pairs with potential synergistic effects, with the combination of trifluridine and monobenzone being the most synergistic. Our in vitro experiments confirmed that the top predicted drug combination exerted a significant synergistic effect in inhibiting TNBC cell growth. In summary, iDOMO is an effective method for the in silico screening of synergistic drug combinations and will be a valuable tool for the development of novel therapeutics for complex diseases.<\/jats:p>","DOI":"10.1093\/bib\/bbaf054","type":"journal-article","created":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T04:55:26Z","timestamp":1740027326000},"source":"Crossref","is-referenced-by-count":1,"title":["iDOMO: identification of drug combinations via multi-set operations for treating diseases"],"prefix":"10.1093","volume":"26","author":[{"given":"Xianxiao","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Wu","sequence":"additional","affiliation":[{"name":"Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine , 4100 John R, Detroit, MI 48201 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minghui","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guojun","family":"Wu","sequence":"additional","affiliation":[{"name":"Barbara Ann Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine , 4100 John R, Detroit, MI 48201 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9549-5653","authenticated-orcid":false,"given":"Bin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place , New York, NY 10029 ,","place":["United States"]},{"name":"Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. 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