{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T09:07:18Z","timestamp":1769764038000,"version":"3.49.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Combinatorial therapies play increasingly important roles in combating complex diseases. Owing to the huge cost associated with experimental methods in identifying optimal drug combinations, computational approaches can provide a guide to limit the search space and reduce cost. However, few computational approaches have been developed for this purpose, and thus there is a great need of new algorithms for drug combination prediction.<\/jats:p><jats:p>Results: Here we proposed to formulate the optimal combinatorial therapy problem into two complementary mathematical algorithms, Balanced Target Set Cover (BTSC) and Minimum Off-Target Set Cover (MOTSC). Given a disease gene set, BTSC seeks a balanced solution that maximizes the coverage on the disease genes and minimizes the off-target hits at the same time. MOTSC seeks a full coverage on the disease gene set while minimizing the off-target set. Through simulation, both BTSC and MOTSC demonstrated a much faster running time over exhaustive search with the same accuracy. When applied to real disease gene sets, our algorithms not only identified known drug combinations, but also predicted novel drug combinations that are worth further testing. In addition, we developed a web-based tool to allow users to iteratively search for optimal drug combinations given a user-defined gene set.<\/jats:p><jats:p>Availability: Our tool is freely available for noncommercial use at http:\/\/www.drug.liuzlab.org\/.<\/jats:p><jats:p>Contact: zhandong.liu@bcm.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu046","type":"journal-article","created":{"date-parts":[[2014,1,25]],"date-time":"2014-01-25T01:24:14Z","timestamp":1390613054000},"page":"1456-1463","source":"Crossref","is-referenced-by-count":56,"title":["Combinatorial therapy discovery using mixed integer linear programming"],"prefix":"10.1093","volume":"30","author":[{"given":"Kaifang","family":"Pang","sequence":"first","affiliation":[{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying-Wooi","family":"Wan","sequence":"additional","affiliation":[{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William T.","family":"Choi","sequence":"additional","affiliation":[{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lawrence A.","family":"Donehower","sequence":"additional","affiliation":[{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingchun","family":"Sun","sequence":"additional","affiliation":[{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, 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3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor College of Medicine, 2Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, 3Department of Pediatrics-Neurology, 4Department of Obstetrics and Gynaecology, 5Department of Molecular Virology and Microbiology, Baylor College of Medicine, 6School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and 7Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Computational and Integrative Biomedical Research Center, Baylor 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