Combinatorial therapy discovery using mixed integer linear programming.
BACKGROUND
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.


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.


BACKGROUND
Our tool is freely available for noncommercial use at http://www.drug.liuzlab.org/.


BACKGROUND
zhandong.liu@bcm.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Department of Pediatrics-Neurology, Department of Obstetrics and Gynaecology, Department of Molecular Virology and Microbiology, Baylor College of Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, and Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Kaifang
K
Pang
Ying-Wooi
YW
Wan
William T
WT
Choi
Lawrence A
LA
Donehower
Jingchun
J
Sun
Dhruv
D
Pant
Zhandong
Z
Liu
D000465:Algorithms; D016208:Databases, Factual; D003924:Diabetes Mellitus, Type 2 / Q000188:drug therapy / Q000235:genetics; D004338:Drug Combinations; D053263:Gene Regulatory Networks; D006801:Humans; D009203:Myocardial Infarction / Q000188:drug therapy / Q000235:genetics; D011382:Programming, Linear; D012985:Software Design
D004338:Drug Combinations