Skip to main content

A community computational challenge to predict the activity of pairs of compounds

Author(s): Bansal, Mukesh; Yang, Jichen; Karan, Charles; Menden, Michael P; Costello, James C; et al

To refer to this page use:
Abstract: Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound pairs, from the most synergistic to the most antagonistic, based on gene-expression profiles of human B cells treated with individual compounds at multiple time points and concentrations. Using scoring metrics based on experimental dose-response curves, we assessed 32 methods (31 community-generated approaches and SynGen), four of which performed significantly better than random guessing. We highlight similarities between the methods. Although the accuracy of predictions was not optimal, we find that computational prediction of compound-pair activity is possible, and that community challenges can be useful to advance the field of in silico compound-synergy prediction.
Publication Date: 2014
Citation: Bansal, Mukesh, Jichen Yang, Charles Karan, Michael P. Menden, James C. Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura M Heiser, Ronald Realubit, Michela Mattioli, Mariano J Alvarez, Yao Shen, NCI-DREAM Community, Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky, and Andrea Califano. "A community computational challenge to predict the activity of pairs of compounds." Nature Biotechnology 32, no. 12 (2014): 1213-1222. doi:10.1038/nbt.3052
DOI: 10.1038/nbt.3052
ISSN: 1087-0156
EISSN: 1546-1696
Pages: 1213 - 1222
Type of Material: Journal Article
Journal/Proceeding Title: Nature Biotechnology
Version: Author's manuscript

Items in OAR@Princeton are protected by copyright, with all rights reserved, unless otherwise indicated.