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Title: A community computational challenge to predict the activity of pairs of compounds
Authors: Bansal, Mukesh
Yang, Jichen
Karan, Charles
Menden, Michael P.
Costello, James C.
Tang, Hao
Xiao, Guanghua
Li, Yajuan
Allen, Jeffrey
Zhong, Rui
Chen, Beibei
Kim, Minsoo
Wang, Tao
Heiser, Laura M.
Realubit, Ronald
Mattioli, Michela
Alvarez, Mariano J.
Shen, Yao
NCI-DREAM Community
Karaçalı, Bilge
Gallahan, Daniel
Singer, Dinah
Saez-Rodriguez, Julio
Xie, Yang
Stolovitzky, Gustavo
Califano, Andrea
Keywords: Gene expression
Scoring metrics
Computational challenges
Synergistic combinations
Drug combinations
Issue Date: Dec-2014
Publisher: Nature Publishing Group
Source: Bansal, M., Yang, J., Karan, C., Menden, M. P., Costello, J. C., Tang, H., ...Califano, A. (2014). A community computational challenge to predict the activity of pairs of compounds. Nature Biotechnology, 32(12), 1213-1222. doi:10.1038/nbt.3052
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.
ISSN: 1087-0156
Appears in Collections:Electrical - Electronic Engineering / Elektrik - Elektronik Mühendisliği
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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