ArticleNature biotechnology2014
A community computational challenge to predict the activity of pairs of compounds.
Abstract read
In one paragraph
Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers.
0numbers the graph read from it
0cells of the map it votes in
173citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
173 citing papers in PubMed.
- Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.The Lancet. Oncology · 2017Trial
- Robust prediction of drug combination side effects in realistic settings.PLoS computational biology · 2026Article
- Beyond Structural Representations: A Semantic-Relational Graph Neural Network for Polypharmacy Side Effect Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
- Deep Learning-Driven Anticancer Drug Discovery: Emodepside as a Potential Therapeutic Candidate for Triple-Negative Breast Cancer.Journal of chemical information and modeling · 2026Article
- Multi agent large language models for biomedical hypothesis generation in drug combination discovery.iScience · 2025Article
- A human metabolic map of pharmacological perturbations reveals drug modes of action.Nature biotechnology · 2025Article
- DeepTarget predicts anti-cancer mechanisms of action of small molecules by integrating drug and genetic screens.NPJ precision oncology · 2025Article
- Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells.iScience · 2025Article
- Single-cell multi-omics reveals that FABP1 + renal cell carcinoma drive tumor angiogenesis through the PLG-PLAT axis under fatty acid reprogramming.Molecular cancer · 2025Article
- HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction.BMC bioinformatics · 2025Article
- AI-driven discovery of synergistic drug combinations against pancreatic cancer.Nature communications · 2025Article
- Computational frameworks transform antagonism to synergy in optimizing combination therapies.NPJ digital medicine · 2025Review
- HPRNA: Predicting synergistic drug combinations for angina pectoris based on human pathway relationship network algorithm.PloS one · 2025Article
- Simulate Scientific Reasoning with Multiple Large Language Models: An Application to Alzheimer's Disease Combinatorial Therapy.medRxiv : the preprint server for health sciences · 2024Article
- iDOMO: identification of drug combinations via multi-set operations for treating diseases.Briefings in bioinformatics · 2024Article
- DRGATAN: Directed relation graph attention aware network for asymmetric drug-drug interaction prediction.iScience · 2024Article
- A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells.Science advances · 2024Article
- MPHGCL-DDI: Meta-Path-Based Heterogeneous Graph Contrastive Learning for Drug-Drug Interaction Prediction.Molecules (Basel, Switzerland) · 2024Article
- Antimalarial Drug Combination Predictions Using the Machine Learning Synergy Predictor (MLSyPred©) tool.Acta parasitologica · 2024Article
- Patient derived tumoroids of high grade neuroendocrine neoplasms for more personalized therapies.NPJ precision oncology · 2024Article
113 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
26 authors.
Mukesh Bansal1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.ORCID 0000000314816767
Jichen YangQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Charles KaranColumbia Genome Center, High Throughput Screening Facility, Columbia University, New York, New York, USA.
Michael P MendenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
James C CostelloHoward Hughes Medical Institute, Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, Massachusetts, USA.
Hao TangQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Guanghua XiaoQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Yajuan LiDepartment of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Jeffrey AllenQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Rui ZhongQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Beibei ChenQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Minsoo Kim1] Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA. [2] Simmons Comprehensive Cancer Center, University of Texas, Southwestern Medical Center, Texas, USA.
Tao WangQuantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA.ORCID 000000024355149X
Laura M HeiserDepartment of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA.
Ronald RealubitColumbia Genome Center, High Throughput Screening Facility, Columbia University, New York, New York, USA.
Michela MattioliCenter for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy.ORCID 0000000216929178
Mariano J Alvarez1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.
Yao Shen1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.
NCI-DREAM Community
Daniel GallahanDivision of Cancer Biology, National Cancer Institute, Bethesda, Maryland, USA.
Dinah SingerDivision of Cancer Biology, National Cancer Institute, Bethesda, Maryland, USA.
Julio Saez-RodriguezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.ORCID 0000000285528976
Yang Xie1] Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA. [2] Simmons Comprehensive Cancer Center, University of Texas, Southwestern Medical Center, Texas, USA.
Gustavo StolovitzkyIBM Computational Biology Center, IBM, T.J. Watson Research Center, Yorktown Heights, New York, USA.
Andrea Califano1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. [3] Department of Biomedical Informatics, Columbia University, New York, New York, USA. [4] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. [5] Institute for Cancer Genetics, Columbia University, New York, New York, USA. [6] Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA.
NCI-DREAM Community
Funding
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8MNation Center: Multi-Scale Study- Cellular Networks(RMI)U54CA121852 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2005 to 2015
$37.4MTissue and Outcomes CoreP50CA058207 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BLACKBURN, ELIZABETH H · 1992 to 2012
$32.7MTargeting the PI3K Signaling Pathway in Endometrial CarcinomaP50CA098258 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI BROADDUS, RUSSELL R · 2003 to 2020
$32.0MSystems-Based Predictions of Responses to Cancer TherapyU54CA112970 · NCI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI GRAY, JOE W. · 2004 to 2014
$27.1MQuantitavie and Computational Biology Graduate ProgramT32HG003284 · NHGRI · PRINCETON UNIVERSITY · PI Joshua Michael Akey, Stanislav Y. Shvartsman · 2004 to 2026
$9.9MSystems Biology of Tumor Progression and Drug ResistanceU01CA168426 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2012 to 2016
$6.5Mlntegration and Visualization of Diverse Biological DataR01GM071966 · NIGMS · PRINCETON UNIVERSITY · PI TROYANSKAYA, OLGA G · 2005 to 2022
$6.4MStructure-Based Prediction of the InteractomeR01GM081871 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BERGER, BONNIE · 2008 to 2020
$4.3MProfiling Signatures of synergistic Chemical Perturbations in Diverse Cellular CU01CA164184 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2011 to 2013
$2.1MPredicting Adjuvant Chemotherapy Response in Lung CancerR01CA152301 · NCI · UT SOUTHWESTERN MEDICAL CENTER · PI XIE, YANG · 2010 to 2014
$1.5MA Systems Approach to Elucidate Mechanisms od Drug Activity and SensivityU01HL111566 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2011 to 2013
$1.1MHoward Hughes Medical InstituteNCI NIH HHS 1U01CA164184-02NCI NIH HHS 5R01CA152301NCI NIH HHS 5U54CA121852-08NCI NIH HHS P30 CA016672NCI NIH HHS P50 CA058207NCI NIH HHS R01 CA152301NCI NIH HHS U01 CA164184NCI NIH HHS U01 CA168426NCI NIH HHS U54 CA112970NCI NIH HHS U54 CA121852NHGRI NIH HHS T32 HG003284NHLBI NIH HHS 3U01HL111566-02NHLBI NIH HHS U01 HL111566NIGMS NIH HHS R01 GM071966NIGMS NIH HHS R01 GM081871Wellcome Trust 104104
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.
Indexed as
Computer SimulationDrug CombinationsDrug SynergismAlgorithmsB-LymphocytesHumansDrug Combinations
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.