ArticleCell reports. Medicine2022
A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.
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Article in Cell reports. Medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36citing papers in PubMed
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Who cites it
36 citing papers in PubMed.
- Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states.Nature genetics · 2026Article
- DrugPTM-Bench: A Large-Scale Dataset for Predictive Modeling of Drug-Induced Cell Type-Specific Protein Post-Translational Modifications.bioRxiv : the preprint server for biology · 2026Article
- A Ponatinib-Associated Transcriptomic Signature: Implications for Cardiovascular Toxicity.International journal of molecular sciences · 2026Article
- Harnessing AI to fuse phenotypic signatures for drug target identification: progress in computational modeling.Briefings in bioinformatics · 2026Review
- Integrating artificial intelligence across the cancer drug discovery pipeline using a design-test-refine workflow.Frontiers in oncology · 2026Review
- Multimodal artificial intelligence and machine learning in oncology: from data integration to precision cancer care.Frontiers in digital health · 2026Review
- 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
- Enhancer RNA-mediated transcriptional regulatory programs reveal the malignant progression of glioma.Science advances · 2025Article
- NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks.Bioinformatics (Oxford, England) · 2025Article
- Benchmarking of protein interaction databases for integration with manually reconstructed signalling network models.The Journal of physiology · 2024Article
- Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results.Nucleic acids research · 2024Article
- Attention-based approach to predict drug-target interactions across seven target superfamilies.Bioinformatics (Oxford, England) · 2024Article
- CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations.Bioinformatics (Oxford, England) · 2024Article
- Deep representation learning of chemical-induced transcriptional profile for phenotype-based drug discovery.Nature communications · 2024Article
- Targeting neddylation and sumoylation in chemoresistant triple negative breast cancer.NPJ breast cancer · 2024Article
- Inference of drug off-target effects on cellular signaling using interactome-based deep learning.iScience · 2024Article
- Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress.Cancer discovery · 2024Article
- The Status Quo of Pharmacogenomics of Tyrosine Kinase Inhibitors in Precision Oncology: A Bibliometric Analysis of the Literature.Pharmaceutics · 2024Article
- Predicting anticancer synergistic drug combinations based on multi-task learning.BMC bioinformatics · 2023Article
Corrections and comments
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Authors and funding
29 authors.
Eugene F DouglassDepartment of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.
Robert J AllawayComputational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA.
Bence SzalaiSemmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary.
Wenyu WangResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Tingzhong TianInstitute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.
Adrià Fernández-TorrasJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Ron RealubitDepartment of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.
Charles KaranDepartment of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.
Shuyu ZhengResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Alberto PessiaResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Ziaurrehman TanoliResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Mohieddin JafariResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Fangping WanInstitute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.
Shuya LiInstitute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.
Yuanpeng XiongDepartment of Computer Science and Technology, Tsinghua University, Beijing 100084, China.
Miquel Duran-FrigolaJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Martino BertoniJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Pau Badia-I-MompelJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Lídia MateoJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Oriol Guitart-PlaJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Verena ChungComputational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA.
DREAM CTD-squared Pancancer Drug Activity Challenge Consortium
Jing TangResearch Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Jianyang ZengInstitute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.
Patrick AloyJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Julio Saez-RodriguezHeidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
Justin GuinneyComputational Oncology Group, Sage Bionetworks, 2901 Third Ave., Ste 330, Seattle, WA 98121, USA.
Daniela S GerhardOffice of Cancer Genomics, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
Andrea CalifanoDepartment of Systems Biology, Columbia University Irving Medical Center, 1130 Saint Nicholas Ave., New York, NY 10032, USA.
Funding
Systems Biology of Tumor Progression and Drug ResistanceU01CA168426 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2012 to 2016
$6.5MSystematic Identification and Pharmacological Targeting of Tumor Dependencies for Precision Cancer MedicineU01CA217858 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2017 to 2021
$6.1MFunctional Genomic Discovery of Pathway Targeted and Immune Modulatory Therapeutic Combinations in Hematologic MalignanciesU01CA217862 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI DRUKER, BRIAN J, TYNER, JEFFREY WALLACE · 2017 to 2021
$5.3MHigh-performance compute cluster for biomedical computingS10OD012351 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2012 to 2012
$2.0MStorage System for High Performance ComputingS10OD021764 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2016 to 2016
$600kNCI NIH HHS U01 CA168426NCI NIH HHS U01 CA217858NCI NIH HHS U01 CA217862NIH HHS S10 OD012351NIH HHS S10 OD021764
Abstract
The Columbia Cancer Target Discovery and Development (CTD2) Center is developing PANACEA, a resource comprising dose-responses and RNA sequencing (RNA-seq) profiles of 25 cell lines perturbed with ∼400 clinical oncology drugs, to study a tumor-specific drug mechanism of action. Here, this resource serves as the basis for a DREAM Challenge assessing the accuracy and sensitivity of computational algorithms for
Indexed as
PolypharmacologyAlgorithmsGene Expression ProfilingGene Expression Regulation, NeoplasticHumansNeoplasmsNeural Networks, ComputerProtein KinasesRNA, MessengerTranscription, GeneticProtein KinasesRNA, Messengercommunity challengeDREAM challengepharmacogenomicspolypharmacology
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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.