SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets

Vasan, 2019, A view on drug resistance in cancer, Nature, 575, 299, 10.1038/s41586-019-1730-1 Nathan, 2020, Resisting antimicrobial resistance, Nat Rev Microbiol, 18, 259, 10.1038/s41579-020-0348-5 Boshuizen, 2020, Rational cancer treatment combinations: an urgent clinical need, Mol Cell, 78, 1002, 10.1016/j.molcel.2020.05.031 Berenbaum, 1989, What is synergy?, Pharmacol Rev, 41, 93 Loewe, 1953, The problem of synergism and antagonism of combined drugs, Arzneimittelforschung, 3, 285 Bliss, 1939, The toxicity of poisons applied jointly, Ann App Biol, 26, 585, 10.1111/j.1744-7348.1939.tb06990.x Yadav, 2015, Searching for drug synergy in complex dose–response landscapes using an interaction potency model, Comput Struct Biotechnol J, 13, 504, 10.1016/j.csbj.2015.09.001 Malyutina, 2019, Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer, PLoS Computat Biol, 15, e1006752, 10.1371/journal.pcbi.1006752 Chou, 2010, Drug combination studies and their synergy quantification using the Chou-Talalay method, Cancer Res, 70, 440, 10.1158/0008-5472.CAN-09-1947 Twarog, 2016, BRAID: a unifying paradigm for the analysis of combined drug action, Sci Rep, 6, 25523, 10.1038/srep25523 Di Veroli, 2016, Combenefit: an interactive platform for the analysis and visualization of drug combinations, Bioinformatics, 32, 2866, 10.1093/bioinformatics/btw230 Ianevski, 2017, SynergyFinder: a web application for analyzing drug combination dose–response matrix data, Bioinformatics, 33, 2413, 10.1093/bioinformatics/btx162 Wooten, 2021, Synergy: a Python library for calculating, analyzing, and visualizing drug combination synergy, Bioinformatics, 37, 1473, 10.1093/bioinformatics/btaa826 Ianevski, 2020, SynergyFinder 2.0: visual analytics of multi-drug combination synergies, Nucleic Acids Res, 48, W488, 10.1093/nar/gkaa216 Cokol-Cakmak, 2020, Guided screen for synergistic three-drug combinations, PLoS One, 15, e0235929, 10.1371/journal.pone.0235929 Meyer, 2020, Charting the fragmented landscape of drug synergy, Trends Pharmacol Sci, 41, 266, 10.1016/j.tips.2020.01.011 Vlot, 2019, Applying synergy metrics to combination screening data: agreements, disagreements and pitfalls, Drug Discov Today, 24, 2286, 10.1016/j.drudis.2019.09.002 Bazgir, 2020, Representation of features as images with neighborhood dependencies for compatibility with convolutional neural networks, Nat Commun, 11, 4391, 10.1038/s41467-020-18197-y Altman, 2011, How to obtain the P value from a confidence interval, BMJ, 343, d2304, 10.1136/bmj.d2304 Kim, 2021, PubChem in 2021: new data content and improved web interfaces, Nucleic Acids Res, 49, D1388, 10.1093/nar/gkaa971 Mendez, 2019, ChEMBL: towards direct deposition of bioassay data, Nucleic Acids Res, 47, D930, 10.1093/nar/gky1075 Hastings, 2016, ChEBI in 2016: improved services and an expanding collection of metabolites, Nucleic Acids Res, 44, D1214, 10.1093/nar/gkv1031 Wishart, 2018, DrugBank 5.0: a major update to the DrugBank database for 2018, Nucleic Acids Res, 46, D1074, 10.1093/nar/gkx1037 Gilson, 2016, BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology, Nucleic Acids Res, 44, D1045, 10.1093/nar/gkv1072 Whirl‐Carrillo, 2021, An evidence-based framework for evaluating pharmacogenomics knowledge for personalized medicine, Clin Pharmacol Ther, 110, 563, 10.1002/cpt.2350 Armstrong, 2020, The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY, Nucleic Acids Res, D1006 Sterling, 2015, ZINC 15 – ligand discovery for everyone, J Chem Inf Model, 55, 2324, 10.1021/acs.jcim.5b00559 Tanoli, 2022, Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments, Brief Bioinform, 23, bbab350, 10.1093/bib/bbab350 Bairoch, 2018, The Cellosaurus, a cell-line knowledge resource, J Biomol Tech, 29, 25, 10.7171/jbt.18-2902-002 Ansbro, 2020, Modulation of triple artemisinin-based combination therapy pharmacodynamics by plasmodium falciparum genotype, ACS Pharmacol Transl Sci, 3, 1144, 10.1021/acsptsci.0c00110 Zagidullin, 2019, DrugComb: an integrative cancer drug combination data portal, Nucleic Acids Res, 47, W43, 10.1093/nar/gkz337 O'Neil, 2016, An unbiased oncology compound screen to identify novel combination strategies, Mol Cancer Ther, 15, 1155, 10.1158/1535-7163.MCT-15-0843 Preuer, 2018, DeepSynergy: predicting anti-cancer drug synergy with deep learning, Bioinformatics, 34, 1538, 10.1093/bioinformatics/btx806 Menden, 2019, Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen, Nat Commun, 10, 2674, 10.1038/s41467-019-09799-2 Li, 2018, Network propagation predicts drug synergy in cancers, Cancer Res, 78, 5446, 10.1158/0008-5472.CAN-18-0740 Zheng, 2021, DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal, Nucleic Acids Res, 49, W174, 10.1093/nar/gkab438 Liu, 2020, DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy, Nucleic Acids Res, 48, D871 Douglass, 2022, A community challenge for pancancer drug mechanism of action inference from perturbational profile data, Cell Rep Med, 3, 100492, 10.1016/j.xcrm.2021.100492 Zhang, 2021, The tumor therapy landscape of synthetic lethality, Nat Commun, 12, 1275, 10.1038/s41467-021-21544-2 Shah, 2021, The Aurora kinase/β-catenin axis contributes to dexamethasone resistance in leukemia, NPJ Precis Oncol, 5, 13, 10.1038/s41698-021-00148-5 Jones, 2019, Epigenetic therapy in immune-oncology, Nat Rev Cancer, 19, 151, 10.1038/s41568-019-0109-9 Fernandes Neto, 2020, Multiple low dose therapy as an effective strategy to treat EGFR inhibitor-resistant NSCLC tumours, Nat Commun, 11, 3157, 10.1038/s41467-020-16952-9 Ozkan-Dagliyan, 2020, Low-dose vertical inhibition of the RAF-MEK-ERK cascade causes apoptotic death of KRAS mutant cancers, Cell Rep, 31, 107764, 10.1016/j.celrep.2020.107764 Caumanns, 2019, Low-dose triple drug combination targeting the PI3K/AKT/mTOR pathway and the MAPK pathway is an effective approach in ovarian clear cell carcinoma, Cancer Lett, 461, 102, 10.1016/j.canlet.2019.07.004 Van Cutsem, 2019, Binimetinib, encorafenib, and cetuximab triplet therapy for patients with BRAF V600E–mutant metastatic colorectal cancer: safety lead-in results from the phase III BEACON colorectal cancer study, J Clin Oncol, 37, 1460, 10.1200/JCO.18.02459 Greco, 1992, Consensus on concepts and terminology for combined-action assessment: the Saariselkä agreement, Arch Complex Environ Stud, 4, 65 Tang, 2015, What is synergy? the Saariselkä agreement revisited, Front Pharmacol, 6, 181, 10.3389/fphar.2015.00181 Wood, 2012, Mechanism-independent method for predicting response to multidrug combinations in bacteria, Proc Natl Acad Sci U S A, 109, 12254, 10.1073/pnas.1201281109 Adam, 2020, Machine learning approaches to drug response prediction: challenges and recent progress, NPJ Precis Oncol, 4, 19, 10.1038/s41698-020-0122-1 Kim, 2021, Anticancer drug synergy prediction in understudied tissues using transfer learning, J Am Med Inform Assoc, 28, 42, 10.1093/jamia/ocaa212