利用大数据变革药物研发。
Leveraging Big Data to Transform Drug Discovery.
作者信息
Glicksberg Benjamin S, Li Li, Chen Rong, Dudley Joel, Chen Bin
机构信息
Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
Department of Genetics and Genomic Sciences, Institute of Next Generation Healthcare, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
出版信息
Methods Mol Biol. 2019;1939:91-118. doi: 10.1007/978-1-4939-9089-4_6.
Abstract
The surge of public disease and drug-related data availability has facilitated the application of computational methodologies to transform drug discovery. In the current chapter, we outline and detail the various resources and tools one can leverage in order to perform such analyses. We further describe in depth the in silico workflows of two recent studies that have identified possible novel indications of existing drugs. Lastly, we delve into the caveats and considerations of this process to enable other researchers to perform rigorous computational drug discovery experiments of their own.
摘要
公共疾病和药物相关数据可用性的激增推动了计算方法在药物发现中的应用。在本章中，我们概述并详细介绍了可用于进行此类分析的各种资源和工具。我们还深入描述了两项近期研究的计算机模拟工作流程，这些研究确定了现有药物可能的新适应症。最后，我们深入探讨了这一过程中的注意事项，以使其他研究人员能够开展自己严谨的计算机辅助药物发现实验。
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本文引用的文献
1
Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.
Nat Commun. 2017 Jul 12;8:16022. doi: 10.1038/ncomms16022.
2
Celebrating parasites.
Nat Genet. 2017 Mar 30;49(4):483-484. doi: 10.1038/ng.3830.
3
Reproducibility of computational workflows is automated using continuous analysis.
Nat Biotechnol. 2017 Apr;35(4):342-346. doi: 10.1038/nbt.3780. Epub 2017 Mar 13.
4
Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling.
Gastroenterology. 2017 Jun;152(8):2022-2036. doi: 10.1053/j.gastro.2017.02.039. Epub 2017 Mar 8.
5
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.
Brief Bioinform. 2018 Jul 20;19(4):656-678. doi: 10.1093/bib/bbw136.
6
Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets.
Nat Genet. 2017 Mar;49(3):416-425. doi: 10.1038/ng.3787. Epub 2017 Feb 6.
7
Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach.
Sci Rep. 2017 Jan 4;7:39487. doi: 10.1038/srep39487.
8
Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study.
Science. 2016 Dec 23;354(6319). doi: 10.1126/science.aaf6814.
9
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Oncotarget. 2017 Jan 17;8(3):4079-4095. doi: 10.18632/oncotarget.13385.
10
Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses.
CPT Pharmacometrics Syst Pharmacol. 2016 Nov;5(11):599-607. doi: 10.1002/psp4.12108. Epub 2016 Nov 14.
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