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The COVID-19 Drug and Gene Set Library

Maxim V. Kuleshov, Daniel J. Stein, Daniel J.B. Clarke, Eryk Kropiwnicki, Kathleen M. Jagodnik, Alon Bartal, John E. Evangelista, Jason Hom, Minxuan Cheng, Allison Bailey, Abigail Zhou, Laura B. Ferguson (+2 others)
2020 Patterns  
Graphical Abstract Highlights d Collections of drug and gene sets relevant to COVID-19 research d Detailed comparison of results from six in vitro SARS-CoV-2 drug screens d Analysis of hits that up-or  ...  downregulate the ACE2 expression module d Machine-learning framework to further prioritize hits and other similar drugs  ...  The COVID-19 Drug and Gene Set Library provides such utility.  ... 
doi:10.1016/j.patter.2020.100090 pmid:32838343 pmcid:PMC7381899 fatcat:ef7ph4xztzcyfesgrfrt3jjuyq

COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics

Dmitry Tworowski, Alessandro Gorohovski, Sumit Mukherjee, Gon Carmi, Eliad Levy, Rajesh Detroja, Sunanda Biswas Mukherjee, Milana Frenkel-Morgenstern
2020 Nucleic Acids Research  
To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar.  ...  The recent outbreak of COVID-19 has generated an enormous amount of Big Data.  ...  ACKNOWLEDGEMENTS E.L. has been working as a volunteer at the Frenkel-Morgenstern's lab in the COVID-19 related project.  ... 
doi:10.1093/nar/gkaa969 pmid:33166390 fatcat:bq6txwroufcz7dmjn36ygll3bm

Androgen regulates SARS-CoV-2 receptor levels and is associated with severe COVID-19 symptoms in men [article]

Zaniar Ghazizadeh, Homa Majd, Mikayla Richter, Ryan Samuel, Seyedeh Maryam Zekavat, Hosseinali Asgharian, Sina Farahvashi, Ali Kalantari, Jonathan Ramirez, Hongyu Zhao, Pradeep Natarajan, Hani Goodarzi (+1 others)
2020 biorxiv/medrxiv  
These findings provide important insights on the mechanism of increased disease susceptibility in male COVID-19 patients and identify androgen receptor inhibition as a potential therapeutic strategy.  ...  Finally, clinical data on coronavirus disease 2019 (COVID-19) patients demonstrated that abnormal androgen states are significantly associated with severe disease complications and cardiac injury as measured  ...  Acknowledgements We are grateful to the UCSF program for breakthrough biomedical research and Sandler foundation for the grant to F.F. that supported this work.  ... 
doi:10.1101/2020.05.12.091082 pmid:32511360 pmcid:PMC7263488 fatcat:vkxkxf2trvdxxpa2rgdm63jn6e

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning

Eryk Kropiwnicki, John E Evangelista, Daniel J Stein, Daniel J B Clarke, Alexander Lachmann, Maxim V Kuleshov, Minji Jeon, Kathleen M Jagodnik, Avi Ma'ayan
2021 Database: The Journal of Biological Databases and Curation  
In addition, drug set libraries can be used as the underlying database for drug set enrichment analysis.  ...  Drugmonizome-ML enables users to construct customized machine learning pipelines using the drug set libraries from Drugmonizome.  ...  The COVID-19 Drug and Gene Set Library (46) was developed to collect drug and gene sets related to COVID-19, including drug sets extracted from 12 publications that describe SARS-CoV-2 in vitro drug screens  ... 
doi:10.1093/database/baab017 pmid:33787872 pmcid:PMC8011435 fatcat:s542rexyqvecppvlfcz467liey

Gene Signature-Based Drug Repositioning [chapter]

Zhilong Jia, Xinyu Song, Jinlong Shi, Weidong Wang, Kunlun He
2021 Drug Repurposing - Molecular Aspects and Therapeutic Applications [Working Title]  
We will cover the following topics in this chapter. 1) An introduction to the basic discipline of gene signature-based drug repurposing; 2) databases of genes, drugs and diseases; 3) gene signature databases  ...  of the approved drugs; 4) gene signature databases of various diseases; 5) gene signature-based methods and tools for drug repositioning; 6) new omics technology for drug repositioning; 7) drug repositioning  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China [grant number 31701155].  ... 
doi:10.5772/intechopen.101377 fatcat:s4w2wts33bewfcnnbplvjr5efq

Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men

Ryan M. Samuel, Homa Majd, Mikayla N. Richter, Zaniar Ghazizadeh, Seyedeh Maryam Zekavat, Albertas Navickas, Jonathan T. Ramirez, Hosseinali Asgharian, Camille R. Simoneau, Luke R. Bonser, Kyung Duk Koh, Miguel Garcia-Knight (+12 others)
2020 Cell Stem Cell  
These findings offer insights on the mechanism of disproportionate disease susceptibility in men and identify antiandrogenic drugs as candidate therapeutics for COVID-19.  ...  Finally, clinical data on COVID-19 patients demonstrated that prostate diseases, which are linked to elevated androgen, are significant risk factors and that genetic variants that increase androgen levels  ...  (E) Gene set enrichment analysis of androgen signaling genes on COVID-19 hospitalization using the COVID-19 host genetics initiative GWAS results.  ... 
doi:10.1016/j.stem.2020.11.009 pmid:33232663 pmcid:PMC7670929 fatcat:d7rxvl24g5cgrfdokj5wtbq2lq

Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates

Takahiro Konuma, Kotaro Ogawa, Yukinori Okada
2021 Human Molecular Genetics  
in broad disease categories, we applied GWAS summary statistics of large-scale European meta-analysis (17 traits; naverage = 201 849) and the hospitalized COVID-19 (n = 900 687), which has urgent need  ...  After confirmation of the statistical robustness by the application of the null GWAS data and of enrichment in true-positive drug-disease relationships by the application of UK-Biobank GWAS summary statistics  ...  Acknowledgements We acknowledge the members of the COVID-19 Host Genetics Initiative for kindly releasing the GWAS summary statistics.  ... 
doi:10.1093/hmg/ddab049 pmid:33577681 pmcid:PMC7928862 fatcat:yjhi3uga3jc27i6uctish7wltm

Towards Preparing a Knowledgebase to Explore Potential Drugs and Biomedical Entities Related to COVID-19 (Preprint)

Junaed Younus Khan, Md. Tawkat Islam Khondaker, Iram Tazim Hoque, Hamada R. H. Al-Absi, Mohammad Saifur Rahman, Reto Guler, Tanvir Alam, M. Sohel Rahman
2020 JMIR Medical Informatics  
Six topic-specific dictionaries, including human genes, human miRNAs, diseases, Protein Databank, drugs, and drug side effects, were integrated to mine all scientific evidence related to COVID-19.  ...  Based on the literature mining, we identified 1805 diseases, 2454 drugs, 1910 genes that are related to coronavirus related diseases including COVID-19.  ...  Acknowledgments The open access publication of this article was funded by the College of Science and Engineering, Hamad Bin Khalifa University. Conflicts of Interest None declared.  ... 
doi:10.2196/21648 pmid:33055059 fatcat:327vqcjfm5f7hnxtozqi2j2g2e

Drug repurposing for COVID-19 based on an integrative meta-analysis of SARS-CoV-2 induced gene signature in human airway epithelium

Rajaneesh K. Gupta, Enyinna L. Nwachuku, Benjamin E. Zusman, Ruchira M. Jha, Ava M. Puccio, Etsuro Ito
2021 PLoS ONE  
Drug database, extracted from the Metacore and IPA, identified 15 drug targets (with information on COVID-19 pathogenesis) with 46 existing drugs as potential-novel candidates for repurposing for COVID  ...  We found 35 novel drugs that inhibit targets (ALPL, CXCL8, and IL6) already in clinical trials for COVID-19.  ...  Acknowledgments Authors thank to Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh for support on data analysis by CLC Workbench Genomics 20 and Ingenuity  ... 
doi:10.1371/journal.pone.0257784 pmid:34582497 fatcat:e2mg3b3jrbchlbmpenkm3del4q

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Anna C. Aschenbrenner, German COVID-19 Omics Initiative (DeCOI), Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki (+44 others)
2021 Genome Medicine  
Methods In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed  ...  Background The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world.  ...  Deutsche COVID- 19 The study was funded in part by the Hellenic Institute for the Study of Sepsis.  ... 
doi:10.1186/s13073-020-00823-5 pmid:33441124 fatcat:iyj3fktsuvhh7o5eno33xawlci

Bioinformatics and System Biology Approach to Reveal the Interaction Network and the Therapeutic Implications for Non-Small Cell Lung Cancer Patients With COVID-19

Zhenjie Zhuang, Xiaoying Zhong, Qianying Chen, Huiqi Chen, Zhanhua Liu
2022 Frontiers in Pharmacology  
-19 and NSCLC.Results: A total of 122 COVID-19/NSCLC interactional genes and 21 interactional hub genes were identified.  ...  With the increasing number of non-small-cell lung cancer (NSCLC) patients with COVID-19, there is an urgent need of efficacious drugs for the treatment of COVID-19/NSCLC.Methods: Based on a comprehensive  ...  Enrichr, containing 192 gene-set libraries and counting, is a comprehensive web portal for gene-set enrichment analysis ( Kuleshov et al., 2016) .  ... 
doi:10.3389/fphar.2022.857730 pmid:35721149 pmcid:PMC9201692 fatcat:s4w6jrp3gzc63arnh6cxkunwcy

The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization [article]

Bruce T Schultz, Andrea Zaliani, Christian Ebeling, Jeanette Reinshagen, Denisa Bojkova, Vanessa Lage-Rupprecht, Reagon Karki, Soeren Lukassen, Yojana Gadiya, Neal Giri Ravindra, Sayoni Das, Shounak Baksi (+19 others)
2020 bioRxiv   pre-print
In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of several disease maps and experimental data focused on SARS-CoV-2 / COVID-19  ...  However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from  ...  Briefly, gene symbol lists were assembled from their respective subgraph or dataset and compared against multiple pathway gene set libraries including Reactome, KEGG, and WikiPathways.  ... 
doi:10.1101/2020.09.23.308239 fatcat:ygkngehsq5crdmq7cqp54zwsae

COVID-19Base: A knowledgebase to explore biomedical entities related to COVID-19 [article]

Junaed Younus Khan, Md. Tawkat Islam Khondaker, Iram Tazim Hoque, Hamada Al-Absi, Mohammad Saifur Rahman, Tanvir Alam, M. Sohel Rahman
2020 arXiv   pre-print
We considered seven topic-specific dictionaries, including human genes, human miRNAs, human lncRNAs, diseases, Protein Databank, drugs, and drug side effects, are integrated to mine all scientific evidence  ...  related to COVID-19.  ...  Informatively, although the US Food and Drugs Administration (FDA) had previously granted authorization to use this drug for Covid-19, it recently cautions against its use outside of the hospital setting  ... 
arXiv:2005.05954v1 fatcat:sygw22nuszafjmybkhdlgrmzjq

Network-Based Approach to Repurpose Approved Drugs for COVID-19 by Integrating GWAS and Text Mining Data

Shuang Liang, Hui-Min Liu, Dan-Yang Liu, Wan-Qiang Lv, Sheng-Ran Wang, Jia-Chen Liu, Jonathan Greenbaum, Hui Shen, Hong-Mei Xiao, Hong-Wen Deng
2022 Processes  
By applying an integrated network-based approach to quantify the interactions of the COVID-19-related gene modules and drug-related gene modules, we prioritized 13 approved drugs (e.g., alitretinoin, clocortolone  ...  Here, we first identified lung-specific gene regulatory/interaction subnetworks (COVID-19-related genes modules) enriched for COVID-19-associated genes obtained from GWAS and text mining.  ...  Step 1: Significant COVID-19-associated genes are identified by combining the GWAS results and literature findings, followed by a filtering step based on the gene set enrichment analysis.  ... 
doi:10.3390/pr10020326 fatcat:lurs46f3wrd7jlwe7fkvvgmaki

Drug Repurposing for COVID-19 using Graph Neural Network with Genetic, Mechanistic, and Epidemiological Validation [article]

Kanglin Hsieh, Yinyin Wang, Luyao Chen, Zhongming Zhao, Sean Savitz, Xiaoqian Jiang, Jing Tang, Yejin Kim
2020 arXiv   pre-print
We built a SARS-CoV-2 knowledge graph based on the interactions among virus baits, host genes, pathways, drugs, and phenotypes.  ...  We first collected all the available drugs (n= 3,635) involved in COVID-19 patient treatment through CTDbase.  ...  Drug A Drug B # COVID-19 genes that Drug A hits # COVID-19 genes that Drug B hits # COVID-19 genes that either Drug A or B hit Etoposide Sirolimus 2 22 24 Mefloquine Sirolimus 1  ... 
arXiv:2009.10931v1 fatcat:ivy62qxdqrguveoczyuyaia6ra
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