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For: Taguchi YH, Turki T. A new advanced in silico drug discovery method for novel coronavirus (SARS-CoV-2) with tensor decomposition-based unsupervised feature extraction. PLoS One 2020;15:e0238907. [PMID: 32915876 PMCID: PMC7485840 DOI: 10.1371/journal.pone.0238907] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Guan J, Fan Y, Wang S, Zhou F. Functions of MAP3Ks in antiviral immunity. Immunol Res 2023;71:814-832. [PMID: 37286768 PMCID: PMC10247270 DOI: 10.1007/s12026-023-09401-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/01/2023] [Indexed: 06/09/2023]
2
Mohamed EAR, Abdel-Rahman IM, Zaki MEA, Al-Khdhairawi A, Abdelhamid MM, Alqaisi AM, Rahim LBA, Abu-Hussein B, El-Sheikh AAK, Abdelwahab SF, Hassan HA. In silico prediction of potential inhibitors for SARS-CoV-2 Omicron variant using molecular docking and dynamics simulation-based drug repurposing. J Mol Model 2023;29:70. [PMID: 36808314 PMCID: PMC9939377 DOI: 10.1007/s00894-023-05457-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
3
A systematic review of artificial intelligence-based COVID-19 modeling on multimodal genetic information. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023;179:1-9. [PMID: 36809830 PMCID: PMC9938959 DOI: 10.1016/j.pbiomolbio.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/21/2023]
4
Turki T, Taguchi YH. A new machine learning based computational framework identifies therapeutic targets and unveils influential genes in pancreatic islet cells. Gene 2023;853:147038. [PMID: 36503891 DOI: 10.1016/j.gene.2022.147038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/19/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022]
5
Adapted tensor decomposition and PCA based unsupervised feature extraction select more biologically reasonable differentially expressed genes than conventional methods. Sci Rep 2022;12:17438. [PMID: 36261574 PMCID: PMC9580456 DOI: 10.1038/s41598-022-21474-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/27/2022] [Indexed: 01/12/2023]  Open
6
Taguchi YH, Turki T. Projection in genomic analysis: A theoretical basis to rationalize tensor decomposition and principal component analysis as feature selection tools. PLoS One 2022;17:e0275472. [PMID: 36173994 PMCID: PMC9521941 DOI: 10.1371/journal.pone.0275472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]  Open
7
Fuzo CA, Martins RB, Fraga-Silva TFC, Amstalden MK, Canassa De Leo T, Souza JP, Lima TM, Faccioli LH, Okamoto DN, Juliano MA, França SC, Juliano L, Bonato VLD, Arruda E, Dias-Baruffi M. Celastrol: A lead compound that inhibits SARS-CoV-2 replication, the activity of viral and human cysteine proteases, and virus-induced IL-6 secretion. Drug Dev Res 2022;83:1623-1640. [PMID: 35989498 PMCID: PMC9539158 DOI: 10.1002/ddr.21982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022]
8
Barati N, Motavallihaghi S, Nikfar B, Chaichian S, Momtazi-Borojeni AA. Potential therapeutic effects of Ivermectin in COVID-19. Exp Biol Med (Maywood) 2022;247:1388-1396. [PMID: 35686662 PMCID: PMC9442455 DOI: 10.1177/15353702221099579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
9
Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. Mol Divers 2022;27:959-985. [PMID: 35819579 DOI: 10.1007/s11030-022-10489-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 12/11/2022]
10
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. Pathogens 2022;11:pathogens11070743. [PMID: 35889989 PMCID: PMC9320269 DOI: 10.3390/pathogens11070743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/11/2022] [Accepted: 06/25/2022] [Indexed: 01/25/2023]  Open
11
Kumari P, Pradhan B, Koromina M, Patrinos GP, Steen KV. Discovery of new drug indications for COVID-19: A drug repurposing approach. PLoS One 2022;17:e0267095. [PMID: 35609015 PMCID: PMC9129022 DOI: 10.1371/journal.pone.0267095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/03/2022] [Indexed: 11/19/2022]  Open
12
Vázquez-Mendoza LH, Mendoza-Figueroa HL, García-Vázquez JB, Correa-Basurto J, García-Machorro J. In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking. Int J Mol Sci 2022;23:ijms23073987. [PMID: 35409348 PMCID: PMC8999907 DOI: 10.3390/ijms23073987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023]  Open
13
Qu N, Hui Z, Shen Z, Kan C, Hou N, Sun X, Han F. Thyroid Cancer and COVID-19: Prospects for Therapeutic Approaches and Drug Development. Front Endocrinol (Lausanne) 2022;13:873027. [PMID: 35600591 PMCID: PMC9114699 DOI: 10.3389/fendo.2022.873027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/04/2022] [Indexed: 02/05/2023]  Open
14
Kashid S, Suttee A, Kadam P, Khatik GL, Kasarla R. An In- Silico Studies for Immunomodulatory Potential of Phytoconstituents from a Naturally Occurring Herb Nigella Sativa. PHARMACOPHORE 2022. [DOI: 10.51847/e6ckqdrhe4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
15
Aronskyy I, Masoudi-Sobhanzadeh Y, Cappuccio A, Zaslavsky E. Advances in the computational landscape for repurposed drugs against COVID-19. Drug Discov Today 2021;26:2800-2815. [PMID: 34339864 PMCID: PMC8323501 DOI: 10.1016/j.drudis.2021.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/30/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
16
Lucchetta M, Pellegrini M. Drug repositioning by merging active subnetworks validated in cancer and COVID-19. Sci Rep 2021;11:19839. [PMID: 34615934 PMCID: PMC8494853 DOI: 10.1038/s41598-021-99399-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023]  Open
17
Asada K, Komatsu M, Shimoyama R, Takasawa K, Shinkai N, Sakai A, Bolatkan A, Yamada M, Takahashi S, Machino H, Kobayashi K, Kaneko S, Hamamoto R. Application of Artificial Intelligence in COVID-19 Diagnosis and Therapeutics. J Pers Med 2021;11:886. [PMID: 34575663 PMCID: PMC8471764 DOI: 10.3390/jpm11090886] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]  Open
18
Taguchi YH, Turki T. Application of Tensor Decomposition to Gene Expression of Infection of Mouse Hepatitis Virus Can Identify Critical Human Genes and Efffective Drugs for SARS-CoV-2 Infection. IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING 2021;15:746-758. [PMID: 34812273 PMCID: PMC8545047 DOI: 10.1109/jstsp.2021.3061251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/06/2020] [Accepted: 02/18/2021] [Indexed: 01/19/2023]
19
Mathematical formulation and application of kernel tensor decomposition based unsupervised feature extraction. Knowl Based Syst 2021. [DOI: 10.1016/j.knosys.2021.106834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
20
Wu YH, Yeh IJ, Phan NN, Yen MC, Hung JH, Chiao CC, Chen CF, Sun Z, Hsu HP, Wang CY, Lai MD. Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021;54:845-857. [PMID: 34176764 PMCID: PMC7997684 DOI: 10.1016/j.jmii.2021.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/03/2020] [Accepted: 03/07/2021] [Indexed: 12/23/2022]
21
Goris T, Pérez‐Valero Á, Martínez I, Yi D, Fernández‐Calleja L, San León D, Bornscheuer UT, Magadán‐Corpas P, Lombó F, Nogales J. Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids. Microb Biotechnol 2021;14:94-110. [PMID: 33047877 PMCID: PMC7675739 DOI: 10.1111/1751-7915.13675] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022]  Open
22
Lardone RD, Garay YC, Parodi P, de la Fuente S, Angeloni G, Bravo EO, Schmider AK, Irazoqui FJ. How glycobiology can help us treat and beat the COVID-19 pandemic. J Biol Chem 2021;296:100375. [PMID: 33548227 PMCID: PMC7857991 DOI: 10.1016/j.jbc.2021.100375] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022]  Open
23
Seoane R, Vidal S, Bouzaher YH, El Motiam A, Rivas C. The Interaction of Viruses with the Cellular Senescence Response. BIOLOGY 2020;9:E455. [PMID: 33317104 PMCID: PMC7764305 DOI: 10.3390/biology9120455] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
24
Mousavi SZ, Rahmanian M, Sami A. A connectivity map-based drug repurposing study and integrative analysis of transcriptomic profiling of SARS-CoV-2 infection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020;86:104610. [PMID: 33130005 PMCID: PMC7598903 DOI: 10.1016/j.meegid.2020.104610] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/29/2020] [Accepted: 10/23/2020] [Indexed: 12/15/2022]
25
De Vita S, Chini MG, Lauro G, Bifulco G. Accelerating the repurposing of FDA-approved drugs against coronavirus disease-19 (COVID-19). RSC Adv 2020;10:40867-40875. [PMID: 35519188 PMCID: PMC9057693 DOI: 10.1039/d0ra09010g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022]  Open
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