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For: Wekesa JS, Kimwele M. A review of multi-omics data integration through deep learning approaches for disease diagnosis, prognosis, and treatment. Front Genet 2023;14:1199087. [PMID: 37547471 PMCID: PMC10398577 DOI: 10.3389/fgene.2023.1199087] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]  Open
Number Cited by Other Article(s)
1
Fan X, He Z, Guo J, Bu D, Han D, Qu X, Li Q, Cheng S, Han A, Guo J. Leveraging TME features and multi-omics data with an advanced deep learning framework for improved Cancer survival prediction. Sci Rep 2025;15:14282. [PMID: 40275021 PMCID: PMC12022115 DOI: 10.1038/s41598-025-98565-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Accepted: 04/14/2025] [Indexed: 04/26/2025]  Open
2
Danaei M, Rashnavadi H, Yeganegi M, Dastgheib SA, Bahrami R, Azizi S, Jayervand F, Masoudi A, Shahbazi A, Shiri A, Aghili K, Mazaheri M, Neamatzadeh H. Advancements in machine learning and biomarker integration for prenatal Down syndrome screening. Turk J Obstet Gynecol 2025;22:75-82. [PMID: 40062699 PMCID: PMC11894766 DOI: 10.4274/tjod.galenos.2025.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 02/09/2025] [Indexed: 03/14/2025]  Open
3
Ali SS, Li Q, Agrawal PB. Implementation of multi-omics in diagnosis of pediatric rare diseases. Pediatr Res 2025;97:1337-1344. [PMID: 39562738 DOI: 10.1038/s41390-024-03728-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 10/24/2024] [Accepted: 10/28/2024] [Indexed: 11/21/2024]
4
Alharbi F, Vakanski A, Zhang B, Elbashir MK, Mohammed M. Comparative Analysis of Multi-Omics Integration Using Graph Neural Networks for Cancer Classification. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2025;13:37724-37736. [PMID: 40123934 PMCID: PMC11928009 DOI: 10.1109/access.2025.3540769] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
5
Alemu R, Sharew NT, Arsano YY, Ahmed M, Tekola-Ayele F, Mersha TB, Amare AT. Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues. Hum Genomics 2025;19:8. [PMID: 39891174 PMCID: PMC11786457 DOI: 10.1186/s40246-025-00718-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 01/16/2025] [Indexed: 02/03/2025]  Open
6
Kaushik AC, Talware SK, Siddiqi MI. Integrative machine learning approach for identification of new molecular scaffold and prediction of inhibition responses in cancer cells using multi-omics data. Brief Funct Genomics 2025;24:elaf006. [PMID: 40251828 PMCID: PMC12008120 DOI: 10.1093/bfgp/elaf006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/07/2025] [Accepted: 03/20/2025] [Indexed: 04/21/2025]  Open
7
Che Y, Zhao M, Gao Y, Zhang Z, Zhang X. Application of machine learning for mass spectrometry-based multi-omics in thyroid diseases. Front Mol Biosci 2024;11:1483326. [PMID: 39741929 PMCID: PMC11685090 DOI: 10.3389/fmolb.2024.1483326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 12/02/2024] [Indexed: 01/03/2025]  Open
8
Du L, Gao P, Liu Z, Yin N, Wang X. TMODINET: A trustworthy multi-omics dynamic learning integration network for cancer diagnostic. Comput Biol Chem 2024;113:108202. [PMID: 39243551 DOI: 10.1016/j.compbiolchem.2024.108202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/23/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
9
Oh VKS, Li RW. Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2400458. [PMID: 39535493 DOI: 10.1002/advs.202400458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 09/16/2024] [Indexed: 11/16/2024]
10
Cai Z, Apolinário S, Baião AR, Pacini C, Sousa MD, Vinga S, Reddel RR, Robinson PJ, Garnett MJ, Zhong Q, Gonçalves E. Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning. Nat Commun 2024;15:10390. [PMID: 39614072 PMCID: PMC11607321 DOI: 10.1038/s41467-024-54771-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 11/18/2024] [Indexed: 12/01/2024]  Open
11
Tang X, Prodduturi N, Thompson K, Weinshilboum R, O’Sullivan C, Boughey J, Tizhoosh H, Klee E, Wang L, Goetz M, Suman V, Kalari K. OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks. Nucleic Acids Res 2024;52:e99. [PMID: 39445795 PMCID: PMC11602161 DOI: 10.1093/nar/gkae915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/14/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024]  Open
12
Vidanagamachchi SM, Waidyarathna KMGTR. Opportunities, challenges and future perspectives of using bioinformatics and artificial intelligence techniques on tropical disease identification using omics data. Front Digit Health 2024;6:1471200. [PMID: 39654982 PMCID: PMC11625773 DOI: 10.3389/fdgth.2024.1471200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 11/06/2024] [Indexed: 12/12/2024]  Open
13
Sanches PHG, de Melo NC, Porcari AM, de Carvalho LM. Integrating Molecular Perspectives: Strategies for Comprehensive Multi-Omics Integrative Data Analysis and Machine Learning Applications in Transcriptomics, Proteomics, and Metabolomics. BIOLOGY 2024;13:848. [PMID: 39596803 PMCID: PMC11592251 DOI: 10.3390/biology13110848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/19/2024] [Accepted: 07/25/2024] [Indexed: 11/29/2024]
14
Ballard JL, Wang Z, Li W, Shen L, Long Q. Deep learning-based approaches for multi-omics data integration and analysis. BioData Min 2024;17:38. [PMID: 39358793 PMCID: PMC11446004 DOI: 10.1186/s13040-024-00391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 09/06/2024] [Indexed: 10/04/2024]  Open
15
Cirinciani M, Da Pozzo E, Trincavelli ML, Milazzo P, Martini C. Drug Mechanism: A bioinformatic update. Biochem Pharmacol 2024;228:116078. [PMID: 38402909 DOI: 10.1016/j.bcp.2024.116078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
16
Wang Y, Hong J, Lu Y, Sheng N, Fu Y, Yang L, Meng L, Huang L, Wang H. A Controllability Reinforcement Learning Method for Pancreatic Cancer Biomarker Identification. IEEE Trans Nanobioscience 2024;23:556-563. [PMID: 39133596 DOI: 10.1109/tnb.2024.3441689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2024]
17
Vitorino R. Transforming Clinical Research: The Power of High-Throughput Omics Integration. Proteomes 2024;12:25. [PMID: 39311198 PMCID: PMC11417901 DOI: 10.3390/proteomes12030025] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/26/2024]  Open
18
Abbasi AF, Asim MN, Ahmed S, Vollmer S, Dengel A. Survival prediction landscape: an in-depth systematic literature review on activities, methods, tools, diseases, and databases. Front Artif Intell 2024;7:1428501. [PMID: 39021434 PMCID: PMC11252047 DOI: 10.3389/frai.2024.1428501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024]  Open
19
Lyu C, Joehanes R, Huan T, Levy D, Li Y, Wang M, Liu X, Liu C, Ma J. Enhancing selection of alcohol consumption-associated genes by random forest. Br J Nutr 2024;131:2058-2067. [PMID: 38606596 PMCID: PMC11216877 DOI: 10.1017/s0007114524000795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
20
Aljarallah NA, Dutta AK, Sait ARW. A Systematic Review of Genetics- and Molecular-Pathway-Based Machine Learning Models for Neurological Disorder Diagnosis. Int J Mol Sci 2024;25:6422. [PMID: 38928128 PMCID: PMC11203850 DOI: 10.3390/ijms25126422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]  Open
21
Chakraborty S, Sharma G, Karmakar S, Banerjee S. Multi-OMICS approaches in cancer biology: New era in cancer therapy. Biochim Biophys Acta Mol Basis Dis 2024;1870:167120. [PMID: 38484941 DOI: 10.1016/j.bbadis.2024.167120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/01/2024]
22
Labarga A, Martínez-Gonzalez J, Barajas M. Integrative Multi-Omics Analysis for Etiology Classification and Biomarker Discovery in Stroke: Advancing towards Precision Medicine. BIOLOGY 2024;13:338. [PMID: 38785820 PMCID: PMC11149453 DOI: 10.3390/biology13050338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
23
Tang X, Prodduturi N, Thompson KJ, Weinshilboum RM, O'Sullivan CC, Boughey JC, Tizhoosh H, Klee EW, Wang L, Goetz MP, Suman V, Kalari KR. OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586001. [PMID: 38585820 PMCID: PMC10996492 DOI: 10.1101/2024.03.21.586001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
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