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For: Wani N, Raza K. Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods. Comput Biol Chem 2019;83:107120. [PMID: 31499298 DOI: 10.1016/j.compbiolchem.2019.107120] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/22/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Rabotnick MH, Ehlinger J, Haidari A, Goodrich JM. Prenatal exposures to endocrine disrupting chemicals: The role of multi-omics in understanding toxicity. Mol Cell Endocrinol 2023;578:112046. [PMID: 37598796 PMCID: PMC10592024 DOI: 10.1016/j.mce.2023.112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
2
Heuts BMH, Martens JHA. Understanding blood development and leukemia using sequencing-based technologies and human cell systems. Front Mol Biosci 2023;10:1266697. [PMID: 37886034 PMCID: PMC10598665 DOI: 10.3389/fmolb.2023.1266697] [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: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023]  Open
3
Erfanian N, Heydari AA, Feriz AM, Iañez P, Derakhshani A, Ghasemigol M, Farahpour M, Razavi SM, Nasseri S, Safarpour H, Sahebkar A. Deep learning applications in single-cell genomics and transcriptomics data analysis. Biomed Pharmacother 2023;165:115077. [PMID: 37393865 DOI: 10.1016/j.biopha.2023.115077] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/04/2023]  Open
4
Mu C, Zhao Q, Zhao Q, Yang L, Pang X, Liu T, Li X, Wang B, Fung SY, Cao H. Multi-omics in Crohn's disease: New insights from inside. Comput Struct Biotechnol J 2023;21:3054-3072. [PMID: 37273853 PMCID: PMC10238466 DOI: 10.1016/j.csbj.2023.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023]  Open
5
Wang Y, Tang S, Ma R, Zamit I, Wei Y, Pan Y. Multi-modal intermediate integrative methods in neuropsychiatric disorders: A review. Comput Struct Biotechnol J 2022;20:6149-6162. [DOI: 10.1016/j.csbj.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]  Open
6
Gupta S, Vundavilli H, Osorio RSA, Itoh MN, Mohsen A, Datta A, Mizuguchi K, Tripathi LP. Integrative Network Modeling Highlights the Crucial Roles of Rho-GDI Signaling Pathway in the Progression of Non-Small Cell Lung Cancer. IEEE J Biomed Health Inform 2022;26:4785-4793. [PMID: 35820010 DOI: 10.1109/jbhi.2022.3190038] [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: 11/08/2022]
7
Monroy Kuhn JM, Miok V, Lutter D. Correlation-guided Network Integration (CoNI), an R package for integrating numerical omics data that allows multiform graph representations to study molecular interaction networks. BIOINFORMATICS ADVANCES 2022;2:vbac042. [PMID: 36699352 PMCID: PMC9710706 DOI: 10.1093/bioadv/vbac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/09/2022] [Accepted: 06/01/2022] [Indexed: 02/01/2023]
8
Translational multi-omics microbiome research for strategies to improve cattle production and health. Emerg Top Life Sci 2022;6:201-213. [PMID: 35311904 DOI: 10.1042/etls20210257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/27/2022]
9
Correa R, Alonso-Pupo N, Hernández Rodríguez EW. Multi-omics data integration approaches for precision oncology. Mol Omics 2022;18:469-479. [DOI: 10.1039/d1mo00411e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
10
Wani N, Barh D, Raza K. Modular network inference between miRNA-mRNA expression profiles using weighted co-expression network analysis. J Integr Bioinform 2021;18:jib-2021-0029. [PMID: 34800012 PMCID: PMC8709739 DOI: 10.1515/jib-2021-0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022]  Open
11
Naseri A, Sharghi M, Hasheminejad SMH. Enhancing gene regulatory networks inference through hub-based data integration. Comput Biol Chem 2021;95:107589. [PMID: 34673384 DOI: 10.1016/j.compbiolchem.2021.107589] [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: 05/21/2021] [Revised: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 12/09/2022]
12
Yang L, Zheng S, Xu X, Sun Y, Wang X, Li J. Medical Data Mining Course Development in Postgraduate Medical Education: Web-Based Survey and Case Study. JMIR MEDICAL EDUCATION 2021;7:e24027. [PMID: 34596575 PMCID: PMC8520135 DOI: 10.2196/24027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/16/2020] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
13
Conard AM, Goodman N, Hu Y, Perrimon N, Singh R, Lawrence C, Larschan E. TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. Nucleic Acids Res 2021;49:W641-W653. [PMID: 34125906 PMCID: PMC8262710 DOI: 10.1093/nar/gkab384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 01/17/2023]  Open
14
Fiorentino G, Visintainer R, Domenici E, Lauria M, Marchetti L. MOUSSE: Multi-Omics Using Subject-Specific SignaturEs. Cancers (Basel) 2021;13:cancers13143423. [PMID: 34298641 PMCID: PMC8304726 DOI: 10.3390/cancers13143423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/06/2023]  Open
15
Picard M, Scott-Boyer MP, Bodein A, Périn O, Droit A. Integration strategies of multi-omics data for machine learning analysis. Comput Struct Biotechnol J 2021;19:3735-3746. [PMID: 34285775 PMCID: PMC8258788 DOI: 10.1016/j.csbj.2021.06.030] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022]  Open
16
Zhao N, Jia L, He X, Zhang B. Proteomics of mucosal exosomes of Cynoglossus semilaevis altered when infected by Vibrio harveyi. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021;119:104045. [PMID: 33582105 DOI: 10.1016/j.dci.2021.104045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
17
Zhou M, Varol A, Efferth T. Multi-omics approaches to improve malaria therapy. Pharmacol Res 2021;167:105570. [PMID: 33766628 DOI: 10.1016/j.phrs.2021.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023]
18
Cava C, Sabetian S, Castiglioni I. Patient-Specific Network for Personalized Breast Cancer Therapy with Multi-Omics Data. ENTROPY 2021;23:e23020225. [PMID: 33670375 PMCID: PMC7918754 DOI: 10.3390/e23020225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/06/2023]
19
Wani N, Raza K. MKL-GRNI: A parallel multiple kernel learning approach for supervised inference of large-scale gene regulatory networks. PeerJ Comput Sci 2021;7:e363. [PMID: 33817013 PMCID: PMC7924726 DOI: 10.7717/peerj-cs.363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
20
Labory J, Fierville M, Ait-El-Mkadem S, Bannwarth S, Paquis-Flucklinger V, Bottini S. Multi-Omics Approaches to Improve Mitochondrial Disease Diagnosis: Challenges, Advances, and Perspectives. Front Mol Biosci 2020;7:590842. [PMID: 33240932 PMCID: PMC7667268 DOI: 10.3389/fmolb.2020.590842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/14/2020] [Indexed: 01/06/2023]  Open
21
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms. Sci Rep 2020;10:14149. [PMID: 32843692 PMCID: PMC7447758 DOI: 10.1038/s41598-020-70941-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 07/22/2020] [Indexed: 01/01/2023]  Open
22
Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020;594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
23
Rigoglio NN, Rabelo ACS, Borghesi J, de Sá Schiavo Matias G, Fratini P, Prazeres PHDM, Pimentel CMMM, Birbrair A, Miglino MA. The Tumor Microenvironment: Focus on Extracellular Matrix. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020;1245:1-38. [PMID: 32266651 DOI: 10.1007/978-3-030-40146-7_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
24
Jiang D, Armour CR, Hu C, Mei M, Tian C, Sharpton TJ, Jiang Y. Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Front Genet 2019;10:995. [PMID: 31781153 PMCID: PMC6857202 DOI: 10.3389/fgene.2019.00995] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022]  Open
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