Network-based analyses of multiomics data in biomedicine
Abstract Network representations of data are designed to encode relationships between concepts as sets of edges between nodes. Human biology is inherently complex and is represented by data that often exists in a hierarchical nature. One canonical example is the relationship that exists within and b...
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| Format: | Article |
| Language: | English |
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BMC
2025-05-01
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| Series: | BioData Mining |
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| Online Access: | https://doi.org/10.1186/s13040-025-00452-x |
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| author | Rachit Kumar Joseph D. Romano Marylyn D. Ritchie |
| author_facet | Rachit Kumar Joseph D. Romano Marylyn D. Ritchie |
| author_sort | Rachit Kumar |
| collection | DOAJ |
| description | Abstract Network representations of data are designed to encode relationships between concepts as sets of edges between nodes. Human biology is inherently complex and is represented by data that often exists in a hierarchical nature. One canonical example is the relationship that exists within and between various -omics datasets, including genomics, transcriptomics, and proteomics, among others. Encoding such data in a network-based or graph-based representation allows the explicit incorporation of such relationships into various biomedical big data tasks, including (but not limited to) disease subtyping, interaction prediction, biomarker identification, and patient classification. This review will present various existing approaches in using network representations and analysis of data in multiomics in the framework of deep learning and machine learning approaches, subdivided into supervised and unsupervised approaches, to identify benefits and drawbacks of various approaches as well as the possible next steps for the field. |
| format | Article |
| id | doaj-art-d9c639bee7374ef6979a8f6dc3a2e08a |
| institution | DOAJ |
| issn | 1756-0381 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BioData Mining |
| spelling | doaj-art-d9c639bee7374ef6979a8f6dc3a2e08a2025-08-20T03:16:50ZengBMCBioData Mining1756-03812025-05-0118112210.1186/s13040-025-00452-xNetwork-based analyses of multiomics data in biomedicineRachit Kumar0Joseph D. Romano1Marylyn D. Ritchie2Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of PennsylvaniaDivision of Informatics, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of PennsylvaniaDivision of Informatics, Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of PennsylvaniaAbstract Network representations of data are designed to encode relationships between concepts as sets of edges between nodes. Human biology is inherently complex and is represented by data that often exists in a hierarchical nature. One canonical example is the relationship that exists within and between various -omics datasets, including genomics, transcriptomics, and proteomics, among others. Encoding such data in a network-based or graph-based representation allows the explicit incorporation of such relationships into various biomedical big data tasks, including (but not limited to) disease subtyping, interaction prediction, biomarker identification, and patient classification. This review will present various existing approaches in using network representations and analysis of data in multiomics in the framework of deep learning and machine learning approaches, subdivided into supervised and unsupervised approaches, to identify benefits and drawbacks of various approaches as well as the possible next steps for the field.https://doi.org/10.1186/s13040-025-00452-xReviewMultiomicsNetworksGraphsDeep learningMachine learning |
| spellingShingle | Rachit Kumar Joseph D. Romano Marylyn D. Ritchie Network-based analyses of multiomics data in biomedicine BioData Mining Review Multiomics Networks Graphs Deep learning Machine learning |
| title | Network-based analyses of multiomics data in biomedicine |
| title_full | Network-based analyses of multiomics data in biomedicine |
| title_fullStr | Network-based analyses of multiomics data in biomedicine |
| title_full_unstemmed | Network-based analyses of multiomics data in biomedicine |
| title_short | Network-based analyses of multiomics data in biomedicine |
| title_sort | network based analyses of multiomics data in biomedicine |
| topic | Review Multiomics Networks Graphs Deep learning Machine learning |
| url | https://doi.org/10.1186/s13040-025-00452-x |
| work_keys_str_mv | AT rachitkumar networkbasedanalysesofmultiomicsdatainbiomedicine AT josephdromano networkbasedanalysesofmultiomicsdatainbiomedicine AT marylyndritchie networkbasedanalysesofmultiomicsdatainbiomedicine |