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- Mathema, Vivek Bhakta, et al.
(author)
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Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine
- 2023
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In: Computational and Structural Biotechnology Journal. - : Elsevier. - 2001-0370. ; 21, s. 1372-1382
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Research review (peer-reviewed)abstract
- Cancer progression is linked to gene-environment interactions that alter cellular homeostasis. The use of biomarkers as early indicators of disease manifestation and progression can substantially improve diagnosis and treatment. Large omics datasets generated by high-throughput profiling technologies, such as microarrays, RNA sequencing, whole-genome shotgun sequencing, nuclear magnetic resonance, and mass spectrometry, have enabled data-driven biomarker discoveries. The identification of differentially expressed traits as molecular markers has traditionally relied on statistical techniques that are often limited to linear parametric modeling. The heterogeneity, epigenetic changes, and high degree of polymorphism observed in oncogenes demand biomarker-assisted personalized medication schemes. Deep learning (DL), a major subunit of machine learning (ML), has been increasingly utilized in recent years to investigate various diseases. The combination of ML/DL approaches for performance optimization across multi-omics datasets produces robust ensemble-learning prediction models, which are becoming useful in precision medicine. This review focuses on the recent development of ML/DL methods to provide integrative solutions in discovering cancer-related biomarkers, and their utilization in precision medicine.
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| 2. |
- Sen, Partho, 1983-, et al.
(author)
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Integrating Omics Data in Genome-Scale Metabolic Modeling : A Methodological Perspective for Precision Medicine
- 2023
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In: Metabolites. - : MDPI. - 2218-1989 .- 2218-1989. ; 13:7
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Research review (peer-reviewed)abstract
- Recent advancements in omics technologies have generated a wealth of biological data. Integrating these data within mathematical models is essential to fully leverage their potential. Genome-scale metabolic models (GEMs) provide a robust framework for studying complex biological systems. GEMs have significantly contributed to our understanding of human metabolism, including the intrinsic relationship between the gut microbiome and the host metabolism. In this review, we highlight the contributions of GEMs and discuss the critical challenges that must be overcome to ensure their reproducibility and enhance their prediction accuracy, particularly in the context of precision medicine. We also explore the role of machine learning in addressing these challenges within GEMs. The integration of omics data with GEMs has the potential to lead to new insights, and to advance our understanding of molecular mechanisms in human health and disease.
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