Omics data integration
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Despite growing numbers of immune checkpoint blockade (ICB) trials with available omics data, it remains challenging to evaluate the robustness of ICB response and immune evasion mechanisms comprehensively. To address these challenges, we integrated large-scale omics data and biomarkers on published ICB trials, nonimmunotherapy tumor profiles.
8p vibransone 28-03-2024 7 2 Download
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The rising prevalence of type 2 diabetes (T2D) poses a major global challenge. It remains unresolved to what extent transcriptomic signatures of metabolic dysregulation and T2D can be observed in easily accessible tissues such as blood. Additionally, large-scale human studies are required to further our understanding of the putative inflammatory component of insulin resistance and T2D.
17p vibransone 28-03-2024 3 2 Download
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Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. Methods: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play.
20p vioraclene 31-03-2024 4 2 Download
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Precision medicine (PM) can be defined as a predictive, preventive, personalized, and participatory healthcare service delivery model. Recent developments in molecular biology and information technology make PM a reality today through the use of massive amounts of genetic, ‘omics’, clinical, environmental, and lifestyle data.
12p vioraclene 31-03-2024 3 2 Download
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Multi-omics data are good resources for prognosis and survival prediction; however, these are difficult to integrate computationally. We introduce DeepProg, a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data.
15p vibransone 28-03-2024 6 2 Download
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Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a complex organ that is susceptible to numerous disorders.
27p vibransone 28-03-2024 7 2 Download
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In this study, we dissect the subcutaneous adipose tissue (SAT) methylome signature relevant to metabolic health by focusing on VF as the major risk factor of metabolic disease. We integrate results with genetic, blood methylation, SAT gene expression, blood metabo‑ lomic, dietary intake and metabolic phenotype data to assess and quantify genetic and environmental drivers of the identified signals, as well as their potential functional roles.
22p viellison 28-03-2024 4 2 Download
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Molecular measurements of the genome, the transcriptome, and the epigenome, often termed multi-omics data, provide an in-depth view on biological systems and their integration is crucial for gaining insights in complex regulatory processes.
21p viellison 28-03-2024 8 2 Download
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Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches.
17p vicwell 29-02-2024 5 2 Download
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Part 2 book "Comprehensive analysis of parasite biology" includes content: Methods to investigate metabolic systems in trypanosoma; the role of metabolomics in antiparasitic drug discovery; the importance of targeting lipid metabolism in parasites for drug discovery; carbon metabolism of plasmodium falciparum; mathematical modeling and omic data integration to understand dynamic adaptation of apicomplexan parasites and identify pharmaceutical targets; ... and other contents.
255p muasambanhan03 02-01-2024 7 2 Download
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Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF’s auto-inhibitory domain and subsequent constitutive kinase activation.
13p vileonardodavinci 23-12-2023 4 3 Download
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Lipid metabolism has a profound impact on gastric cancer (GC) progression and is a newly targetable vulnerability for cancer therapy. Given the importance of lipids in cancer cellular processes, in this study we employed lipidomic clinical and transcriptomic data to connect the variations of lipid metabolism changes of GC.
13p vialfrednobel 23-12-2023 6 3 Download
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Prediction of patient survival from tumor molecular ‘-omics’ data is a key step toward personalized medicine. Cox models performed on RNA profiling datasets are popular for clinical outcome predictions. But these models are applied in the context of “high dimension”, as the number p of covariates (gene expressions) greatly exceeds the number n of patients and e of events.
16p vialfrednobel 23-12-2023 3 3 Download
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The current management of lung cancer patients has reached a high level of complexity. Indeed, besides the traditional clinical variables (e.g., age, sex, TNM stage), new omics data have recently been introduced in clinical practice, thereby making more complex the decision-making process.
8p visharma 20-10-2023 4 2 Download
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It is common that cancer patients have different molecular signatures even though they have similar clinical features, such as histology, due to the heterogeneity of tumors. To overcome this variability, we previously developed a new approach incorporating prior biological knowledge that identifies knowledge-driven genomic interactions associated with outcomes of interest.
11p visteverogers 24-06-2023 5 3 Download
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Association studies using a single type of omics data have been successful in identifying diseaseassociated genetic markers, but the underlying mechanisms are unaddressed. To provide a possible explanation of how these genetic factors affect the disease phenotype, integration of multiple omics data is needed.
5p vihagrid 30-01-2023 5 3 Download
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Rapidly evolving high-throughput technology has made it cost-effective to collect multilevel omic data in clinical and biological studies. Different types of omic data collected from these studies provide both shared and complementary information, and can be integrated into association analysis to enhance the power of identifying novel disease-associated biomarkers.
4p vihagrid 30-01-2023 5 3 Download
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An accumulation of evidence has revealed the important role of epigenetic factors in explaining the etiopathogenesis of human diseases. Several empirical studies have successfully incorporated methylation data into models for disease prediction. However, it is still a challenge to integrate different types of omics data into prediction models, and the contribution of methylation information to prediction remains to be fully clarified.
5p vihagrid 30-01-2023 6 3 Download
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The advance of high-throughput technologies has made it cost-effective to collect diverse types of omic data in large-scale clinical and biological studies. While the collection of the vast amounts of multi-level omic data from these studies provides a great opportunity for genetic research, the high dimensionality of omic data and complex relationships among multi-level omic data bring tremendous analytic challenges.
12p vihagrid 30-01-2023 10 3 Download
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In studies with multi-omics data available, there is an opportunity to investigate interdependent mechanisms of biological causality. The GAW20 data set includes both DNA genotype and methylation measures before and after fenofibrate treatment. Using change in triglyceride (TG) levels pre- to posttreatment as outcome, we present a mediation analysis that incorporates methylation.
5p vihagrid 30-01-2023 7 3 Download