Integrative Biology Approaches Applied to Human Diseases

Urbanski, Alysson H.; Araújo, José Deney Alves; Creighton, Rachel; Nakaya, Helder I.

doi:10.15586/computationalbiology.2019.ch2

Cited by 2 publications

(2 citation statements)

References 114 publications

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“…With the help of these online platforms, a shortened study curve was presented to researchers regarding omics data analysis. [85][86][87] As an example, MetaboAnalyst (https://www.metaboanalyst.ca/) is a popular online tool that analyzes metabolomics and multiomics data. 88 The website provides online services with coverage from basic statistics, such as quantitative comparisons and principal component analysis, to advanced clustering, enrichment, and pathway analysis.…”

Section: Utilization Of Online Platforms For Statistics In Multiomics...mentioning

confidence: 99%

Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation

Liu

Que³

et al. 2022

J Clin Transl Hepatol

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Omics data address key issues in liver transplantation (LT) as the most effective therapeutic means for end-stage liver disease. The purpose of this study was to review the current application and future direction for omics in LT. We reviewed the use of multiomics to elucidate the pathogenesis leading to LT and prognostication. Future directions with respect to the use of omics in LT are also described based on perspectives of surgeons with experience in omics. Significant molecules were identified and summarized based on omics, with a focus on post-transplant liver fibrosis, early allograft dysfunction, tumor recurrence, and graft failure. We emphasized the importance omics for clinicians who perform LTs and prioritized the directions that should be established. We also outlined the ideal workflow for omics in LT. In step with advances in technology, the quality of omics data can be guaranteed using an improved algorithm at a lower price. Concerns should be addressed on the translational value of omics for better therapeutic effects in patients undergoing LT.

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Section: Utilization Of Online Platforms For Statistics In Multiomics...mentioning

confidence: 99%

Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation

Liu

Que³

et al. 2022

J Clin Transl Hepatol

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“…Multi-omics data broadly cover the domains of "-omes" and can provide useful biological information at several levels and thus help to understand the mechanisms of pathologies, contribute to diagnosis, prognosis and potential therapeutic interventions (Urbanski et al, 2019). There are many examples of massive data production in specific applications for human diseases.…”

Section: Other Public Omics Databasesmentioning

confidence: 99%

Multi-Omics Approaches to Improve Mitochondrial Disease Diagnosis: Challenges, Advances, and Perspectives

Labory

Fierville

Ait-El-Mkadem

et al. 2020

Front. Mol. Biosci.

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Mitochondrial diseases (MD) are rare disorders caused by deficiency of the mitochondrial respiratory chain, which provides energy in each cell. They are characterized by a high clinical and genetic heterogeneity and in most patients, the responsible gene is unknown. Diagnosis is based on the identification of the causative gene that allows genetic counseling, prenatal diagnosis, understanding of pathological mechanisms, and personalized therapeutic approaches. Despite the emergence of Next Generation Sequencing (NGS), to date, more than one out of two patients has no diagnosis in the absence of identification of the responsible gene. Technologies currently used for detecting causal variants (genetic alterations) is far from complete, leading many variants of unknown significance (VUS) and mainly based on the use of whole exome sequencing thus neglecting the identification of non-coding variants. The complexity of human genome and its regulation at multiple levels has led biologists to develop several assays to interrogate the different aspects of biological processes. While one-dimension single omics investigation offers a peek of this complex system, the combination of different omics data allows the discovery of coherent signatures. The community of computational biologists and bioinformaticians, in order to integrate data from different omics, has developed several approaches and tools. However, it is difficult to understand which suits the best to predict diverse phenotypic outcome. First attempts to use multi-omics approaches showed an improvement of the diagnostic power. However, we are far from a complete understanding of MD and their diagnosis. After reviewing multi-omics algorithms developed in the latest years, we are proposing here a novel data-driven classification and we will discuss how multi-omics will change and improve the diagnosis of MD. Due to the growing use of multi-omics approaches in MD, we foresee that this work will contribute to set up good practices to perform multi-omics data integration to improve the prediction of phenotypic outcomes and the diagnostic power of MD.

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Integrative Biology Approaches Applied to Human Diseases

Cited by 2 publications

References 114 publications

Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation

Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation

Multi-Omics Approaches to Improve Mitochondrial Disease Diagnosis: Challenges, Advances, and Perspectives

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