| 1. |
- Lamichhane, Santosh, et al.
(author)
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An Overview of Metabolomics Data Analysis : Current Tools and Future Perspectives
- 2018
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In: Data Analysis for Omic Sciences. - : Elsevier. - 9780444640444 ; , s. 387-413
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Book chapter (peer-reviewed)abstract
- Metabolomics is a study of small molecules in the body and the associated metabolic pathways and is considered to provide a close link between organism's genotype and phenotype. As with other ‘omics’ techniques, metabolomic analysis generates large-scale and complex datasets. Therefore, various data analysis tools are needed to extract biologically relevant information. The data analysis workflows in metabolomics studies are generally complex and involve several steps. In this chapter, we highlight the concept of metabolomics workflow and discuss the data analysis strategies for metabolomics experiments. We also discuss the available tools that can assist in biological interpretation of metabolomics data. We also present an emerging approach of developing genome-scale metabolic models to study cellular metabolism.
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| 2. |
- Lamichhane, Santosh, et al.
(author)
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Gut metabolome meets microbiome : A methodological perspective to understand the relationship between host and microbe
- 2018
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In: Methods. - : Academic Press. - 1046-2023 .- 1095-9130. ; 149, s. 3-12
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Research review (peer-reviewed)abstract
- It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.
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| 3. |
- Sen, Partho, et al.
(author)
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Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells
- 2018
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In: Frontiers in Molecular Biosciences. - : Frontiers Research Foundation. - 2296-889X. ; 4
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Research review (peer-reviewed)abstract
- Human peripheral blood mononuclear cells (PBMCs) are the key drivers of the immune responses. These cells undergo activation, proliferation and differentiation into various subsets. During these processes they initiate metabolic reprogramming, which is coordinated by specific gene and protein activities. PBMCs as a model system have been widely used to study metabolic and autoimmune diseases. Herein we review various omics and systems-based approaches such as transcriptomics, epigenomics, proteomics, and metabolomics as applied to PBMCs, particularly T helper subsets, that unveiled disease markers and the underlying mechanisms. We also discuss and emphasize several aspects of T cell metabolic modeling in healthy and disease states using genome-scale metabolic models.
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