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Metabolites
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Bioinformatics in Metabolomics
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Bioinformatics in Metabolomics

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Bioinformatics and Data Analysis".

Deadline for manuscript submissions: closed (31 December 2018) | Viewed by 9379

Special Issue Editor

Dr. Thusitha W. Rupasinghe

E-Mail Website
Guest Editor
School of BioSciences, University of Melbourne, Parkville, VIC 3052, Australia
Interests: lipidomics; metabolomics; bioanalytics; fluxomics; analytical chemistry; plant physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the past decade and a half, bioinformatics has evolved from the role of being a support science to now becoming an integral part of all areas of metabolomics. Bioinformatic-defined models and solutions are part of the entire workflow of metabolomics, starting from methodically defining and capturing an experiment using standards, managing the vast amount of high-throughput data arising from these experiments, making sense of these data using data processing and statistical analysis methods, and finally relating the findings back to the underlying question using data integration, pathway analysis and visualization models. This Special Issue focuses on bioinformatics methods, tools, systems and solutions in metabolomics. Specific areas include, but not limited to, data standards, data management solution, database systems, data processing and statistical methods, pathway analysis and visualization techniques.

Dr. Thusitha W. Rupasinghe
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolomics bioinformatics
  • data processing
  • statistical analysis
  • data management
  • database systems
  • data visualization

Published Papers (2 papers)

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Research

22 pages, 3082 KiB  
Article
The Fate of Glutamine in Human Metabolism. The Interplay with Glucose in Proliferating Cells
by Jean-Pierre Mazat and Stéphane Ransac
Metabolites 2019, 9(5), 81; https://doi.org/10.3390/metabo9050081 - 26 Apr 2019
Cited by 19 | Viewed by 5032
Abstract
Genome-scale models of metabolism (GEM) are used to study how metabolism varies in different physiological conditions. However, the great number of reactions involved in GEM makes it difficult to understand these variations. In order to have a more understandable tool, we developed a [...] Read more.
Genome-scale models of metabolism (GEM) are used to study how metabolism varies in different physiological conditions. However, the great number of reactions involved in GEM makes it difficult to understand these variations. In order to have a more understandable tool, we developed a reduced metabolic model of central carbon and nitrogen metabolism, C2M2N with 77 reactions, 54 internal metabolites, and 3 compartments, taking into account the actual stoichiometry of the reactions, including the stoichiometric role of the cofactors and the irreversibility of some reactions. In order to model oxidative phosphorylation (OXPHOS) functioning, the proton gradient through the inner mitochondrial membrane is represented by two pseudometabolites DPH (∆pH) and DPSI (∆ψ). To illustrate the interest of such a reduced and quantitative model of metabolism in mammalian cells, we used flux balance analysis (FBA) to study all the possible fates of glutamine in metabolism. Our analysis shows that glutamine can supply carbon sources for cell energy production and can be used as carbon and nitrogen sources to synthesize essential metabolites. Finally, we studied the interplay between glucose and glutamine for the formation of cell biomass according to ammonia microenvironment. We then propose a quantitative analysis of the Warburg effect. Full article
(This article belongs to the Special Issue Bioinformatics in Metabolomics)
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18 pages, 2174 KiB  
Article
PLS2 in Metabolomics
by Matteo Stocchero, Emanuela Locci, Ernesto d’Aloja, Matteo Nioi, Eugenio Baraldi and Giuseppe Giordano
Metabolites 2019, 9(3), 51; https://doi.org/10.3390/metabo9030051 - 15 Mar 2019
Cited by 23 | Viewed by 3762
Abstract
Metabolomics is the systematic study of the small-molecule profiles of biological samples produced by specific cellular processes. The high-throughput technologies used in metabolomic investigations generate datasets where variables are strongly correlated and redundancy is present in the data. Discovering the hidden information is [...] Read more.
Metabolomics is the systematic study of the small-molecule profiles of biological samples produced by specific cellular processes. The high-throughput technologies used in metabolomic investigations generate datasets where variables are strongly correlated and redundancy is present in the data. Discovering the hidden information is a challenge, and suitable approaches for data analysis must be employed. Projection to latent structures regression (PLS) has successfully solved a large number of problems, from multivariate calibration to classification, becoming a basic tool of metabolomics. PLS2 is the most used implementation of PLS. Despite its success, PLS2 showed some limitations when the so called ‘structured noise’ affects the data. Suitable methods have been recently introduced to patch up these limitations. In this study, a comprehensive and up-to-date presentation of PLS2 focused on metabolomics is provided. After a brief discussion of the mathematical framework of PLS2, the post-transformation procedure is introduced as a basic tool for model interpretation. Orthogonally-constrained PLS2 is presented as strategy to include constraints in the model according to the experimental design. Two experimental datasets are investigated to show how PLS2 and its improvements work in practice. Full article
(This article belongs to the Special Issue Bioinformatics in Metabolomics)
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