Metabolomics and Computational Research on Drugs and Diseases

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

Deadline for manuscript submissions: 15 January 2025 | Viewed by 1034

Special Issue Editors


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Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
Interests: networks biology systems; chemoinformatics and biological databases
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
Interests: systems biology; biological databases; metabolomics
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
Interests: systems biology; complex systems models; using statistical models; deep learning models
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
Interests: bioinformatics; machine learning; deep learning; metabolomics

Special Issue Information

Dear Colleagues,

Metabolomics, the comprehensive study of small molecules or metabolites within living systems, offers a unique perspective into cellular function and health. Metabolites are influenced by various factors like diet, the gut microbiome, drugs, and disease. By analyzing metabolite levels, researchers can gain critical insights into disease progression and identify potential drug targets. The metabolome is intricately connected to an organism’s genotype and physiology and the environment where it lives. There are numerous applications of metabolomics in healthcare, including pharmacology, toxicology, health condition monitoring, e.g., after surgery, and drugging. Metabolites can be biomarkers of diseases, and they can be linked to various disease pathways to understand disease mechanisms. Plant metabolites that are commonly known as natural products can be utilized as effective drugs for different diseases. Computational approaches can be utilized to predict the activities of natural products to assess their effectiveness as drugs.

This Special Issue seeks to bridge the gap between metabolomics and computational research for drug discovery and disease diagnosis. We welcome all manuscripts that explore computational metabolomics, including the development and application of machine learning tools and algorithms for analyzing metabolomic data. Topics of interest include, but are not limited to, the following: identifying disease biomarkers; disease diagnosis and pathway analysis; discovering new drugs and drug targets; and monitoring drug efficacy. This Special Issue aims to be a valuable resource for researchers of computational metabolomics. By fostering collaboration between various branches of this field, we aim to accelerate the development of new therapies and diagnostics for various diseases.

We look forward to receiving your submissions and contribution to the advancement of this exciting field.

Dr. Md. Altaf-Ul-Amin
Prof. Dr. Shigehiko Kanaya
Dr. Naoaki Ono
Dr. Ahmad Kamal Nasution
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
  • natural products
  • computational research
  • drug discovery
  • disease diagnosis
  • disease mechanisms
  • machine learning algorithms

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Published Papers (1 paper)

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Research

18 pages, 4848 KiB  
Article
Implementation of Machine Learning-Based System for Early Diagnosis of Feline Mammary Carcinomas through Blood Metabolite Profiling
by Vidhi Kulkarni, Igor F. Tsigelny and Valentina L. Kouznetsova
Metabolites 2024, 14(9), 501; https://doi.org/10.3390/metabo14090501 - 17 Sep 2024
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Abstract
Background: Feline mammary carcinoma (FMC) is a prevalent and fatal carcinoma that predominantly affects unspayed female cats. FMC is the third most common carcinoma in cats but is still underrepresented in research. Current diagnosis methods include physical examinations, imaging tests, and fine-needle aspiration. [...] Read more.
Background: Feline mammary carcinoma (FMC) is a prevalent and fatal carcinoma that predominantly affects unspayed female cats. FMC is the third most common carcinoma in cats but is still underrepresented in research. Current diagnosis methods include physical examinations, imaging tests, and fine-needle aspiration. The diagnosis through these methods is sometimes delayed and unreliable, leading to increased chances of mortality. Objectives: The objective of this study was to identify the biomarkers, including blood metabolites and genes, related to feline mammary carcinoma, study their relationships, and develop a machine learning (ML) model for the early diagnosis of the disease. Methods: We analyzed the blood metabolites of felines with mammary carcinoma using the pathway analysis feature in MetaboAnalyst software, v. 5.0. We utilized machine-learning (ML) methods to recognize FMC using the blood metabolites of sick patients. Results: The metabolic pathways that were elucidated to be associated with this disease include alanine, aspartate and glutamate metabolism, Glutamine and glutamate metabolism, Arginine biosynthesis, and Glycerophospholipid metabolism. Furthermore, we also elucidated several genes that play a significant role in the development of FMC, such as ERBB2, PDGFA, EGFR, FLT4, ERBB3, FIGF, PDGFC, PDGFB through STRINGdb, a database of known and predicted protein-protein interactions, and MetaboAnalyst 5.0. The best-performing ML model was able to predict metabolite class with an accuracy of 85.11%. Conclusion: Our findings demonstrate that the identification of the biomarkers associated with FMC and the affected metabolic pathways can aid in the early diagnosis of feline mammary carcinoma. Full article
(This article belongs to the Special Issue Metabolomics and Computational Research on Drugs and Diseases)
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