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Metabolites
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Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques
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Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 1619

Special Issue Editor

Dr. Priyanka Baloni

E-Mail Website
Guest Editor
School of Health Sciences, Purdue University, West Lafayette, IN 47906, USA
Interests: metabolic modeling; neurodegenerative diseases; toxicology; multi-omics analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, entitled “Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques”, seeks to explore the cutting-edge developments and applications of genome-scale metabolic models (GEMs) and related techniques in understanding complex biological systems. With the rapid advancement of high-throughput omics technologies, GEMs have emerged as powerful tools for mapping and simulating the intricate networks of metabolic pathways across various organisms. This Special Issue invites researchers to submit original research, reviews, and case studies that highlight innovative approaches to genome-scale modeling, including the integration of multi-omics data, machine learning techniques, and novel algorithms. This Special Issue will focus on the integration of the computational biology, systems biology, and bioinformatics fields along with experimental data to analyze and predict the behavior of complex metabolic systems at the cellular level.

Studies exploring innovative methodologies in genome-scale modeling, including constraint-based models, flux balance analysis, and integration with multi-omics data offering novel insights into applications in health, disease, and biotechnology are highly welcomed. This Special Issue aims to showcase how these techniques can be used to understand metabolic regulation, identify potential drug targets, and optimize metabolic engineering efforts. Researchers are invited to contribute original research, reviews, and case studies that advance the understanding of metabolic pathways through the lens of genome-scale modeling.

Dr. Priyanka Baloni
Guest Editor

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

  • metabolism
  • systems biology
  • genome-scale metabolic modeling
  • multi-omics data
  • data integration
  • data analysis
  • metabolic regulation
  • biomarker
  • drug targets

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Published Papers (2 papers)

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Research

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12 pages, 395 KiB  
Article
Adapting OptCouple to Identify Strategies with Increased Product Yields in Community Cohorts of E. coli
by Nicole Pearcy and Jamie Twycross
Metabolites 2025, 15(5), 309; https://doi.org/10.3390/metabo15050309 - 6 May 2025
Viewed by 104
Abstract
Background: Microbesas chemical factories provide an alternative sustainable approach for producing platform chemicals. Until recently, most efforts have involved engineering heterologous pathways into a single microbial chassis to maximise its production of a target chemical. More recently, cohorts of microbes have been used [...] Read more.
Background: Microbesas chemical factories provide an alternative sustainable approach for producing platform chemicals. Until recently, most efforts have involved engineering heterologous pathways into a single microbial chassis to maximise its production of a target chemical. More recently, cohorts of microbes have been used to engineer microbial communities to achieve higher yields than achieved in a single chassis. Full article
(This article belongs to the Special Issue Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques)
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Review

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25 pages, 2912 KiB  
Review
Metabolic Objectives and Trade-Offs: Inference and Applications
by Da-Wei Lin, Saanjh Khattar and Sriram Chandrasekaran
Metabolites 2025, 15(2), 101; https://doi.org/10.3390/metabo15020101 - 6 Feb 2025
Viewed by 1077
Abstract
Background/Objectives: Determining appropriate cellular objectives is crucial for the system-scale modeling of biological networks for metabolic engineering, cellular reprogramming, and drug discovery applications. The mathematical representation of metabolic objectives can describe how cells manage limited resources to achieve biological goals within mechanistic and [...] Read more.
Background/Objectives: Determining appropriate cellular objectives is crucial for the system-scale modeling of biological networks for metabolic engineering, cellular reprogramming, and drug discovery applications. The mathematical representation of metabolic objectives can describe how cells manage limited resources to achieve biological goals within mechanistic and environmental constraints. While rapidly proliferating cells like tumors are often assumed to prioritize biomass production, mammalian cell types can exhibit objectives beyond growth, such as supporting tissue functions, developmental processes, and redox homeostasis. Methods: This review addresses the challenge of determining metabolic objectives and trade-offs from multiomics data. Results: Recent advances in single-cell omics, metabolic modeling, and machine/deep learning methods have enabled the inference of cellular objectives at both the transcriptomic and metabolic levels, bridging gene expression patterns with metabolic phenotypes. Conclusions: These in silico models provide insights into how cells adapt to changing environments, drug treatments, and genetic manipulations. We further explore the potential application of incorporating cellular objectives into personalized medicine, drug discovery, tissue engineering, and systems biology. Full article
(This article belongs to the Special Issue Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques)
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