Lipidomic and Metabolomic Analysis of Neurodegenerative Diseases

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

Deadline for manuscript submissions: 20 June 2026 | Viewed by 913

Special Issue Editor


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Guest Editor
Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
Interests: bioinformatics; computational biomedicine; drug discovery, molecular analysis, biomarkers; neurodegenerative diseases
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Special Issue Information

Dear Colleagues,

Neurodegenerative diseases are characterized by progressive neuronal dysfunction and widespread metabolic alterations. Lipidomic and metabolomic analyses have revealed systemic and cellular metabolic changes that contribute to oxidative stress, impaired energy homeostasis, and disease-specific pathology. Integrating multi-omics approaches with advanced data analysis, bioinformatics pipelines, and artificial intelligence models provides a systems-level understanding of these interconnected pathways and helps identify potential biomarkers and therapeutic targets across different neurodegenerative conditions.

This Special Issue aims to highlight recent studies investigating lipidomic and metabolomic alterations in neurodegenerative diseases using diverse experimental contexts, including patient samples, biofluids, cellular models, in vitro assays, in vivo studies, and animal models. Emphasis is placed on multi-omics integration, AI-driven analyses, and bioinformatics approaches to dissect complex datasets, uncover mechanistic insights, and identify translational biomarkers. Contributions that advance our understanding of metabolic dysregulation and explore innovative strategies for diagnosis, monitoring, and therapeutic intervention are particularly welcome.

Dr. Marios Krokidis
Guest Editor

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Keywords

  • neurodegenerative diseases
  • metabolomics
  • lipidomics
  • biofluids and patient samples
  • cellular models
  • animal models
  • mass-spectrometry
  • nuclear magnetic resonance
  • biomarkers
  • artifical intelligence
  • multi-omics analysis
  • bioinformatics

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Published Papers (1 paper)

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Review

18 pages, 1672 KB  
Review
A Structured Computational Roadmap for Lipidomics in R: Reproducible Workflows from Raw Data to Functional Insight
by Maria-Christina P. Papatheodorou, Panagiotis Vlamos and Marios G. Krokidis
Metabolites 2026, 16(5), 288; https://doi.org/10.3390/metabo16050288 - 22 Apr 2026
Viewed by 581
Abstract
Lipidomics has emerged as a transformative discipline in biomedical research, providing high-resolution insights into metabolic signaling and disease pathophysiology. The R programming language provides a widely adopted framework for extensible analysis of complex lipidomic datasets due to its robust biostatistical infrastructure. Herein, we [...] Read more.
Lipidomics has emerged as a transformative discipline in biomedical research, providing high-resolution insights into metabolic signaling and disease pathophysiology. The R programming language provides a widely adopted framework for extensible analysis of complex lipidomic datasets due to its robust biostatistical infrastructure. Herein, we present a comprehensive roadmap for lipidomics in R, structured around a standardized analytical lifecycle: from raw data acquisition and preprocessing to structural annotation, statistical modeling and functional interpretation. We critically contextualize and integrate a curated suite of widely adopted R packages (version 4.3.0), including xcms and MSnbase for feature extraction, LipidMS 3.0 for fragmentation-based identification, and lipidr for quality control and normalization. Furthermore, we demonstrate how advanced tools such as mixOmics and clusterProfiler can be integrated to bridge the gap between differential lipid abundance and systems-level biological insights. Particular emphasis is placed on reproducibility, nomenclature standardization and the emerging role of machine learning in biomarker discovery. By synthesizing these resources into a coherent pipeline, this guide provides a structured reference for researchers. Further discussion addresses methodological pitfalls, statistical assumptions and reproducibility constraints that frequently compromise lipidomics studies. Ultimately, this structured approach facilitates systematic tool selection, accelerating the translation of complex lipidomic signatures into reproducible and clinically meaningful discoveries. Full article
(This article belongs to the Special Issue Lipidomic and Metabolomic Analysis of Neurodegenerative Diseases)
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