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Machine Learning and Bioinformatics in Human Health and Disease: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 20 August 2025 | Viewed by 4383

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Guest Editor
Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Feldkirch, Austria
Interests: cardiology; epidemiology; virology; adipose tissue; metabolism; nutrition; data science; diabetes; renal disease; biomarker
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Special Issue Information

Dear Colleagues,

Machine learning and bioinformatics have emerged as powerful tools for analyzing complex biological data and driving advances in human health and disease research. These fields offer a range of techniques for learning from and making predictions based on biological data, including genetic sequencing data, protein structure data, and medical imaging data.

In the context of human health and disease, machine learning and bioinformatics can be used to identify biomarkers for diseases, predict treatment outcomes, and develop new therapies. For example, machine learning algorithms can be used to analyze large datasets of patient information and identify patterns and correlations that might be missed by human experts. Bioinformatics techniques can be utilized to analyze genomic data and identify genetic variations that may contribute to disease.

Machine learning and bioinformatics techniques can also be used to analyze medical images, such as MRIs and CT scans, to identify structural changes associated with disease or injury. This can enable earlier and more accurate diagnoses, as well as more personalized treatment plans tailored to the specific needs of each patient.

However, as is the case with any computational method, machine learning and bioinformatics techniques have their limitations and challenges. One challenge is the need for large amounts of high-quality data to train and validate the algorithms. Another challenge is the potential for overfitting, where the algorithms learn patterns specific to the training data that cannot be applied to new data.

Despite these challenges, the potential benefits of applying machine learning and bioinformatics techniques to human health and disease research are extensive. This Special Issue will provide a platform for researchers to share their latest findings, insights, and innovations in this rapidly evolving field.

Potential topics include, but are not limited to, the following:

  • Machine learning approaches for identifying genetic risk factors for common diseases;
  • Analysis of single-cell RNA sequencing data using bioinformatics and machine learning techniques;
  • Machine learning for predicting drug interactions and side effects;
  • Bioinformatics and machine learning for precision medicine in cancer treatment;
  • Machine learning-based diagnosis of neurodegenerative diseases using neuroimaging data;
  • Integrating multi-omics data using machine learning techniques for disease diagnosis and treatment;
  • Development of predictive models for infectious disease outbreaks using machine learning and epidemiological data;
  • Application of machine learning and deep learning techniques in medical image analysis for disease diagnosis and treatment planning;
  • Identifying disease biomarkers using bioinformatics, deep learning, and machine learning approaches;
  • Machine learning approaches for predicting patient outcomes and disease progression.

This Special Issue is supervised by Dr. Andreas Leiherer and assisted by our Topical Advisory Panel Member Dr. Bernhard Bermeitinger (University of St. Gallen).

Dr. Andreas Leiherer
Guest Editor

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • machine learning
  • bioinformatics
  • deep learning
  • multi-omics approaches
  • genetic risk factors
  • drug interactions
  • precision medicine
  • neurodegenerative diseases
  • disease diagnosis
  • epidemic prediction

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Published Papers (3 papers)

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Research

18 pages, 13101 KiB  
Article
Unveiling Novel miRNA–mRNA Interactions and Their Prognostic Roles in Triple-Negative Breast Cancer: Insights into miR-210, miR-183, miR-21, and miR-181b
by Jiatong Xu, Xiaoxuan Cai, Junyang Huang, Hsi-Yuan Huang, Yong-Fei Wang, Xiang Ji, Yuxin Huang, Jie Ni, Huali Zuo, Shangfu Li, Yang-Chi-Dung Lin and Hsien-Da Huang
Int. J. Mol. Sci. 2025, 26(5), 1916; https://doi.org/10.3390/ijms26051916 - 23 Feb 2025
Viewed by 656
Abstract
Triple-negative breast cancer (TNBC) poses a major clinical challenge due to its aggressive progression and limited treatment options, making early diagnosis and prognosis critical. MicroRNAs (miRNAs) are crucial post-transcriptional regulators that influence gene expression. In this study, we unveil novel miRNA–mRNA interactions and [...] Read more.
Triple-negative breast cancer (TNBC) poses a major clinical challenge due to its aggressive progression and limited treatment options, making early diagnosis and prognosis critical. MicroRNAs (miRNAs) are crucial post-transcriptional regulators that influence gene expression. In this study, we unveil novel miRNA–mRNA interactions and introduce a prognostic model based on miRNA–target interaction (MTI), integrating miRNA–mRNA regulatory correlation inference and the machine learning method to effectively predict the survival outcomes in TNBC cohorts. Using this method, we identified four key miRNAs (miR-181b-5p, miR-21-5p, miR-210-3p, miR-183-5p) targeting eight downstream target genes, forming a novel regulatory network of 19 validated miRNA–mRNA pairs. A prognostic model constructed based on the top 10 significant MTI pairs using random forest combination effectively classified patient survival outcomes in both TCGA and independent dataset GSE19783 cohorts, demonstrating good predictive accuracy and valuable prognostic insights for TNBC patients. Further analysis uncovered a complex network of 71 coherent feed-forward loops involving transcription factors, miRNAs, and target genes, shedding light on the mechanisms driving TNBC progression. This study underscores the importance of considering regulatory networks in cancer prognosis and provides a foundation for new therapeutic strategies aimed at improving TNBC treatment outcomes. Full article
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15 pages, 1243 KiB  
Article
Exploring the Pharmacogenomic Map of Croatia: PGx Clustering of 522-Patient Cohort Based on UMAP + HDBSCAN Algorithm
by Petar Brlek, Luka Bulić, Leo Mršić, Mateo Sokač, Eva Brenner, Vid Matišić, Andrea Skelin, Lidija Bach-Rojecky and Dragan Primorac
Int. J. Mol. Sci. 2025, 26(2), 589; https://doi.org/10.3390/ijms26020589 - 12 Jan 2025
Viewed by 1290
Abstract
Pharmacogenetics is a branch of genomic medicine aiming to personalize drug prescription guidelines based on individual genetic information. This concept might lead to a reduction in adverse drug reactions, which place a heavy burden on individual patients’ health and the economy of the [...] Read more.
Pharmacogenetics is a branch of genomic medicine aiming to personalize drug prescription guidelines based on individual genetic information. This concept might lead to a reduction in adverse drug reactions, which place a heavy burden on individual patients’ health and the economy of the healthcare system. The aim of this study was to present insights gained from the pharmacogenetics-based clustering of over 500 patients from the Croatian population. The data used in this article were obtained by the pharmacogenetic testing of 522 patients from the Croatian population. The patients were clustered based on the genotypes of 28 pharmacologically relevant genes. Dimensionality reduction was employed using the UMAP algorithm, after which clusters were defined using HDBSCAN. Validation of clustering was performed by decision tree analysis and predictive modeling using the RandomForest, XGBoost, and ExtraTrees classification algorithms. The clustering algorithm defined six clusters of patients based on two UMAP components (silhouette score = 0.782). Decision tree analysis demonstrated CYP2D6 and SLCO1B1 genotypes as the main points of cluster determination. Predictive modeling demonstrated an excellent ability to discern the cluster of each patient based on all genes (avg. ROC-AUC = 0.998), CYP2D6 and SLCO1B1 (avg. ROC-AUC = 1.000), and CYP2D6 alone (avg. ROC-AUC = 0.910). Membership in each cluster provided clinically relevant information, in the context of ruling out certain favorable or unfavorable phenotypes. However, this study’s main limitation is its cohort size. Through further research and investigation of a larger number of patients, more accurate and clinically applicable associations between pharmacogenetic genotypes and phenotypes might be discovered. Full article
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19 pages, 4302 KiB  
Article
Identification of Oxidative Stress-Related Biomarkers for Pain–Depression Comorbidity Based on Bioinformatics
by Tianyun Zhang, Menglu Geng, Xiaoke Li, Yulin Gu, Wenjing Zhao, Qi Ning, Zijie Zhao, Lei Wang, Huaxing Zhang and Fan Zhang
Int. J. Mol. Sci. 2024, 25(15), 8353; https://doi.org/10.3390/ijms25158353 - 30 Jul 2024
Cited by 1 | Viewed by 1678
Abstract
Oxidative stress has been identified as a major factor in the development and progression of pain and psychiatric disorders, but the underlying biomarkers and molecular signaling pathways remain unclear. This study aims to identify oxidative stress-related biomarkers and signaling pathways in pain–depression comorbidity. [...] Read more.
Oxidative stress has been identified as a major factor in the development and progression of pain and psychiatric disorders, but the underlying biomarkers and molecular signaling pathways remain unclear. This study aims to identify oxidative stress-related biomarkers and signaling pathways in pain–depression comorbidity. Integrated bioinformatics analyses were applied to identify key genes by comparing pain–depression comorbidity-related genes and oxidative stress-related genes. A total of 580 differentially expressed genes and 35 differentially expressed oxidative stress-related genes (DEOSGs) were identified. By using a weighted gene co-expression network analysis and a protein–protein interaction network, 43 key genes and 5 hub genes were screened out, respectively. DEOSGs were enriched in biological processes and signaling pathways related to oxidative stress and inflammation. The five hub genes, RNF24, MGAM, FOS, and TKT, were deemed potential diagnostic and prognostic markers for patients with pain–depression comorbidity. These genes may serve as valuable targets for further research and may aid in the development of early diagnosis, prevention strategies, and pharmacotherapy tools for this particular patient population. Full article
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