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Bioinformatics and Machine Learning for Predicting Biological Processes

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: 30 May 2025 | Viewed by 1370

Special Issue Editor


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Guest Editor
Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
Interests: focused on developing machine learning/deep learning tools for identifying DNA, RNA, and protein modification sites, with current interest in developing computational pipelines to generate embeddings and identify cell types from single-cell Hi-C data
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Special Issue Information

Dear Colleagues,

The rapid advancement of bioinformatics and machine learning has revolutionized the way in which we study and predict complex biological processes. As the volume of biological data continues to grow, novel computational approaches are increasingly required to interpret high-dimensional datasets and discover the mechanisms that underlie biological phenomena. From understanding gene regulation and protein interactions to elucidating disease pathways, bioinformatics tools, combined with cutting-edge machine learning algorithms, offer unprecedented opportunities to accelerate progress in the life sciences. This Special Issue seeks to explore the intersection of these fields, providing insights into how innovative computational methods can address various challenges associated with biology and medicine.

The aim of this Special Issue is to provide a platform for researchers to share advancements in bioinformatics and machine learning methodologies specifically designed to predict biological processes. We welcome original research articles, reviews, and application-focused studies that utilize computational tools to model, predict, and interpret key biological events, such as gene expression, epigenetic modifications, metabolic pathways, and disease progression. Submissions that incorporate novel algorithms, explainable machine learning models, or integrative multi-omics approaches are particularly welcome. By highlighting innovative research, this Special Issue seeks to foster interdisciplinary collaboration and drive innovation at the forefront of bioinformatics and machine learning.

Dr. Lv Hao
Guest Editor

Manuscript Submission Information

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Keywords

  • bioinformatics
  • machine learning
  • multi-omics integration
  • gene regulation
  • biological processes
  • disease processes
  • data-driven discovery

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Published Papers (1 paper)

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Review

19 pages, 274 KiB  
Review
AlphaFold3: An Overview of Applications and Performance Insights
by Marios G. Krokidis, Dimitrios E. Koumadorakis, Konstantinos Lazaros, Ouliana Ivantsik, Themis P. Exarchos, Aristidis G. Vrahatis, Sotiris Kotsiantis and Panagiotis Vlamos
Int. J. Mol. Sci. 2025, 26(8), 3671; https://doi.org/10.3390/ijms26083671 - 13 Apr 2025
Viewed by 1151
Abstract
AlphaFold3, the latest release of AlphaFold developed by Google DeepMind and Isomorphic Labs, was designed to predict protein structures with remarkable accuracy. AlphaFold3 enhances our ability to model not only single protein structures but also complex biomolecular interactions, including protein–protein interactions, protein–ligand docking, [...] Read more.
AlphaFold3, the latest release of AlphaFold developed by Google DeepMind and Isomorphic Labs, was designed to predict protein structures with remarkable accuracy. AlphaFold3 enhances our ability to model not only single protein structures but also complex biomolecular interactions, including protein–protein interactions, protein–ligand docking, and protein-nucleic acid complexes. Herein, we provide a detailed examination of AlphaFold3’s capabilities, emphasizing its applications across diverse biological fields and its effectiveness in complex biological systems. The strengths of the new AI model are also highlighted, including its ability to predict protein structures in dynamic systems, multi-chain assemblies, and complicated biomolecular complexes that were previously challenging to depict. We explore its role in advancing drug discovery, epitope prediction, and the study of disease-related mutations. Despite its significant improvements, the present review also addresses ongoing obstacles, particularly in modeling disordered regions, alternative protein folds, and multi-state conformations. The limitations and future directions of AlphaFold3 are discussed as well, with an emphasis on its potential integration with experimental techniques to further refine predictions. Lastly, the work underscores the transformative contribution of the new model to computational biology, providing new insights into molecular interactions and revolutionizing the fields of accelerated drug design and genomic research. Full article
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