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The field of computational biology and bioinformatics has seen remarkable progress in recent years, driven largely by advancements in artificial intelligence (AI) technologies. This review synthesizes the latest developments in AI methodologies and their applications in addressing key challenges within the field of computational biology and bioinformatics. This review begins by outlining fundamental concepts in AI relevant to computational biology, including machine learning algorithms such as neural networks, support vector machines, and decision trees. It then explores how these algorithms have been adapted and optimized for specific tasks in bioinformatics, such as sequence analysis, protein structure prediction, and drug discovery. AI techniques can be integrated with big data analytics, cloud computing, and high-performance computing to handle the vast amounts of biological data generated by modern experimental techniques. The chapter discusses the role of AI in processing and interpreting various types of biological data, including genomic sequences, protein-protein interactions, and gene expression profiles. This chapter highlights recent breakthroughs in AI-driven precision medicine, personalized genomics, and systems biology, showcasing how AI algorithms are revolutionizing our understanding of complex biological systems and driving innovations in healthcare and biotechnology. Additionally, it addresses emerging challenges and future directions in the field, such as the ethical implications of AI in healthcare, the need for robust validation and reproducibility of AI models, and the importance of interdisciplinary collaboration between computer scientists, biologists, and clinicians. In conclusion, this comprehensive review provides insights into the transformative potential of AI in computational biology and bioinformatics, offering a roadmap for future research and development in this rapidly evolving field.
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http://dx.doi.org/10.1007/978-1-0716-4690-8_6 | DOI Listing |
Genome Biol
September 2025
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
Background: Soil salinization represents a critical global challenge to agricultural productivity, profoundly impacting crop yields and threatening food security. Plant salt-responsive is complex and dynamic, making it challenging to fully elucidate salt tolerance mechanism and leading to gaps in our understanding of how plants adapt to and mitigate salt stress.
Results: Here, we conduct high-resolution time-series transcriptomic and metabolomic profiling of the extremely salt-tolerant maize inbred line, HLZY, and the salt-sensitive elite line, JI853.
Br J Cancer
September 2025
Department of Genetics, Institut Curie, PSL Research University, Paris, France.
Background: Identifying molecular alterations specific to advanced lung adenocarcinomas could provide insights into tumour progression and dissemination mechanisms.
Method: We analysed tumour samples, either from locoregional lesions or distant metastases, from patients with advanced lung adenocarcinoma from the SAFIR02-Lung trial by targeted sequencing of 45 cancer genes and comparative genomic hybridisation array and compared them to early tumours samples from The Cancer Genome Atlas.
Results: Differences in copy-number alterations frequencies suggest the involvement in tumour progression of LAMB3, TNN/KIAA0040/TNR, KRAS, DAB2, MYC, EPHA3 and VIPR2, and in metastatic dissemination of AREG, ZNF503, PAX8, MMP13, JAM3, and MTURN.
Nature
September 2025
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
As a key mitochondrial Ca transporter, NCLX regulates intracellular Ca signalling and vital mitochondrial processes. The importance of NCLX in cardiac and nervous-system physiology is reflected by acute heart failure and neurodegenerative disorders caused by its malfunction. Despite substantial advances in the field, the transport mechanisms of NCLX remain unclear.
View Article and Find Full Text PDFNature
September 2025
Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
Cancer development and response to treatment are evolutionary processes, but characterizing evolutionary dynamics at a clinically meaningful scale has remained challenging. Here we develop a new methodology called EVOFLUx, based on natural DNA methylation barcodes fluctuating over time, that quantitatively infers evolutionary dynamics using only a bulk tumour methylation profile as input. We apply EVOFLUx to 1,976 well-characterized lymphoid cancer samples spanning a broad spectrum of diseases and show that initial tumour growth rate, malignancy age and epimutation rates vary by orders of magnitude across disease types.
View Article and Find Full Text PDFNat Commun
September 2025
Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.
Atherosclerosis, a major cause of cardiovascular diseases, is characterized by the buildup of lipids and chronic inflammation in the arteries, leading to plaque formation and potential rupture. Despite recent advances in single-cell transcriptomics (scRNA-seq), the underlying immune mechanisms and transformations in structural cells driving plaque progression remain incompletely defined. Existing datasets often lack comprehensive coverage and consistent annotations, limiting the utility of downstream analyses.
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