AI and Machine Learning in Cancer Genomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: 25 November 2025 | Viewed by 824

Special Issue Editor


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Guest Editor
College of Integrated Health Sciences, Department of Epidemiology and Biostatistics, State University of New York at Albany, Albany, NY, USA
Interests: cancer genomics and epidemiology; methylation analysis; AI/machine-learning; blind source separation; early disease diagnosis; computational biology

Special Issue Information

Dear Colleagues,

The incorporation of artificial intelligence (AI) and Machine Learning (ML) into the field of cancer genomics has changed our approach toward analyzing and interpreting intricate genomic data. This, in turn, has aided in the understanding of the processes related to the inception, evolution, and prognosis of cancer. Advanced AI techniques, including deep learning and sophisticated models, can help to unravel multidimensional genomic data and tailor treatments for individuals based on their unique disease patterns, which were previously thought to be impossible. Some of the most advanced cancer AI solutions have breathtaking usefulness, and the study of mutational signatures is one of them. Using AI to interpret these complex patterns against the backdrop of different mutagenic mechanisms greatly enhances their clinical value.

This special issue aims to illustrate some of the most impressive synergetic research works that combine AI/ML with cancer genomics. We encourage the submission of works that put forward novel computational techniques, the use of machine learning on genomic projects, and the application of observational studies where AI methods have already been placed into practice in a medical field. Examples of focus include computational analysis of mutational signatures, the functional aspects of oncology, genomic and dynamic spatial biomarker development, and others. The main focus should be directed toward research carried out with the intent of explaining cancer development processes with the help of AI technologies, while cherishing expected improvement in the control of cancer patients for all clinicians.

Dr. S M Ashiqul Islam
Guest Editor

Manuscript Submission Information

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Keywords

  • genomics
  • cancer
  • AI
  • ML
  • tools
  • signatures
  • biomarkers
  • oncology

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Published Papers (1 paper)

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Research

19 pages, 8779 KB  
Article
Bulk and Single-Cell Transcriptomes Reveal Exhausted Signature in Prognosis of Hepatocellular Carcinoma
by Ruixin Chun, Haisen Ni, Ziyi Zhao and Chunlong Zhang
Genes 2025, 16(9), 1034; https://doi.org/10.3390/genes16091034 - 30 Aug 2025
Viewed by 473
Abstract
Background/Objectives: Hepatocellular carcinoma (HCC) is a highly heterogeneous malignancy with poor prognosis. T cell exhaustion (TEX) is a key factor in tumor immune evasion and therapeutic resistance. In this study, we integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) data to [...] Read more.
Background/Objectives: Hepatocellular carcinoma (HCC) is a highly heterogeneous malignancy with poor prognosis. T cell exhaustion (TEX) is a key factor in tumor immune evasion and therapeutic resistance. In this study, we integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) data to characterize TEX-related transcriptional features in HCC. Methods: We first computed TEX scores for each sample using a curated 65-gene signature and classified them into high-TEX and low-TEX groups by the median score. Differentially expressed genes were identified separately in scRNA-seq and bulk RNA-seq data, then intersected to retain shared candidates. A 26-gene prognostic signature was derived from these candidates via univariate Cox and LASSO regression analysis. Results: The high-TEX group exhibited increased expression of immune checkpoint molecules and antigen presentation molecules, suggesting a tumor microenvironment that is more immunosuppressive but potentially more responsive to immunotherapy. Functional enrichment analysis and protein–protein interaction (PPI) network construction further validated the roles of these genes in immune regulation and tumor progression. Conclusions: This study provides a comprehensive characterization of the TEX landscape in HCC and identifies a robust gene signature associated with prognosis and immune infiltration. These findings highlight the potential of targeting TEX-related genes for personalized immunotherapeutic strategies in HCC. Full article
(This article belongs to the Special Issue AI and Machine Learning in Cancer Genomics)
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