{"title":"Illuminating the Noncoding Genome in Cancer Using Artificial Intelligence.","authors":"Maria Del Mar Alvarez-Torres, Xi Fu, Raul Rabadan","doi":"10.1158/0008-5472.CAN-25-0482","DOIUrl":null,"url":null,"abstract":"<p><p>Understanding the vast noncoding cancer genome requires cutting-edge, high-resolution, and accessible strategies. Artificial intelligence is revolutionizing cancer research, enabling advanced models to analyze genome regulation. This review examines illustrative examples of noncoding mutations in cancer, focusing on both key regulatory elements and risk-associated variants that remain poorly understood, and compares key artificial intelligence models developed over the last decade for identifying functional noncoding variants, predicting gene expression impacts, and uncovering cancer-associated mutations. The discussion of the goals, data requirements, features, and outcomes of the models offers practical insights to help cancer researchers integrate these technologies into their work, regardless of computational expertise. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.</p>","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":" ","pages":"2368-2375"},"PeriodicalIF":16.6000,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12214880/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cancer research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1158/0008-5472.CAN-25-0482","RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ONCOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Understanding the vast noncoding cancer genome requires cutting-edge, high-resolution, and accessible strategies. Artificial intelligence is revolutionizing cancer research, enabling advanced models to analyze genome regulation. This review examines illustrative examples of noncoding mutations in cancer, focusing on both key regulatory elements and risk-associated variants that remain poorly understood, and compares key artificial intelligence models developed over the last decade for identifying functional noncoding variants, predicting gene expression impacts, and uncovering cancer-associated mutations. The discussion of the goals, data requirements, features, and outcomes of the models offers practical insights to help cancer researchers integrate these technologies into their work, regardless of computational expertise. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.
期刊介绍：
Cancer Research, published by the American Association for Cancer Research (AACR), is a journal that focuses on impactful original studies, reviews, and opinion pieces relevant to the broad cancer research community. Manuscripts that present conceptual or technological advances leading to insights into cancer biology are particularly sought after. The journal also places emphasis on convergence science, which involves bridging multiple distinct areas of cancer research.
With primary subsections including Cancer Biology, Cancer Immunology, Cancer Metabolism and Molecular Mechanisms, Translational Cancer Biology, Cancer Landscapes, and Convergence Science, Cancer Research has a comprehensive scope. It is published twice a month and has one volume per year, with a print ISSN of 0008-5472 and an online ISSN of 1538-7445.
Cancer Research is abstracted and/or indexed in various databases and platforms, including BIOSIS Previews (R) Database, MEDLINE, Current Contents/Life Sciences, Current Contents/Clinical Medicine, Science Citation Index, Scopus, and Web of Science.
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