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      A Comprehensive Review of Bioinformatics Tools for Genomic Biomarker Discovery Driving Precision Oncology.

      1 , 1
      Genes
      MDPI AG
      RNA-Seq, bioinformatics, biomarker discovery, oncology, predictive algorithms

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          Abstract

          The rapid advancement of high-throughput technologies, particularly next-generation sequencing (NGS), has revolutionized cancer research by enabling the investigation of genetic variations such as SNPs, copy number variations, gene expression, and protein levels. These technologies have elevated the significance of precision oncology, creating a demand for biomarker identification and validation. This review explores the complex interplay of oncology, cancer biology, and bioinformatics tools, highlighting the challenges in statistical learning, experimental validation, data processing, and quality control that underpin this transformative field. This review outlines the methodologies and applications of bioinformatics tools in cancer genomics research, encompassing tools for data structuring, pathway analysis, network analysis, tools for analyzing biomarker signatures, somatic variant interpretation, genomic data analysis, and visualization tools. Open-source tools and repositories like The Cancer Genome Atlas (TCGA), Genomic Data Commons (GDC), cBioPortal, UCSC Genome Browser, Array Express, and Gene Expression Omnibus (GEO) have emerged to streamline cancer omics data analysis. Bioinformatics has significantly impacted cancer research, uncovering novel biomarkers, driver mutations, oncogenic pathways, and therapeutic targets. Integrating multi-omics data, network analysis, and advanced ML will be pivotal in future biomarker discovery and patient prognosis prediction.

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          Author and article information

          Journal
          Genes (Basel)
          Genes
          MDPI AG
          2073-4425
          2073-4425
          Aug 06 2024
          : 15
          : 8
          Affiliations
          [1 ] Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA.
          Article
          genes15081036
          10.3390/genes15081036
          11353282
          39202397
          e74982e5-ccb6-49c9-8758-748359869390
          History

          biomarker discovery,predictive algorithms,oncology,bioinformatics,RNA-Seq

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