The advancements in genomics and biomedical technologies have generated vast amounts of biological and physiological data, which present opportunities for understanding human health. Deep learning (DL) and machine learning (ML) are frontiers and interdisciplinary fields of computer science that consider comprehensive computational models and provide integral roles for disease diagnosis and therapy investigation. DL-based algorithms can discover the intrinsic hierarchies in the training data to show great promise for extracting features and learning patterns from complex datasets and performing various analytical tasks. This review comprehensively discusses the wide-ranging DL approaches for intelligent healthcare systems (IHS) in genomics and biomedicine. This paper explores advanced concepts in deep learning (DL) and discusses the workflow of utilizing role-based algorithms in genomics and biomedicine to integrate intelligent healthcare systems (IHS). The aim is to overcome biomedical obstacles like patient disease classification, core biomedical processes, and empowering patient-disease integration. The paper also highlights how DL approaches are well-suited for addressing critical challenges in these domains, offering promising solutions for improved healthcare outcomes. We also provided a concise concept of DL architectures and model optimization in genomics and bioinformatics at the molecular level to deal with biomedicine classification, genomic sequence analysis, protein structure classification, and prediction. Finally, we discussed DL's current challenges and future perspectives in genomics and biomedicine for future directions.