Institutional Publications

Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11

Browse

Start date: 2020Subject: search.filters.subject.Genomics

Search Results

Now showing 1 - 4 of 4
  • No Thumbnail Available
    Item
    The intersection of AI and genomics in health and disease: Advancements and applications
    (Elsevier B.V., 2026) Kaushik, Love; Vivek, A T; Arora, Simran; Hamid, Fiza; Mukherjee, Kanka; Bisht, Niyati; Chaudhary, Sakshi; Shukla, Jagriti; Nawani, Sakshi; Kumar, Shailesh
    AI and genomics are revolutionizing precision medicine by using machine learning (ML) to analyze large-scale next-generation sequencing (NGS) data, identifying genetic mutations and biomarkers for personalized therapies. In practice, this accelerates drug discovery and enhances variant detection, while in cancer genomics, AI enables early detection via liquid biopsies and refines treatment by integrating multi-omics data to improve therapeutic precision. However, challenges such as data biases in underrepresented populations, limited model interpretability, and ethical concerns regarding privacy and algorithmic inequity hinder clinical adoption and demand robust governance. Efforts to diversify datasets also face standardization hurdles, although explainable AI and federated learning provide promising solutions for improving transparency and privacy. In this chapter, we discuss the role of AI in advancing genomics from diagnostics to novel therapies and emphasize the need for equitable frameworks to ensure responsible implementation, thereby paving the way for breakthroughs in personalized medicine.
  • No Thumbnail Available
    Item
    Foxtail millet (Setaria italica L.): a model for small millets
    (Elsevier B.V., 2023) Pramitha, Lydia; Choudhary, Pooja; Rana, Sumi; Singh, Roshan Kumar; Das, Pronomita; Sharma, Shriya; Ravikesavan, R; Prasad, Manoj; Muthamilarasan, Mehanathan
    Foxtail millet (Setaria italica L.) is a small millet predominantly cultivated in arid and semi-arid regions of the world. India is the second-largest producer of foxtail millet, next to China, and the crop has importance in the history and civilization of the human race in these two countries. Although the foxtail millet was widely cultivated in the ancient era, it has lost its importance with time and became a marginally grown crop catering to the nutritional requirements of a limited population. Despite this, the crop has excellent yield contributing to agronomic traits along with climate-resilient characteristics. Being a C4 panicoid species with a small diploid genome, short lifecycle, in-breeding nature, and close relationship with biofuel grasses, foxtail millet has recently been considered as a C4 model crop to understand several agronomically important traits, including stress tolerance. Given the importance, the genome sequence of foxtail millet and green foxtail (S. viridis) is now available. The postgenome era has seen several crop studies, which provided extensive genetic and genomic resources for crop improvement. Studies including genetic and genomic dissection of nutritional traits, response to biotic and abiotic stresses, water-use and nitrogen-use efficiencies, biofuel traits, and deciphering the photosynthetic machinery have provided insights into the novel genes and pathways underlying the individual traits. This has also provided a roadmap for deploying similar studies in other millets using foxtail millet as a model. In this context, the chapter describes the botany, nutritional significance, global distribution, and production technologies being implemented in foxtail millet cultivation. The chapter also summarizes the outcomes of the studies being pursued to decode complex traits and provide a roadmap for executing similar work in other millet crops.
  • No Thumbnail Available
    Item
    PtRNAdb: a web resource of plant tRNA genes from a wide range of plant species
    (Springer Nature Publishing AG, 2022) Singh, Ajeet; Zahra, Shafaque; Das, Durdam; Kumar, Shailesh
    tRNA, as well as their derived products such as short interspersed nuclear elements (SINEs), pseudogenes, and transfer RNA (tRNA)-derived fragments (tRFs), have now been shown to be vital for cellular life, functioning, and adaptation during different stress conditions in all diverse life forms. In this study, we have developed PtRNAdb (www.nipgr.ac.in/PtRNAdb), a plant-exclusive tRNA database containing 113,849 tRNA gene sequences from phylogenetically diverse plant species. We have analyzed a total of 106 nuclear, 89 plastidial, and 38 mitochondrial genomes of plants by the tRNAscan-SE software package, and after careful curation of the output data, we integrated the data and developed this database. The information about the tRNA gene sequences obtained was further enriched with a consensus sequence-based study of tRNA genes based on their isoacceptors and isodecoders. We have also built covariance models based on the isoacceptors and isodecoders of all the tRNA sequences using the infernal tool. The user can also perform BLAST not only against PtRNAdb entries but also against all the tRNA sequences stored in the PlantRNA database and annotated tRNA genes across the plant kingdom available at NCBI. This resource is believed to be of high utility for plant researchers as well as molecular biologists to carry out further exploration of the plant tRNAome on a wider spectrum, as well as for performing comparative and evolutionary studies related to tRNAs, and their derivatives across all domains of life. Database URL: http://www.nipgr.ac.in/PtRNAdb/
  • Thumbnail Image
    Item
    Genomics approaches to synthesis plant-based biomolecules for therapeutic applications to combat SARS-CoV-2
    (Elsevier B.V., 2020) Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Ashish; Prasad, Manoj
    COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.