Shahid Bahonar University of Kerman and Iranian Biotechnology Society Agricultural Biotechnology Journal 2228-6705 16 2 2024 05 21 The role of artificial intelligence in genomics The role of artificial intelligence in genomics 195 279 4325 10.22103/jab.2024.23558.1575 FA Mohammadreza Mohammadabadi Corresponding Author. Professor, Animal Science Department, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran Hamid Kheyrodin Assistant Professor, Semnan University, Semnan, Iran Volodymyr Afanasenko National University of Life and Environmental Sciences of Ukraine, Ukraine. Olena Babenko Ivanivna Assistant Professor, Department of Animal Science, Bila Tserkva National Agrarian University, Bila Tserkva, Ukraine Nataliia Klopenko Assistant Professor, Department of Animal Science, Bila Tserkva National Agrarian University, Bila Tserkva, Ukraine. Oleksandr Kalashnyk Sumy National Agrarian University, Sumy, Ukraine. Yulia Ievstafiieva Associate professor, Department of Technologies of Livestock Production and processing, Higher Educational Institution “Podillia State University”, Ukraine Vita Buchkovska Associate Professor, Department of Technologies of Livestock Production and processing, Higher Educational Institution “Podillia State University”, Ukraine Journal Article 2024 03 04 Objective Data generation in biology and biotechnology has greatly increased in recent years due to the very rapid development of high-performance technologies. These data are obtained by studying biological molecules, such as metabolites, proteins, RNA, and DNA, to understand the role of these molecules in determining the structure, function, and dynamics of living systems. Functional genomics is a field of research that aims to characterize the function and interaction of all the major components (DNA, RNA, proteins, and metabolites, along with their modifications) that contribute to the set of observable characteristics of a cell or individual (i.e., phenotype). Furthermore, in a breeding program, genetic improvement can be maximized through accurate identification of superior animals that are selected as parents of the next generation, thereby achieving breeding goals. Artificial neural networks have been proposed to alleviate this limitation of traditional regression methods and can be used to handle nonlinear and complex data, even when the data is imprecise and noisy. Omics data can be too large and complex to handle through visual analysis or statistical correlations. This has encouraged the use of machine intelligence or artificial intelligence. The objectives of this study was to review the main applications of artificial intelligence methods in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics and metabolomics, discuss important aspects of data management, such as data integration, , cleaning, noise removal, balancing and ratio of missing data, functional genomics-system modeling, artificial intelligence and systems biology, addressing legal, ethical and economic issues related to the application of artificial intelligence methods in the field of genomics and presenting a view of possible scenarios in the future. Materials and methods In this review, all the researches conducted in the field of artificial intelligence application in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics and metabolomics, were tried, focusing on the applications of recent years after Increase production of big data to be studied and used. Results The studies showed that the application of artificial intelligence in all fields, including functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e., epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics, is increasing rapidly and has many benefits. Objective Data generation in biology and biotechnology has greatly increased in recent years due to the very rapid development of high-performance technologies. These data are obtained by studying biological molecules, such as metabolites, proteins, RNA, and DNA, to understand the role of these molecules in determining the structure, function, and dynamics of living systems. Functional genomics is a field of research that aims to characterize the function and interaction of all the major components (DNA, RNA, proteins, and metabolites, along with their modifications) that contribute to the set of observable characteristics of a cell or individual (i.e., phenotype). Furthermore, in a breeding program, genetic improvement can be maximized through accurate identification of superior animals that are selected as parents of the next generation, thereby achieving breeding goals. Artificial neural networks have been proposed to alleviate this limitation of traditional regression methods and can be used to handle nonlinear and complex data, even when the data is imprecise and noisy. Omics data can be too large and complex to handle through visual analysis or statistical correlations. This has encouraged the use of machine intelligence or artificial intelligence. The objectives of this study was to review the main applications of artificial intelligence methods in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics and metabolomics, discuss important aspects of data management, such as data integration, , cleaning, noise removal, balancing and ratio of missing data, functional genomics-system modeling, artificial intelligence and systems biology, addressing legal, ethical and economic issues related to the application of artificial intelligence methods in the field of genomics and presenting a view of possible scenarios in the future. Materials and methods In this review, all the researches conducted in the field of artificial intelligence application in functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e. epigenomics, transcriptomics, epitranscriptomics, proteomics and metabolomics, were tried, focusing on the applications of recent years after Increase production of big data to be studied and used. Results The studies showed that the application of artificial intelligence in all fields, including functional genomics, cancer, agriculture, domestic animals and its intertwined fields, i.e., epigenomics, transcriptomics, epitranscriptomics, proteomics, and metabolomics, is increasing rapidly and has many benefits.

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