AI applications in functional genomics
We review the current applications of artificial intelligence (AI) in functional genomics. The recent explosion of AI follows the remarkable achievements made possible by “deep learning”, along with a burst of “big data” that can meet its hunger. Biology is about to overthrow astronomy as the paradi...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037021004311 |
| _version_ | 1818979542004400128 |
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| author | Claudia Caudai Antonella Galizia Filippo Geraci Loredana Le Pera Veronica Morea Emanuele Salerno Allegra Via Teresa Colombo |
| author_facet | Claudia Caudai Antonella Galizia Filippo Geraci Loredana Le Pera Veronica Morea Emanuele Salerno Allegra Via Teresa Colombo |
| author_sort | Claudia Caudai |
| collection | DOAJ |
| description | We review the current applications of artificial intelligence (AI) in functional genomics. The recent explosion of AI follows the remarkable achievements made possible by “deep learning”, along with a burst of “big data” that can meet its hunger. Biology is about to overthrow astronomy as the paradigmatic representative of big data producer. This has been made possible by huge advancements in the field of high throughput technologies, applied to determine how the individual components of a biological system work together to accomplish different processes. The disciplines contributing to this bulk of data are collectively known as functional genomics. They consist in studies of: i) the information contained in the DNA (genomics); ii) the modifications that DNA can reversibly undergo (epigenomics); iii) the RNA transcripts originated by a genome (transcriptomics); iv) the ensemble of chemical modifications decorating different types of RNA transcripts (epitranscriptomics); v) the products of protein-coding transcripts (proteomics); and vi) the small molecules produced from cell metabolism (metabolomics) present in an organism or system at a given time, in physiological or pathological conditions. After reviewing main applications of AI in functional genomics, we discuss important accompanying issues, including ethical, legal and economic issues and the importance of explainability. |
| first_indexed | 2024-12-20T17:01:11Z |
| format | Article |
| id | doaj.art-51ae253844e64a12b6a64863e6a7b82b |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-20T17:01:11Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-51ae253844e64a12b6a64863e6a7b82b2022-12-21T19:32:31ZengElsevierComputational and Structural Biotechnology Journal2001-03702021-01-011957625790AI applications in functional genomicsClaudia Caudai0Antonella Galizia1Filippo Geraci2Loredana Le Pera3Veronica Morea4Emanuele Salerno5Allegra Via6Teresa Colombo7CNR, Institute of Information Science and Technologies “A. Faedo” (ISTI), Pisa, Italy; Corresponding authors.CNR, Institute of Applied Mathematics and Information Technologies (IMATI), Genoa, ItalyCNR, Institute for Informatics and Telematics (IIT), Pisa, ItalyCNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy; CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, ItalyCNR, Institute of Molecular Biology and Pathology (IBPM), Rome, ItalyCNR, Institute of Information Science and Technologies “A. Faedo” (ISTI), Pisa, ItalyCNR, Institute of Molecular Biology and Pathology (IBPM), Rome, ItalyCNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy; Corresponding authors.We review the current applications of artificial intelligence (AI) in functional genomics. The recent explosion of AI follows the remarkable achievements made possible by “deep learning”, along with a burst of “big data” that can meet its hunger. Biology is about to overthrow astronomy as the paradigmatic representative of big data producer. This has been made possible by huge advancements in the field of high throughput technologies, applied to determine how the individual components of a biological system work together to accomplish different processes. The disciplines contributing to this bulk of data are collectively known as functional genomics. They consist in studies of: i) the information contained in the DNA (genomics); ii) the modifications that DNA can reversibly undergo (epigenomics); iii) the RNA transcripts originated by a genome (transcriptomics); iv) the ensemble of chemical modifications decorating different types of RNA transcripts (epitranscriptomics); v) the products of protein-coding transcripts (proteomics); and vi) the small molecules produced from cell metabolism (metabolomics) present in an organism or system at a given time, in physiological or pathological conditions. After reviewing main applications of AI in functional genomics, we discuss important accompanying issues, including ethical, legal and economic issues and the importance of explainability.http://www.sciencedirect.com/science/article/pii/S2001037021004311Artificial intelligenceFunctional genomicsGenomicsProteomicsEpigenomicsTranscriptomics |
| spellingShingle | Claudia Caudai Antonella Galizia Filippo Geraci Loredana Le Pera Veronica Morea Emanuele Salerno Allegra Via Teresa Colombo AI applications in functional genomics Computational and Structural Biotechnology Journal Artificial intelligence Functional genomics Genomics Proteomics Epigenomics Transcriptomics |
| title | AI applications in functional genomics |
| title_full | AI applications in functional genomics |
| title_fullStr | AI applications in functional genomics |
| title_full_unstemmed | AI applications in functional genomics |
| title_short | AI applications in functional genomics |
| title_sort | ai applications in functional genomics |
| topic | Artificial intelligence Functional genomics Genomics Proteomics Epigenomics Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2001037021004311 |
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