RNA and DNA-Based Gene Fusion Detection: Unveiling Genomic Rearrangements

Gene fusions, resulting from genomic rearrangements, have emerged as important drivers of oncogenesis and potential therapeutic targets in various types of cancer. Detecting gene fusions accurately is crucial for understanding tumor biology and developing targeted therapies. In recent years, advancements in RNA and DNA-based approaches have significantly improved gene fusion detection capabilities. 

Our aim is to unravel genomic rearrangements through RNA and DNA-based gene fusion detection tools, which are promising for advancing precision medicine in oncology and improving patient outcomes.

A gene fusion is a biological event in which two distinct regions in the DNA create a new fused gene. Gene fusions are a relevant issue in medicine because many gene fusions are involved in cancer, and some of them can even be used as cancer predictors. However, not all of them are necessarily oncogenic.

This research area aims to provide up-to-date gene fusion detection tools and prioritizers to facilitate biologists' works. The tools mainly exploit ML and DL architectures to integrate multiple data sources useful for gene fusion prediction (e.g., from transcription factors, gene ontologies, the structure of the gene fusion).

Publications

1	Lovino, Marta; Gianvito, Urgese; Enrico, Macii; Santa Di Cataldo, ; Ficarra, Elisa "Predicting the oncogenic potential of gene fusions using convolutional neural networks" Computational Intelligence Methods for Bioinformatics and Biostatistics, vol. 11925, Caparica, pp. 277 -284 , 6 - 8 September 2018, 2020 | DOI: 10.1007/978-3-030-34585-3_24 Conference
2	Lovino, Marta; Ciaburri, Maria Serena; Urgese, Gianvito; Di Cataldo, Santa; Ficarra, Elisa "DEEPrior: a deep learning tool for the prioritization of gene fusions" BIOINFORMATICS, vol. 36, pp. 3248 -3250 , 2020 | DOI: 10.1093/bioinformatics/btaa069 Journal
3	Lovino, Marta; Urgese, Gianvito; Macii, Enrico; Di Cataldo, Santa; Ficarra, Elisa "A Deep Learning Approach to the Screening of Oncogenic Gene Fusions in Humans" INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 20, pp. 1 -13 , 2019 | DOI: 10.3390/ijms20071645 Journal