TY - JOUR A1 - Anteghini, Marco A1 - Gualdi, Francesco A1 - Oliva, Baldo T1 - How did we get there? AI applications to biological networks and sequences T2 - Computers in Biology and Medicine N2 - The rapidly advancing field of artificial intelligence (AI) has transformed numerous scientific domains, including biology, where a vast and complex volume of data is available for analysis. This paper provides a comprehensive overview of the current state of AI-driven methodologies in genomics, proteomics, and systems biology. We discuss how machine learning algorithms, particularly deep learning models, have enhanced the accuracy and efficiency of embedding sequences, motif discovery, and the prediction of gene expression and protein structure. Additionally, we explore the integration of AI in the embedding and analysis of biological networks, including protein–protein interaction networks and multi-layered networks. By leveraging large-scale biological data, AI techniques have enabled unprecedented insights into complex biological processes and disease mechanisms. This work underlines the potential of applying AI to complex biological data, highlighting current applications and suggesting directions for future research to further explore AI in this rapidly evolving field. Y1 - 2025 UR - https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/10010 SN - 0010-4825 VL - 190 PB - Elsevier BV ER -