Artificial Intelligence in Transcriptomics: From Human-in-the-Loop to Agentic AI

To better understand the complexity of biological systems, research has shifted from a reductionist to a holistic approach, expanding the focus from single genes to a genome-scale view of gene activity and regulation. This is known as transcriptomics, a continuously growing field generating gene expression signatures from different technologies. A comparable paradigm shift has occurred in computational systems biology with the implementation of Artificial Intelligence (AI) learning models for gene expression analysis and integration. These models enable transcriptome-based profiling to address challenges of data heterogeneity, integration, and updating, assisting human intelligence and enhancing their ability to retrieve, analyze, integrate, and generate data recursively, thanks to their intrinsic predictive, inferential, reinforcement, and generative capabilities. Additionally, while scientists worldwide are still learning how to leverage AI methods that can maintain the human-in-the-loop, a new fundamental change is emerging: agentic AI, which can autonomously act and employ other AI methods to pursue its objectives. As a futuristic perspective, the proposed data analysis pipeline imagines agentic AI systems allowing the automated retrieval and pre-processing of heterogeneous transcriptomics data, analysis and integration with other omics datasets, performed with an incremental updating and recurrent analysis (IURA) model that could allow the detection of guideline updates (e.g., disease reclassification) and the generation of new hypotheses, such as candidate biomarkers or transcriptome-phenotype correlations. Since personalized medicine could derive profound benefits from its use, this scenario also raises important considerations regarding the advantages and concerns associated with the use of scientific AI agents in research and clinical practice.