Italy
Technologist position in RNA Technologies Flagship – Artificial Intelligence Expert – RNA-Based Applications
Contract: Fixed-term contract, full time, up to 3 years
Location: Genova/Milano/Roma

ESSENTIAL REQUIREMENTS

• PhD or equivalent research experience in computational biology, machine learning, bioinformatics, physics or related fields;
• High proficiency level in programming languages (e.g., Python, R, SQL), in Linux environment, and High-Performance Computing infrastructures, in handling workflow/workload managers and containers;
• High proficiency level in Python and relevant deep learning libraries (such as TensorFlow, PyTorch), along with experience in structural modeling tools (e.g., Vienna, Rosetta, RNAstructure) and graph neural networks or transformers applied to molecular modeling;
• A solid understanding of molecular simulations, especially in relation to RNA systems, and capable of handling large-scale biological data;
• Ability to communicate scientific concepts, analytical reasoning, and scientific creativity;
• Ability to work and think independently, and collaboratively in a highly interdisciplinary environment, with a pro-active attitude;
• Fluency in both spoken and written English.

The RNA Technologies Flagship at Fondazione Istituto Italiano di Tecnologia (IIT) is seeking a highly motivated and experienced Technologist with a strong background in applying machine learning and deep learning techniques to the biological sciences. The ideal candidate will have advanced expertise in artificial intelligence, with a specific focus on deep learning applications in structural biology. This is a unique opportunity to join a dynamic, interdisciplinary team operating at the intersection of computational genomics, RNA biology, and precision medicine. The goal is to build a strategic institutional resource for advancing discoveries in cancer, neurodevelopmental, and neurodegenerative disorders, through the integration of computational modeling of RNA and understanding RNA interactions.
The ideal candidate has a strong background in molecular biology, genetics, and biochemistry, and is familiar with complex experimental data generated from omics studies or laboratory-based research. A collaborative mindset is essential, as the role involves working closely within multidisciplinary teams of biologists, chemists, engineers, and medical professionals, with the goal of translating AI-driven insights into practical and potentially clinical applications.
The RNA Technologies Flagship is a cornerstone of IIT’s strategic plan, bringing together over 20 Principal Investigators and more than 200 scientists. This ambitious interdisciplinary program is aiming to drive technological innovation and clinical translation by advancing RNA-based diagnostics, therapeutics, and precision medicine tools.
For more information about the RNA Technologies Flagship, visit: https://www.rna.iit.it
The Artificial Intelligence Expert will play a pivotal role in the RNA Technologies Flagship by developing and applying cutting-edge deep learning methods to model RNA structures and RNA-based molecular complexes. The primary goal of this position is to enable the rational design of RNA-targeting molecules, such as aptamers, antisense oligonucleotides (ASOs), and next-generation RNA-modulating agents like RIBOTACs and PROTACs. Through advanced modeling of RNA structure, folding dynamics, and interaction interfaces, the AI expert will directly contribute to identifying novel therapeutic targets and guiding the engineering of RNA-binding molecules with high specificity and functionality.
The successful candidate will be responsible for integrating AI-driven approaches—including graph neural networks, generative models, and transformer-based architectures—into the RNA design pipeline, with a strong emphasis on explainability, predictive accuracy, and experimental validation. A central component of the work will involve simulating the conformational dynamics of RNA molecules, predicting the effects of sequence variation (including mutations), and mapping the structural basis for interactions with small molecules, peptides, or protein partners.
This position offers a unique opportunity to influence the development of novel RNA-based therapeutic strategies and contribute to shaping the computational backbone of a flagship national initiative in RNA technologies.

Within the team, your main responsibilities will be:

• Design and implement deep learning frameworks for modeling RNA structure and dynamics, using state-of-the-art computational tools and AI architectures.
• Predict and evaluate RNA-ligand interactions to support the discovery of molecules capable of binding or degrading RNA or RNA-protein complexes (e.g., aptamers, RIBOTACs, RNA-targeting PROTACs).
• Contribute to the development of in silico pipelines for high-throughput screening of candidate RNA-targeting molecules and optimization of their binding interfaces.
• Collaborate with wet-lab researchers and clinicians to validate AI-generated predictions and integrate results into iterative design-experimentation cycles.
• Assist in the interpretation of multi-modal biological data (e.g., transcriptomics, structural genomics, interactomics) and incorporate these datasets into machine learning models to improve their biological relevance and robustness.
• Contribute to publications, patent generation, and technology transfer initiatives stemming from AI-driven discoveries in RNA biology and designing and management of initiatives aimed at the valorization of intellectual property rights and technology transfer
• Support internal strategic efforts to build institutional capabilities in RNA modeling, AI-based drug discovery, and synthetic biology, particularly within WP3 of the Flagship program.