The ARC Centre of Excellence for the Mathematical Analysis of Cellular Systems (MACSYS) at the Australian National University (ANU) is offering two fully funded, 3.5-year PhD positions for 2026. These positions focus on cutting-edge research at the intersection of artificial intelligence, computational biology, and mathematical modelling, with the goal of advancing whole cell modelling and the design of RNA-interacting molecules.

Project 1 explores hybrid whole cell modelling, agentic AI virtual cells, genomic and RNA foundation models, and multi-omics modelling. The research aims to combine mechanistic cell models with modern machine learning to deliver robust predictions, integrate molecular foundation models with single-cell multi-omics data, train genome/RNA foundation models, and fuse various omics data to infer cell states and dynamics. This project is ideal for students with backgrounds in computer science, mathematics, or computational biology, especially those with strong machine learning and mathematical modelling skills.

Project 2 focuses on AI-driven decoding and design of RNA-interacting molecules. The goal is to develop integrated AI systems for biomedicine to decode and engineer molecules that specifically target RNA, addressing key challenges in cell biology, biotechnology, and RNA-targeting therapeutics. The research leverages RNA-aware deep learning models, diffusion-based molecular generation, and agentic reasoning to design synthetic RNA-interacting molecules, incorporating multimodal training and domain-specific biological constraints.

Both projects are supervised by leading academics at ANU: Associate Professor Jiayu (Jean) Wen and Professor Eduardo Eyras. The positions are fully funded, covering tuition and providing a stipend for 3.5 years. Application rounds are open for April (international & domestic), August (international), and October (domestic) 2026. Interested candidates should contact the relevant supervisor with a cover letter (email format acceptable), CV, and academic transcripts. For more information and application instructions, visit the MACSYS website.

Key research areas include AI-driven whole cell modelling, hybrid cell modelling, agentic AI, genomic foundation models, multi-omics modelling, RNA-interacting molecules, computational biology, machine learning, synthetic biology, and biotechnology.