AI tool reveals single-cell structure of chromosomes in 3D

Jun 2, 2025 | General news

An example of 3D modeling generated by new AI tool. Credit: Yanli Wang
An example of 3D modeling generated by new AI tool. Credit: Yanli Wang

In a leap forward for genetic and biomedical research, two scientists at the University of Missouri have developed a powerful new artificial intelligence tool that can predict the 3D shape of chromosomes inside individual cells, helping researchers gain a new view of how our genes work.Historically, scientists have relied on data that averaged results from millions of cells at once. That makes it almost impossible to see the unique differences between individual cells. But the new AI model developed by Yanli Wang and Jianlin “Jack” Cheng at Mizzou’s College of Engineering changes that. Studying single cells is tricky because the data is often messy or incomplete. But the new AI tool is specially designed to work with those challenges. It’s smart enough to spot weak patterns in noisy data, and it knows how to estimate a chromosome’s 3D shape even when some information is missing. The team has made the software free and available to scientists around the world. That means researchers can now use it to better understand how genes function, how diseases start and how to design better treatments. The researchers now plan to improve the AI tool even further by expanding it to build the high-resolution structures of entire genomes. Their goal: to give scientists the clearest picture yet of the genetic blueprint inside our cells.

More information: Yanli Wang et al, Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks, NAR Genomics and Bioinformatics (2025). DOI: 10.1093/nargab/lqaf027

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Article can be accessed on: phys.org