Fast, flexible tools to map how viruses like SARS-CoV-2 spread
Fast and flexible Bayesian phylogenetics via modern machine learning
This project builds fast computer methods that use thousands of viral genomes to track how the coronavirus spreads and support public health response.
Quick facts
| Grant type | R01 grant |
|---|---|
| Study type | NIH-funded research |
| Funding institution | Fred Hutchinson Cancer Center NIH-funded |
| Lab location | 1 site (Seattle, United States) |
| Project ID | NIH-11099997 on NIH RePORTER |
What this research studies
From a patient perspective, researchers are creating new machine-learning versions of Bayesian phylogenetics so they can analyze thousands of viral genomes quickly and with reliable uncertainty estimates. They'll develop mathematical tools and fast algorithms (including online updates and convergence checks) and implement them in popular frameworks like TensorFlow and PyTorch. The methods will let scientists combine genome sequences with data such as sampling location and migration patterns to produce clearer pictures of how outbreaks move. Those improved maps are intended to inform strategies for controlling viral spread.
Who could benefit from this research
Good fit: People with confirmed SARS-CoV-2 infection whose viral samples are sequenced and shared in public or research databases are the individuals whose data could be included.
Not a fit: Patients without viral genome sequencing or people with conditions unrelated to viral infections would not directly benefit from this computational work.
Why it matters
Potential benefit: If successful, this work could give public health teams faster and clearer information about outbreak spread, helping reduce infections and target interventions sooner.
How similar studies have performed: Traditional phylogenetic and genomic-tracing methods have helped map outbreaks, but applying scalable variational machine-learning methods to thousands of genomes is a newer and less-tested approach.
Where this research is happening
Seattle, United States
- Fred Hutchinson Cancer Center — Seattle, United States (Active)
Researchers
- Principal investigator: Matsen, Frederick Albert — Fred Hutchinson Cancer Center
- Study coordinator: Matsen, Frederick Albert
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.