Institute for Genomics & Evolutionary Medicine · Temple University

Steven Weaver

I build systems that turn genomic data into research and public-health tools. Off the clock, I point the same curiosity at fast food, old anime, and books.

Software used by the U.S. Centers for Disease Control and Prevention for HIV molecular surveillance. Research published in Nature, Cell, and Science Translational Medicine.

Software

Datamonkey A web application for detecting natural selection and other evolutionary processes in gene sequences. Supported by the NIH and NSF.HyPhy An open-source platform for phylogenetic hypothesis testing, and the analysis engine behind Datamonkey. Open source, written in C++.HIV-TRACE Reconstructs genetic-distance transmission networks for molecular epidemiology. Used by the U.S. CDC for HIV cluster detection and response.phylotree.js A JavaScript library for interactive visualization of phylogenetic trees. Open source, embedded in tools across the field.

Steven Weaver

About

I’m a Senior Programming Analyst at Temple University’s Institute for Genomics and Evolutionary Medicine (CV). I develop and maintain bioinformatics software for analyzing molecular evolution and natural selection in pathogen genomes. This includes Datamonkey and the HyPhy platform for selection analysis, the phylotree.js visualization library, and HIV-TRACE, a tool for molecular epidemiology. The software is written primarily in C++, Python, and JavaScript.

Beyond building these tools, I conduct research on the molecular epidemiology of viral pathogens, including HIV and hepatitis C, using genetic-distance methods to reconstruct transmission networks. I develop and maintain the systems that public-health agencies, including the U.S. Centers for Disease Control and Prevention, use for HIV molecular surveillance and cluster detection. During the COVID-19 pandemic, I also contributed to the characterization of SARS-CoV-2, including its variants of concern and the Omicron lineages.

These analyses run at scale on high-performance computing, which I provision and administer at the San Diego Supercomputer Center and at Temple University.

Current work is focused on modernizing the platform: compiling HyPhy to WebAssembly so that selection analyses can run directly in a web browser, and connecting the analysis platform to large language models through the Model Context Protocol.