We have a new paper out that performs a detailed comparison of computational methods for inferring enzyme function. This is collaborative work with Saeedeh Davoudi and Farnoush Banaei-Kashani in Computer Science at CU Denver, and also involved Chris Henry at Argonne National Lab. There are so many methods out there to do these kinds of predictions of function, but little bioinformatics research that explores how to objectively evaluate the methods. Read more in our Bioinformatics Advances paper here: EC-Bench: a benchmark for enzyme commission number prediction.

The Lowry Landfill is an EPA Superfund site that operates a very unique microbial solution for cleaning up contaminated groundwater. The Biological Treatment System uses natural microbes to degrade 1,4-dioxane, and is a system that is pretty much unique in the US. Thanks in large part to the hard work of Jessie Romero, MS, we have a new publication out that gets us closer to a mechanistic understanding of how the system works, thanks to shotgun metagenomics and marker gene sequencing. In addition to data generated and analyzed by Jessie and the rest of the co-authors, this work also includes data generated by our first year General Biology students here at CU Denver! Read more here: Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.

Congratulations to Derick, who defended his MS Thesis. Derick used the GROW river microbiome dataset to explore the distribution of antimicrobial resistance genes in US rivers. He was also a co-author on the Nature paper describing these U.S. river microbial communities. Congratulations, Derick!

Alyssa Cruz, an outstanding undergraduate researcher in the lab, has won the… Outstanding Undergraduate in Public Health Award, and won a poster award at the 2024 CU Denver Research and Creative Activities symposium. After graduation this semester, she’s headed off to do a PhD at the Sanford Burnham Prebys Medical Discovery Institute. Congratulations, Alyssa!