In an open-source research paper, a UVA Engineering professor and her former Ph.D. student share a new, more accurate method for...
Approaching Tyrosine Phosphorylation as a Design Problem
The Naegle Lab seeks to understand the regulation and function of tyrosine phosphorylation in complex networks. We combine systems biology, computation, and experiments to test predict and test the function of tyrosine phosphorylation in proteins and protein networks. We hope to tackle the outsized challenge of understanding the role of 46,000 phosphotyrosines in the human proteome, while developing molecular and computational tools that are open source and broadly applicable to other fields of molecular research.
“I am very excited to be part of a department whose faculty members routinely use data- and computationally driven approaches to gain...
- Crowl, S., Jordan, B., Ma, C., & Naegle, K.M (2021). KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. Nature Communications
- Ronan, T., Anastasio, S., Qi, Z., Tavares, P. H. da S., Sloutsky, R., & Naegle, K. M. (2018). OpenEnsembles : A Python Resource for Ensemble Clustering. Journal of Machine Learning Research, 26, 1–6.
- Matlock, M. K., Holehouse, A. S., & Naegle, K. M. (2015). ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.ABS Nucleic Acids Research, 43(D1), D521–D530.
- Schaberg, K. E., Shirure, V. S., Worley, E. A., George, S. C., & Naegle, K. M. (2017). Ensemble clustering of phosphoproteomic data identifies differences in protein interactions and cell-cell junction integrity of HER2-overexpressing cells.ABS Integr. Biol., 9, 539–547.
- Ronan, T., Qi, Z., & Naegle, K. M. (2016). Avoiding common pitfalls when clustering biological data. Sci. Signal, 9(432), 1–12.
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open source software packages
undergrads mentored since 2012
active NIH R21 awards