Research

All of our research deals with the fundamental questions posed on the home page. However, to help you find the specific techniques or projects we pursue, please choose one of the following topics.

A foundation of our work is the ability to have proteome information at our fingertips. This includes the current knowledge of tyrosine phosphorylation, quantitative measurements measured on those sites, and related protein annotations.  In enabling this research for our own lab, we also construct tools that can be used by the broader research community, with a focus on extendibility and reproducibility. ProteomeScout ProteomeScout is our database of post-translational modifications and their protein annotations.  The major features of ProteomeScout …
A major barrier to the study of protein phosphorylation is the ability to create phosphorylated proteins for in vitro study. The Naegle lab has been developing a cheap and fast method for producing phosphorylated proteins that capitalizes on observations made of enzymatic specificity.
Clustering is a type of unsupervised learning approach to identify underlying structure in multidimensional data, based on exploring the data alone (i.e. without labels as occurs in supervised learning).  Ultimately, the structure uncovered in a solution is a hypothetical relationship of the data that may indicate meaning. This structure is different when the relationships of the data are perturbed, such as by transforming the data, or when alternate criteria are considered in the process (like using a different measure of distance between points or algorithms). …
A major piece of ongoing work in the lab is to develop methods that will allow us to identify what phosphotyrosines will be recognized by a binding domain. Specifically, we hope to push this area of research into arenas that allow us to predict the relative competition between domains for phosphotyrosine sequences and phosphotyrosine sequences for domains. This information will enable us to begin to predict the consequence of context differences between cells in response to the same extracellular cue. We will feel we have succeeded when these predictions can be …