Ph.D. Biological Engineering, MIT, 2010S.M. Biological Engineering, MIT, 2006M.S. Electrical Engineering, University of Washington, 2004B.S. Electrical Engineering, University of Washington, 2001

"Our overriding interest is tackling the challenge of tyrosine phosphorylation, and we cross disciplines as necessary to achieve this goal."

Kristen Naegle, PhD, Associate Professor

Kristen Naegle uses data- and computational-driven approaches to predict, and experimental approaches to test, the regulation and function of tyrosine phosphorylation in complex networks. Tyrosine phosphorylation is a protein modification that can occur during or after translation of a protein.The phosphate addition to a tyrosine residue, regulated by tyrosine kinases and phosphatases, can result in changes in protein function, regulation and localization. It is key to important cell signaling processes, which are the processes that convert extracellular cues, like growth factors and insulin, into biochemical networks that result in a change to the cell.  Tyrosine phosphorylation is specifically utilized in the early events of receptor tyrosine kinase (RTK) networks, which are fundamental to many processes in the development and homeostasis of complex organisms.  Improvements in measurement technologies have enabled the ability to detect and monitor tyrosine phosphorylation and now we know that tyrosine phosphorylation is extensive — occurring on thousands of tyrosines in the human proteome.

Given the sheer size of the challenge, we use both computational and molecular technologies to predict and test the role of tyrosine phosphorylation on proteins and in cellular networks.  Although we incorporate new mathematical and computational methods as needed to tackle the fundamental problems of our research, those techniques always have a foundation in statistical robustness. Hypotheses are tested in molecular and cellular systems, closing the loop between computation and experimentation.

The questions that drive us include:

  • How do we increase the capabilities of research to gain new understanding of tyrosine phosphorylation rapidly, i.e. in a high-throughput manner that matches the rate of discovery of these modifications?
  • How do we develop new capabilities to understand how these networks act in specific contexts? Cell context refers to the differences we see between tissue types and the states of the network components that lead to differential responses of tissues to the same cue. As a philosophy, we approach network dysregulation that occurs in disease as an alteration in cell context.

Research Interests

  • Machine Learning and Data Science
  • Systems Biology
  • Bioinformatics and Computational Biology
  • Biotechnology
  • Cellular and Molecular Engineering
  • Synthetic Biology
  • Cancer

In the News

Courses Taught

  • BME 4550/6550: Molecular Data Science

Featured Grants & Projects

  • NIH/NCI Development of Innovative Informatics Methods and Algorithms for Cancer Research and Management (R21)

    Inferring kinase activity profiles from phosphoproteomic data

    Phosphorylation can regulate protein function, which is a cornerstone of normal tissue development and home- ostasis. However, kinases, the enzymes that catalyze protein phosphorylation, are often dysregulated in cancer. Recently, advances have been made to measure global phosphorylation within human patient tumor samples. The hope is that this data holds the key to identifying patient-specific targets in cancer therapy. Unfortunately, challenges exist in interpreting phosphorylation data and its reflection of the underlying dysregulation of signaling networks. The goal of this project is to develop an algorithm that translates the measurements of phosphorylation in human samples to a prediction of kinase activity profiles. The kinase activity profiles could then be used to identify new targets and classify tumor types. This goal will be achieved by: the development of graph-based score, based on predicted kinase-substrate relationships, interpretation of that score through statistical frameworks, and testing and improvement of the algorithms on available control and patient data.

    Read More
  • NIH/NCI Innovative Molecular and Cellular Analysis Technologies for Basic and Clinical Cancer Research (R21)

    A molecular toolkit for the production of tyrosine phosphorylated proteins

    yrosine phosphorylation can regulate protein function, and this is a cornerstone of cell signaling networks. Ty- rosine phosphorylation often becomes dysregulated in cancer and therefore, understanding the effect of phos- phorylation on protein function will be paramount to identifying therapeutic interventions in cancer. Unfortunately, an important tool in the basic research of phosphorylation – testing the effect of protein phosphorylation by com- paring the function of the phosphorylated form with an unphosphorylated form of the protein in in vitro assays – is significantly hindered by our limited knowledge in how to make a phosphorylated protein. This project seeks to build a molecular technology, inspired by previous observations of biochemistry in cell networks, to overcome this requirement and improve the pace of basic research. The goal of this research is to build a fast, accessible and inexpensive method for producing phosphorylated and soluble proteins in a bacterial system. The goals will be achieved by: development of a molecular toolkit for the enhancement and control of precise phosphorylation on protein substrates using secondary kinase-substrate targeting approaches, testing the toolkit on a set of sub- strates, and comparing the outcome with current technologies. It is anticipated that this technology will be less expensive, more physiologically-relevant, and capable of producing a larger variety of phosphorylated forms of proteins than current molecular approaches to studying the effect of protein phosphorylation.

    Read More