The Naegle Lab Group

We use data- and computationally-driven approaches to predict - and experimental approaches to test - the regulation and function of tyrosine phosphorylation in complex networks.

Principal Investigator

  • Kristen Naegle, Ph.D.

    Kristen Naegle, Ph.D.

    Associate Professor of Biomedical Engineering

    Research Interests: Molecular/Cell Bioengineering; Quantitative Cell Biology; Systems Biology – proteomics, post-translational modifications, cell signaling, cell networks, machine learning, domain-motif interactions, protein-protein interactions.

    Faculty Profile

Postdocs and Professional Research Staff

  • Adrian Shimpi, Ph.D.

    Adrian Shimpi, Ph.D.

    Postdoctoral Researcher

    Studying tumor heterogeneity by developing tools to understand the evolution of signaling networks and the intersection of  protein domain architectures and post-translational modifications in regulating pathway activity.

    Email: yzv6ek@virginia.edu

    LinkedIn

  • Margaret Ryan

    Research Specialist

    Developing a synthetic toolkit to drive phosphorylation in proteins.

Graduate Students

  • Sam Crowl

    Sam Crowl

    Ph.D. Candidate

    Studying kinase activity in cancer and how changes to kinase activity can give rise to drug resistance in hopes of identifying effective therapeutic targets.

    Email: sc8wf@virginia.edu

    LinkedIn

  • Gabi Martinez

    Gabi Martinez

    Ph.D. Candidate

    Understanding the effects of tyrosine phosphorylation on SH2 domain function and binding specificity with hopes of better understanding the role of this modification in the progression of cancer.

    Email: gem6va@virginia.edu

    LinkedIn

  • Reagan Portelance

    Reagan Portelance

    Ph.D. Candidate

    Utilizing a synthetic toolkit to drive phosphorylation across recombinant proteins. This work has implications for cancer biomarker detection and understanding intracellular signaling pathways.

    Email: rlp5fh@virginia.edu

    LinkedIn

  • Alekhya Abhiram Kandoor

    Alekhya Abhiram Kandoor

    Ph.D. Candidate

    Developing a structure-based framework to compare inter- and intra- protein contact conservation

    Email: adk9hq@virginia.edu

    LinkedIn

  • Candace Lei

    Candace Lei

    Ph.D. Student

    Studying the roles of kinase-substrate networks in cancer progression and in characterizing the tumor microenvironment.

    Email: spw4mt@virginia.edu

    LinkedIn

Undergraduate Students

  • Hamza Ahmed

    Fourth-Year Undergraduate

    Modifying KSTAR for SH2 domains.

  • Julianna Hitchcock

    Fourth-Year Undergraduate

    Expanding CoDIAC for PH domain analysis

  • Swathi Shekharan

    Fourth-Year Undergraduate

    Designing and testing new plasmid constructs optimize protein expression, solubility, and purification.

  • Carol Wu

    Third-Year Undergraduate

    Working with the kinase toolkit to produce phosphorylated, recombinant proteins

  • Michael Park

    Second-Year Undergraduate

    Expanding CODIAC for SH3 domain analysis.

Naegle Lab Alumni

 

Postdoctoral Associates

  1. Zeenat Shyr, joint with Maria Remedi (2017-2018) through NIH training grant (WUSTL)

Ph.D. Students Trained

  1. Roman Sloutsky (PhD, August 2017 at WUSTL): Robust algorithms for detecting hidden structure in biological data. Current Position: Postdoctoral Associate at University of Massachusetts Amherst with Dr. Margaret Stratton.
  2. Tom Ronan (PhD, November 2017 at WUSTL): Binding Affinity and Specificity of SH2 Domain Interactions in Receptor Tyrosine Kinase Signaling Networks.

M.S. & M.E. Students Trained

  1. Summer Elias, (M.S. 2018, WUSTL): Reevaluating kinase evolution.

Undergraduate Students Trained

  1. Elizabeth Worley (WUSTL BME), 2012-2014
  2. Tedan Hu (UMSL Biochemistry), Summer 2012
  3. Nikolay Shenkov (University of Richmond), Summer 2012
  4. Kellie Stoka (WUSTL BME), Spring Semester 2013
  5. Cong Zhang (WUSTL BME), Spring 2013
  6. Jennifer Flynn (Truman Biology, Siteman Cancer Center), Summer 2013
  7. Junwoo Suh (WUSTL BME), Summer/Fall 2013
  8. Emily Gale (Swarthmore), Summer 2014 Amgen
  9. Zhijie Qi (WUSTL BME), 2014-2015
  10. Jordan Banks (University of Illinois), BiomedRAP
  11. Pedro de Silva Vierira Taveres (Brazil Scientific Mobility Program), Summer 2015
  12. Shweta Ravi (WUSTL BME), Spring/Summer 2016
  13. Ramya Palaniappan (Case Western), Summer 2016
  14. Varun Krishnamurthy (WUSTL CSE), Fall 2016
  15. Erin Tevonian (UIUC BME), Siteman Cancer Center, Summer 2017
  16. Liezel Tiples (Univ. of Guam), Genome Institute, Summer 2017
  17. Yuanyuan He (WUSTL BME), Spring and Summer 2018
  18. Yunli Chu (WUSTL BME), Spring 2018
  19. Dylan May (UVA), Spring 2019
  20. Savannah Angel (UVA), Spring 2021
  21. Bella Coleman (UVA), Spring 2021
  22. Saqib Rizvi (UVA), Spring 2021
  23. Andrew Chaphiv (UVA), Spring 2023
  24. Nico Paredes (Yale), Summer 2023 REU
  25. Joel Moses (Drew University), Summer 2023 SRIP