Team

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.

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.

Postdoctoral Fellow

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, M.S.

Research Specialist

Developing a synthetic toolkit to drive phosphorylation in proteins.

Graham Newman, B.S.

Research Technician

Levi Custer, M.S.

Software Engineer

Graduate Students

Sam Crowl

Ph.D. Candidate

Studying how kinase activity and alternative splicing drive changes to cancer cell behavior in various cancer types (including breast cancer and glioblastoma), with a long term goal of better identifying when a cancer patient may respond to kinase inhibitor therapies.

Email: SC8WF@VIRGINIA.EDU

LINKEDIN

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

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

Ph.D. Candidate

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

Email: ADK9HQ@VIRGINIA.EDU

LINKEDIN

Candace Lei

Ph.D. Candidate

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

Email: SPW4MT@VIRGINIA.EDU

LINKEDIN

Gabby Salazar-Lopez

Ph.D. Candidate

Studying kinase signaling in the context of cancer using mainly computational techniques. One of her goals is to help enhance the KSTAR algorithm, and use it to study how kinase activity contributes to the development and progression of cancerous tumors.

Undergraduate Students

Mindolay Fike

Madhuri Sosale

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
  26. Hamza Ahmed (UVA), Spring 2024
  27. Julianna Hitchcock (UVA), Spring 2024
  28. Swathi Shekharan (UVA), Spring 2024
  29. Riko Mukoyama (Smith College), Summer 2024 REU
  30. Carol Wu (UVA), Spring 2025
  31. Alysha Akhtar (UVA), Spring 2025
  32. Kayenat Peera (UVA), Spring 2025