Faculty Spotlight

naegle.jpgKristen Naegle, PhD
Assistant Professor of Biomedical Engineering
Assistant Professor of Computer Science and Engineering
B.S. (Electrical Engineering), University of Washington, 2001
M.S. (Electrical Engineering) University of Washington, 2004
S.M. (Bioengineering) Massachusetts Institute of Technology, 2006
Ph.D. (Bioengineering) Massachusetts Institute of Technology, 2010
What do you enjoy most about being part of the Washington University DBBS team?
I immensely enjoy interacting with the students of DBBS and colleagues affiliated with DBBS who are doing so much diverse and interesting research in a collaborative manner.
What are your research interests? What are your research goals?
I am interested in understanding how tyrosine phosphorylation functions within proteins and within cell signaling networks. There are 46,000 phosphotyrosines that have been identified in the human proteome (currently) and my goal is to develop both computational and experimental approaches to identify and test the function of phosphotyrosine -- specifically developing methods and understanding that begins to approach the scale of the problem.
How has your time at Washington University helped further your research goals?
I have had amazing students and staff, great colleagues, and fabulous facilities that have allowed me to establish a research program and build into new areas. I would not have guessed five years ago that I would be publishing an algorithm in evolution and developing synthetic biology approaches to producing phosphorylated proteins in E. coli.
What is your favorite part about living in St. Louis?
I grew up in a truly small city (Boise, Idaho) and most recently lived in a big city (Boston, Massachusetts). I really appreciate how St. Louis is a blend of both of these types of metropolitan areas.  It has all of the trappings of a larger city (theater, opera, museums, gardens, and great food), but with the expense and ease of access as a small city.
What hobbies do you enjoy?
My husband would tell you that my hobby is trying new hobbies.
What is your favorite quote?
Zora Neale Hurston is my favorite author and it's for reasons like these (from “Their Eyes Were Watching God”):
"She was a rut in the road. Plenty of life beneath the surface but it was kept beaten down by the wheels. Sometimes she stuck out into the future, imagining her life different from what it was. But mostly she lived between her hat and her heels, with her emotional disturbances like shade patterns in the woods — come and gone with the sun."
A second quote, a line that will haunt me the rest of my days is from Ta-Nehisi Coates' "Between the World and Me"; a letter to his son: "Never forget that we were enslaved in this country longer than we have been free. Never forget that for 250 years black people were born into chains — whole generations followed by more generations who knew nothing but chains.”
What is the most ridiculous fact you know?
I know that there is an animal in Asia, the bearcat, whose urine smells like hot buttered popcorn. Also, octopuses don't stick to themselves because of a process (likely chemical) between their skin and their suckers.
Who is your biggest role model?
I try not to judge people by their size.
What advice would you give to both prospective and current graduate students?
To prospective students: There is never one path and don't believe people when they tell you there is a best path.
To current graduate students, if you haven't yet: Cultivate your communities — the scientific community that will push your boundaries and keep you curious every day and the personal community that will support you every step of the way and keep you rooted in what is truly important. 
Fellowships, awards, and publications while at Washington University:
NCI/SAGE Integrative Approaches to Cancer Metastasis workshop, June 2017 (invited participant)
Publication Ronan, Qi, and Naegle in “Science Signaling” made the home page of science and was the most tweeted
article in the history of “Science Signaling.”
Publication Ronan et al. in “Journal of Biological Chemistry” was article of the week, a highlight of the year in 2016, and rated "Exceptional" by Faculty of 1000.
Keynote Speaker, 4th Midwest Quantitative Biology Symposium, Purdue, October 22, 2016.
Keynote Speaker, Biomedical Computation at Stanford (BCATS) Symposium, April 6, 2015.
1.         Sloutsky, Roman, and Kristen M. Naegle. “Accuracy through Subsampling of Protein EvolutioN: An Ensemble Approach to Testing Accuracy and Reconstructing the History of Protein Family Divergence.” (BioRXiv Preprint: doi: https://doi.org/10.1101/170787, 2017)
2.         Sloutsky, Roman, and Kristen M. Naegle. “Proteome-level analysis indicates global mechanisms for post-translational regulation of RRM domains”. Journal of Molecular Biology, 2017
3.         Mooradian, Arshag D., Jason M. Held, and Kristen M. Naegle. “Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins They Annotate.” Current Protocols in Bioinformatics, 2017
4.         Schaberg, Katherine E., Venktesh S Shirure, Elizabeth A Worley, Steven C George, and Kristen M Naegle. “Ensemble Clustering of Phosphoproteomic Data Identifies Differences in Protein Interactions and Cell-Cell Junction Integrity of HER2-Overexpressing Cells.” Integr. Biol. 9 (2017): 539–47. doi:10.1039/C7IB00054E.
5.         Sloutsky, Roman, and Kristen M. Naegle. “High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments.” Plos One 11, no. 9 (2016): e0162579.
6.         Noren, David P., Byron L. Long, Raquel Norel, Kahn Rrhissorrakrai, Kenneth Hess, Chenyue Wendy Hu, Alex J. Bisberg, et al. “A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.” PLOS Computational Biology 12, no. 6 (2016): e1004890. *Naegle lab (Tom Ronan, Jennifer Flynn, Kristen M. Naegle) participated as a team in the AML consortium.
7.         Ronan, Thomas, Zhijie Qi, and Kristen M Naegle, “Avoiding pitfalls when clustering biological data”, Science Signaling, 9, no. 432 (2016): re6. Invited Review.
8.         Ronan, Thomas, Jennifer L. McDonnell-Obermann, Laurel Huelsmann, *Kristen M. Naegle, and  *Linda J. Pike. “The seven EGF receptor agonists each elicit a unique signature of recruitment of downstream signaling proteins”, Journal of Biological Chemistry 291, no. 12 (2016): 5528-5540 *co-corresponding
9.         Holehouse, Alex S, and Kristen M. Naegle. “Reproducible Analysis of Post-Translational Modifications in Proteomes—Application to Human Mutations.” PLoS ONE 10, no. 12 (2015): 1–19.
10.       *Naegle, Kristen M., Nancy R Gough, and *Michael B Yaffe. “Criteria for Biological Reproducibility : What Does ‘n’ Mean ?” Science Signaling 8, no. 371 (2015): 2–5. *co-corresponding
11.       Matlock, Matthew K, Alex S Holehouse, and Kristen M Naegle. “ProteomeScout: A Repository and Analysis Resource for Post-Translational Modifications and Proteins.” Nucleic Acids Research 43, no. D1 (November 20, 2015): D521–30.
12.       Cho, Yongcheol, Roman Sloutsky, Kristen M Naegle, and Valeria Cavalli. “Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration.” Cell 155, no. 4 (November 2013): 894–908.
13.       Iwai, Leo K, Leo S Payne, Maciej T Luczynski, Francis Chang, Huifang Xu, Ryan W Clinton, Angela Paul, Edward A. Esposito, Scott Gridley, Birgit Leitinger, Kristen M Naegle, and Paul H. Huang.  “Phosphoproteomics of Collagen Receptor Networks Reveals SHP-2 Phosphorylation Downstream of Wild-Type DDR2 and Its Lung Cancer Mutants.” The Biochemical Journal 454, no. 3 (September 15, 2013): 501–13.
14.       Sloutsky, Roman, Nicolas Jimenez, S Joshua Swamidass, and Kristen M Naegle. “Accounting for Noise When Clustering Biological Data.” Briefings in Bioinformatics 14, no. 4 (July 2013): 423–36. doi:10.1093/bib/bbs057.

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