PDF version: tamasnagy_cv.pdf
Tamas L. Nagy
University of California, San Francisco
Cardiovascular Research Building, Room 384, MC 3120
555 Mission Bay Blvd. South
San Francisco, CA 94158-9001
Email: iam [at] tamasnagy.com
Twitter: @tlngy
Website: https://tamasnagy.com
Education
2015— Graduate student, Biomedical Informatics, University of California, San Francisco
2011—2015 B.S. in Chemistry, B.S. in Mathematics, University of Kentucky, Lexington
Research Interests
Systems Biology & Computational Biology; Machine Vision; Cell-to-Cell Heterogeneity and Cell Decision Making; Data Visualization
Awards & Grants
2017 Graduate Division TA Award, University of California, San Francisco
2017 Moritz-Heyman Discovery Fellow, University of California, San Francisco
2015 NSF Graduate Research Fellow, National Science Foundation
2014 Undergraduate Research Abroad Scholar w/Lucas Pelkmans, University of Zurich
2013 AMGEN/CRSB Fellow w/Jennifer Doudna, University of California, Berkeley
2012 Chellgren Fellow, University of Kentucky
2011 Otis A. Singletary Scholar, University of Kentucky (Tuition, Board, & stipend)
Publications
Graziano, B. R., Town, J. P., Sitarska, E., Nagy, T. L., Fošnarič, M., Penič, S., Iglič, A., Kralj-Iglič, V., Gov, N. S., Diz-Muñoz, A., & Weiner, O. D. (2019). Cell confinement reveals a branched-actin independent circuit for neutrophil polarity. PLoS Biology, 17(10), e3000457. https://doi.org/10.1371/journal.pbio.3000457
Saha, S., Nagy, T. L. & Weiner, O. D. Joining forces: crosstalk between biochemical signalling and physical forces orchestrates cellular polarity and dynamics. Philos. Trans. R. Soc. Lond. B Biol. Sci. 373, (2018). https://doi.org/10.1098/rstb.2017.0145
Nagy, T. & Kampmann, M. CRISPulator: a discrete simulation tool for pooled genetic screens. BMC Bioinformatics 18, 347 (2017). https://doi.org/10.1186/s12859-017-1759-9
Webb, S., Nagy, T., Moseley, H., Fried, M. & Dutch, R. E. Hendra virus fusion protein transmembrane domain contributes to pre-fusion protein stability. J. Biol. Chem. (2017). https://doi.org/10.1074/jbc.M117.777235
Software
I develop or maintain the following open-source libraries:
Gadfly.jl
: Premier grammar of graphics library in the Julia languageWeave.jl
: Literate programming environment for Julia; generate reproducible scientific reportsCrispulator.jl
: Simulation tool for designing pooled CRISPR screensOMETIFF.jl
: Read and interact with high-dimensional imagesjekyll-lab-notebook
: Simple and flexible electronic lab notebook based on the Jekyll static site generator
Talks & Posters
2020 “Leveraging Julia for Data Science”, invited speaker, 2020 Computational Biology Skills Seminar, UC Berkeley, remote
2019 “Dissecting the mechanistic basis of the chemoattractant-induced volume increase in neutrophils”, 2019 Gordon Research Conference on Directed Cell Migration, Galveston, TX
2018 “Dissecting the mechanistic basis of the chemoattractant-induced volume increase in neutrophils”, 2018 Ion Channels & Immunity Symposium, NYU Langone Health, New York City, NY
2018 “Active control of cell volume during immune cell migration”, 2018 Training Grantees Meeting, National Institute of Biomedical Imaging and Bioengineering, Bethesda, MD
2016 “Leveraging CRISPR for Precision Biology”, Workshop with Jacob Corn and Martin Kampmann, American Society for Cell Biology Annual Meeting, San Francisco, CA
2014 “Investigating the Expanding Role of Transmembrane Domains in Enveloped Virus Entry,” Bioinformatics Summit, UT-KBRIN, Lake Barkley, KY
2014 “Investigating Common Transmembrane Motifs in Enveloped Virus Entry,” National Conference of Undergraduate Research, Lexington, KY
2013 “Engineered CRISPR/Cas-based System for RNA-guided, Tag-less, Spatiotemporal Imaging of Endogeneous RNA,” AMGEN symposium, Berkeley, CA
Service
2018 Teaching Assistant, Algorithms, University of California, San Francisco
2017 Teaching Assistant, Algorithms, University of California, San Francisco
2014 Teaching Assistant, Organic Chemistry II, University of Kentucky
2013 Teaching Assistant, Organic Chemistry I, University of Kentucky
2013—2014 Public Relations, Society for the Promotion of Undergraduate Research (SPUR)
References (Alphabetical)
Steven J. Altschuler, UCSF, steven.altschuler [at] ucsf.edu
Jennifer A. Doudna, UC Berkeley, doudna [at] berkeley.edu
Rebecca E. Dutch, University of Kentucky, rdutc2 [at] uky.edu
Jerzy Jaromczyk, University of Kentucky, jurek [at] cs.uky.edu
Martin Kampmann, UCSF, martin.kampmann [at] ucsf.edu
Hunter Moseley, University of Kentucky, hunter.moseley [at] uky.edu
Lucas Pelkmans, University of Zurich, lucas.pelkmans [at] imls.uzh.ch
Orion Weiner, UCSF, orion.weiner [at] ucsf.edu
Lani Wu, UCSF, lani.wu [at] ucsf.edu