​MR5 Room 2220
​Box 800759
Charlottesville, VA 22908
Google Scholar Zunder Lab


Eli Zunder analyzes stem cell fate using single cell mass cytometry and high-dimensional modeling of cell lineage trajectories. He received his Ph.D. in Biophysics from UCSF in 2009. There, he worked in Kevan Shokat’s lab studying the role of PI3K signaling in insulin responsecancer, and drug resistance.  Eli did his postdoc in Garry Nolan’s lab at Stanford University. There, he developed a cell barcoding method for mass cytometry that he used to study kinase inhibitor specificity across the human immune system, developed a graph-based mapping algorithm to track iPS cell reprogramming and identify early reprogramming intermediates, and applied these generalizable methods to map AML patient samples by prognosis and organism-level organization of the mouse immune system.

In January 2016, Eli began his independent career as an Assistant Professor in the Department of Biomedical Engineering at the University of Virginia.


​B.A. Dartmouth College, 2002

​Ph.D. University of California San Francisco, 2008

Research Interests

Biotechnology and Biomolecular Engineering Biomolecular Design, Cellular and Molecular Bioengineering
Computational Systems Biology

Selected Publications

Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nature Methods. 2016. Frei A.P.*, Bava F.A.*, Zunder E.R., Hsieh E.W., Chen S.Y., Nolan G.P., Gherardini P.F. *contributed equally
A dynamic immune system reference map: system-wide organization with functional correlates. Science. 2015. Spitzer M.H.*, Gherardini P.F.*, Fragiadakis G.K., Bhattacharya N., Yuan R.T., Hotson A.N., Finck R., Carmi Y., Zunder E.R, Fantl W.J., Bendall S.C., Engleman E.G., Nolan G.P. *contributed equally
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell. 2015. Levine JH*, Simonds EF*, Bendall SC*, Davis KL, Amir ED, Litvin O, Fienberg H, Jager A, Pinkus L, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe’er D, Nolan GP. *contributed equally
Early regulators of iPSC reprogramming identified by a novel set of transient intermediates. Nature. 2015. Kujan E*, Zunder ER*, Nolan GP, Wernig M. *contributed equally
A Continuous Molecular Roadmap to iPSC Reprogramming Through Progression Analysis of Single Cell Mass Cytometry. Cell Stem Cell. 2015. Zunder ER*, Lujan E*, Goltsev Y, Wernig M, and Nolan GP. *contributed equally
Palladium-based Mass-Tag Cell Barcoding with a Doublet-Filtering Scheme and Single Cell Deconvolution Algorithm. Nature Protocols. 2015. Zunder ER*, Finck R*, Behbehani GK, Amir ED, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe’er D, Nolan GP. *contributed equally
"Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining." Cytometry Part A. 2014. Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP.
"Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators." Nature Biotechnology. 2012. Bodenmiller B*, Zunder ER*, Finck R*, Chen TJ, Savig ES, Bruggner RV, Simonds EF, Bendall SC, Sachs K, Krutzik PO, Nolan GP. *contributed equally
"Dual blockade of lipid and cyclin-dependent kinases induces synthetic lethality in malignant glioma." Proceedings of the National Academy of Sciences, USA. 2012. Cheng CK, Gustafson WC, Charron E, Houseman BT, Zunder ER, Goga A, Gray NS, Pollok B, Oakes SA, James CD, Shokat KM, Weiss WA, Fan QW.
"Discovery of drug-resistant and drug-sensitizing mutations in the oncogenic PI3K isoform p110alpha." Cancer Cell. 2008. Zunder ER, Knight ZA, Houseman BT, Apsel B, Shokat KM.
"A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling." Cell. 2006 Knight ZA, Gonzalez B, Feldman ME, Zunder ER, Goldenberg DD, Williams O, Loewith R, Stokoe D, Balla A, Toth B, Balla T, Weiss WA, Williams RL, Shokat KM.

Courses Taught

BME 2104 Cell and Molecular Biology for Engineers
BME 6550 Stem Cell Engineering

Featured Grants & Projects

In Vitro Differentiation Research Research in our laboratory is focused on discovering the mechanisms that control stem cell fate. We study in vitro differentiation to gain insight into stem cell behavior during normal development and disease, and we study in vivo development to gain insight into the derivation of clinically relevant cell types for regenerative therapy. In order to study the complex mixtures of rapidly changing cell types that exist in these in vitro and in vivo systems, we are building experimental and computational tools that track cell populations as they change over time with molecular characterization at the single-cell level. Using these tools, our goal is to define the fundamental principles of cellular pluripotency and differentiation.