Eli Zunder


  • PhD, University of California, San Francisco
  • BA, Dartmouth College

Primary Appointment

  • Assistant Professor, Biomedical Engineering


Research Interest(s)

Stem Cell Behavior

Research Description

Research in our laboratory is focused on discovering the mechanisms that control stem cell fate. Specifically, we seek to identify factors that control the progression and branch points of cellular differentiation. To accomplish this, we are building experimental and computational tools that track cell populations as they change over time, using molecular characterization at the single-cell level. Our goal is to define the fundamental principles of stem cell differentiation, and apply this knowledge to the development of regenerative transplantation therapies.

Selected Publications

  • Levine J, Simonds E, Bendall S, Davis K, Amir e, Tadmor M, Litvin O, Fienberg H, Jager A, Zunder E, Finck R, Gedman A, Radtke I, Downing J, Pe'er D, Nolan G. Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell. 2015;162(1): 184-97. PMID: 26095251 | PMCID: PMC4508757
  • Lujan E, Zunder E, Ng Y, Goronzy I, Nolan G, Wernig M. Early reprogramming regulators identified by prospective isolation and mass cytometry. Nature. 2015;521(7552): 352-6. PMID: 25830878 | PMCID: PMC4441548
  • Spitzer M, Gherardini P, Fragiadakis G, Bhattacharya N, Yuan R, Hotson A, Finck R, Carmi Y, Zunder E, Fantl W, Bendall S, Engleman E, Nolan G. IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science (New York, N.Y.). 2015;349(6244): 1259425. PMID: 26160952 | PMCID: PMC4537647
  • Zunder E, Finck R, Behbehani G, Amir e, Krishnaswamy S, Gonzalez V, Lorang C, Bjornson Z, Spitzer M, Bodenmiller B, Fantl W, Pe'er D, Nolan G. Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nature protocols. 2015;10(2): 316-33. PMID: 25612231 | PMCID: PMC4347881
  • Zunder E, Lujan E, Goltsev Y, Wernig M, Nolan G. A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. Cell stem cell. 2015;16(3): 323-37. PMID: 25748935 | PMCID: PMC4401090
  • Behbehani G, Thom C, Zunder E, Finck R, Gaudilliere B, Fragiadakis G, Fantl W, Nolan G. Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2014;85(12): 1011-9. PMID: 25274027 | PMCID: PMC4361015
  • Bodenmiller B, Zunder E, Finck R, Chen T, Savig E, Bruggner R, Simonds E, Bendall S, Sachs K, Krutzik P, Nolan G. Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nature biotechnology. 2012;30(9): 858-67. PMID: 22902532 | PMCID: PMC3627543
  • Zunder E, Knight Z, Houseman B, Apsel B, Shokat K. Discovery of drug-resistant and drug-sensitizing mutations in the oncogenic PI3K isoform p110 alpha. Cancer cell. 2008;14(2): 180-92. PMID: 18691552 | PMCID: PMC2720137
  • Knight Z, Gonzalez B, Feldman M, Zunder E, Goldenberg D, Williams O, Loewith R, Stokoe D, Balla A, Toth B, Balla T, Weiss W, Williams R, Shokat K. A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling. Cell. 2006;125(4): 733-47. PMID: 16647110 | PMCID: PMC2946820