Eli Zunder


Primary Appointment

Assistant Professor, Biomedical Engineering


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

Research Disciplines

Biochemistry, Bioinformatics and Genomics, Biotechnology, Cancer Biology, Immunology, Neuroscience

Research Interests

Single Cell Analysis

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.


  • Basic Cardiovascular Research Training Grant
  • Biotechnology Training Grant
  • Interdisciplinary Training Program in Immunology
  • Predoctoral Training in Neuroscience

Selected Publications

Ko ME, Williams CM, Fread KI, Goggin SM, Rustagi RS, Fragiadakis GK, Nolan GP, Zunder ER, FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets., 2020; Nature protocols. 15(2) 398-420. PMID: 31932774

Balogh P, Adelman ER, Pluvinage JV, Capaldo BJ, Freeman KC, Singh S, Elagib KE, Nakamura Y, Kurita R, Sashida G, Zunder ER, Li H, Gru AA, Price EA, Schrier SL, Weissman IL, Figueroa ME, Pang WW, Goldfarb AN, RUNX3 levels in human hematopoietic progenitors are regulated by aging and dictate erythroid-myeloid balance., 2019; Haematologica. () . PMID: 31171641 | PMCID: PMC7109730

Lammert CR, Frost EL, Bolte AC, Paysour MJ, Shaw ME, Bellinger CE, Weigel TK, Zunder ER, Lukens JR, Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism., 2018; Journal of immunology (Baltimore, Md. : 1950). 201(3) 845-850. PMID: 29967099 | PMCID: PMC6057827

Han G, Chen SY, Gonzalez VD, Zunder ER, Fantl WJ, Nolan GP, Atomic mass tag of bismuth-209 for increasing the immunoassay multiplexing capacity of mass cytometry., 2017; Cytometry. Part A : the journal of the International Society for Analytical Cytology. 91(12) 1150-1163. PMID: 29205767 | PMCID: PMC5802970

Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF, Highly multiplexed simultaneous detection of RNAs and proteins in single cells., 2016; Nature methods. 13(3) 269-75. PMID: 26808670 | PMCID: PMC4767631

Fread KI, Strickland WD, Nolan GP, Zunder ER, AN UPDATED DEBARCODING TOOL FOR MASS CYTOMETRY WITH CELL TYPE-SPECIFIC AND CELL SAMPLE-SPECIFIC STRINGENCY ADJUSTMENT., 2016; Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 22() 588-598. PMID: 27897009

Levine JH, Simonds EF, Bendall SC, Davis KL, Amir el-, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP, Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis., 2015; Cell. 162(1) 184-97. PMID: 26095251 | PMCID: PMC4508757

Spitzer MH, Gherardini PF, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP, IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system., 2015; Science (New York, N.Y.). 349(6244) 1259425. PMID: 26160952 | PMCID: PMC4537647

Lujan E, Zunder ER, Ng YH, Goronzy IN, Nolan GP, Wernig M, Early reprogramming regulators identified by prospective isolation and mass cytometry., 2015; Nature. 521(7552) 352-6. PMID: 25830878 | PMCID: PMC4441548

Zunder ER, Lujan E, Goltsev Y, Wernig M, Nolan GP, A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry., 2015; Cell stem cell. 16(3) 323-37. PMID: 25748935 | PMCID: PMC4401090

Zunder ER, Finck R, Behbehani GK, Amir el-, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe'er D, Nolan GP, Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm., 2015; Nature protocols. 10(2) 316-33. PMID: 25612231 | PMCID: PMC4347881

Behbehani GK, Thom C, Zunder ER, Finck R, Gaudilliere B, Fragiadakis GK, Fantl WJ, Nolan GP, Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining., 2014; Cytometry. Part A : the journal of the International Society for Analytical Cytology. 85(12) 1011-9. PMID: 25274027 | PMCID: PMC4361015

Bodenmiller B, Zunder ER, Finck R, Chen TJ, Savig ES, Bruggner RV, Simonds EF, Bendall SC, Sachs K, Krutzik PO, Nolan GP, Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators., 2012; Nature biotechnology. 30(9) 858-67. PMID: 22902532 | PMCID: PMC3627543

Cheng CK, Gustafson WC, Charron E, Houseman BT, Zunder E, Goga A, Gray NS, Pollok B, Oakes SA, James CD, Shokat KM, Weiss WA, Fan QW, Dual blockade of lipid and cyclin-dependent kinases induces synthetic lethality in malignant glioma., 2012; Proceedings of the National Academy of Sciences of the United States of America. 109(31) 12722-7. PMID: 22802621 | PMCID: PMC3411950

Zunder ER, Knight ZA, Houseman BT, Apsel B, Shokat KM, Discovery of drug-resistant and drug-sensitizing mutations in the oncogenic PI3K isoform p110 alpha., 2008; Cancer cell. 14(2) 180-92. PMID: 18691552 | PMCID: PMC2720137

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, A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling., 2006; Cell. 125(4) 733-47. PMID: 16647110 | PMCID: PMC2946820