Erin Simonds, PhD

TitleAssistant Professor
InstitutionUniversity of California San Francisco
Address1450 Third St
San Francisco CA 94158
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    Collapse Biography 
    Collapse Awards and Honors
    Damon Runyon Cancer Research Foundation2014  - 2018Damon Runyon Postdoctoral Fellowship
    Alex's Lemonade Stand Foundation2013  - 2015Young Investigator Award
    Stanford University Dept. of Microbiology & Immunology2012  - 2012Sidney Raffel Award for Outstanding PhD Dissertation

    Collapse Overview 
    Collapse Overview
    Coming from an immunology background, I have a longstanding interest in cellular phenotypic heterogeneity and the relationship between different cell fates and their underlying signaling biology. Now, as a cancer biologist, I am applying single-cell analysis techniques to understand how phenotypic heterogeneity contributes to cancer growth and resistance to therapy.

    As a PhD student, I helped develop single-cell assays to study signaling in the healthy immune system (Science 2011), and in childhood leukemias (Cell 2015). As a postdoc, I am applying these same approaches to investigate phenotypic plasticity and immune infiltration in glioblastoma, the most common and lethal brain tumor.

    Many of my projects are enabled by a next-generation flow cytometry platform (CyTOF mass cytometry), which can measure up to 42 protein expression and intracellular signaling markers at the single-cell level in millions of cancer cells. This platform provides detailed biochemical profiles of rare and complex samples, uncovering subpopulations that would have been overlooked by classical bulk protein and genetic assays.

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Aghaeepour N, Simonds E, Knapp DJHF, Bruggner R, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis G, Bendall S, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl W, Nolan G. GateFinder: Projection-based Gating Strategy Optimization for Flow and Mass Cytometry. Bioinformatics. 2018 May 29. PMID: 29850785.
      View in: PubMed
    2. Good Z, Sarno J, Jager A, Samusik N, Aghaeepour N, Simonds E, White L, Lacayo NJ, Fantl WJ, Fazio G, Gaipa G, Biondi A, Tibshirani R, Bendall SC, Nolan GP, Davis KL. Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nat Med. 2018 May; 24(4):474-483. PMID: 29505032.
      View in: PubMed
    3. Fan Q, Aksoy O, Wong RA, Ilkhanizadeh S, Novotny CJ, Gustafson WC, Truong AY, Cayanan G, Simonds E, Haas-Kogan D, Phillips JJ, Nicolaides T, Okaniwa M, Shokat KM, Weiss WA. A Kinase Inhibitor Targeted to mTORC1 Drives Regression in Glioblastoma. Cancer Cell. 2017 03 13; 31(3):424-435. PMID: 28292440.
      View in: PubMed
    4. Jones C, Karajannis MA, Jones DTW, Kieran MW, Monje M, Baker SJ, Becher OJ, Cho YJ, Gupta N, Hawkins C, Hargrave D, Haas-Kogan DA, Jabado N, Li XN, Mueller S, Nicolaides T, Packer RJ, Persson AI, Phillips JJ, Simonds E, Stafford JM, Tang Y, Pfister SM, Weiss WA. Pediatric high-grade glioma: biologically and clinically in need of new thinking. Neuro Oncol. 2017 02 01; 19(2):153-161. PMID: 27282398.
      View in: PubMed
    5. Transforming Big Data into Cancer-Relevant Insight: An Initial, Multi-Tier Approach to Assess Reproducibility and Relevance. Mol Cancer Res. 2016 08; 14(8):675-82. PMID: 27401613; PMCID: PMC4987219 [Available on 08/01/17].
    6. Levine JH, Simonds E, Bendall SC, Davis KL, Amir el-AD, 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. Cell. 2015 Jul 02; 162(1):184-97. PMID: 26095251; PMCID: PMC4508757.
    7. Gustafson WC, Meyerowitz JG, Nekritz EA, Chen J, Benes C, Charron E, Simonds E, Seeger R, Matthay KK, Hertz NT, Eilers M, Shokat KM, Weiss WA. Drugging MYCN through an allosteric transition in Aurora kinase A. Cancer Cell. 2014 Sep 08; 26(3):414-427. PMID: 25175806; PMCID: PMC4160413.
    8. Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds E, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 2014 Apr 24; 157(3):714-25. PMID: 24766814; PMCID: PMC4045247.
    9. Amir el-AD, Davis KL, Tadmor MD, Simonds E, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat Biotechnol. 2013 Jun; 31(6):545-52. PMID: 23685480.
      View in: PubMed
    10. Finck R, Simonds E, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC. Normalization of mass cytometry data with bead standards. Cytometry A. 2013 May; 83(5):483-94. PMID: 23512433; PMCID: PMC3688049.
    11. Bodenmiller B, Zunder ER, Finck R, Chen TJ, Savig ES, Bruggner RV, Simonds E, Bendall SC, Sachs K, Krutzik PO, Nolan GP. Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nat Biotechnol. 2012 Sep; 30(9):858-67. PMID: 22902532; PMCID: PMC3627543.
    12. Linderman MD, Bjornson Z, Simonds E, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP. CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data. Bioinformatics. 2012 Sep 15; 28(18):2400-1. PMID: 22782546; PMCID: PMC3436846.
    13. Fienberg HG, Simonds E, Fantl WJ, Nolan GP, Bodenmiller B. A platinum-based covalent viability reagent for single-cell mass cytometry. Cytometry A. 2012 Jun; 81(6):467-75. PMID: 22577098; PMCID: PMC3808967.
    14. Qiu P, Simonds E, Bendall SC, Gibbs KD, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol. 2011 Oct 02; 29(10):886-91. PMID: 21964415; PMCID: PMC3196363.
    15. Bendall SC, Simonds E, Qiu P, Amir el-AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011 May 06; 332(6030):687-96. PMID: 21551058; PMCID: PMC3273988.
    16. O'Gorman WE, Sampath P, Simonds E, Sikorski R, O'Malley M, Krutzik PO, Chen H, Panchanathan V, Chaudhri G, Karupiah G, Lewis DB, Thorne SH, Nolan GP. Alternate mechanisms of initial pattern recognition drive differential immune responses to related poxviruses. Cell Host Microbe. 2010 Aug 19; 8(2):174-85. PMID: 20709294; PMCID: PMC2940993.
    17. Oh ST, Simonds E, Jones C, Hale MB, Goltsev Y, Gibbs KD, Merker JD, Zehnder JL, Nolan GP, Gotlib J. Novel mutations in the inhibitory adaptor protein LNK drive JAK-STAT signaling in patients with myeloproliferative neoplasms. Blood. 2010 Aug 12; 116(6):988-92. PMID: 20404132; PMCID: PMC2924231.
    18. Simonds E, Davis KL, Lacayo NJ. Speeding the flow toward personalized therapy in childhood acute leukemia. Pediatr Blood Cancer. 2009 Oct; 53(4):525-6. PMID: 19642213.
      View in: PubMed
    19. O'Gorman WE, Dooms H, Thorne SH, Kuswanto WF, Simonds E, Krutzik PO, Nolan GP, Abbas AK. The initial phase of an immune response functions to activate regulatory T cells. J Immunol. 2009 Jul 01; 183(1):332-9. PMID: 19542444; PMCID: PMC2753472.
    20. Kotecha N, Flores NJ, Irish JM, Simonds E, Sakai DS, Archambeault S, Diaz-Flores E, Coram M, Shannon KM, Nolan GP, Loh ML. Single-cell profiling identifies aberrant STAT5 activation in myeloid malignancies with specific clinical and biologic correlates. Cancer Cell. 2008 Oct 07; 14(4):335-43. PMID: 18835035; PMCID: PMC2647559.