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Items: 23


Mechanisms of Resistance to EGFR Inhibition Reveal Metabolic Vulnerabilities in Human GBM.

McKinney A, Lindberg OR, Engler JR, Chen KY, Kumar A, Gong H, Lu KV, Simonds EF, Cloughesy TF, Liau LM, Prados M, Bollen AW, Berger MS, Shieh JTC, James CD, Nicolaides TP, Yong WH, Lai A, Hegi ME, Weiss WA, Phillips JJ.

Mol Cancer Ther. 2019 Sep;18(9):1565-1576. doi: 10.1158/1535-7163.MCT-18-1330. Epub 2019 Jul 3.


Scalable Conjugation and Characterization of Immunoglobulins with Stable Mass Isotope Reporters for Single-Cell Mass Cytometry Analysis.

Hartmann FJ, Simonds EF, Vivanco N, Bruce T, Borges L, Nolan GP, Spitzer MH, Bendall SC.

Methods Mol Biol. 2019;1989:55-81. doi: 10.1007/978-1-4939-9454-0_5.


Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints.

Andor N, Simonds EF, Czerwinski DK, Chen J, Grimes SM, Wood-Bouwens C, Zheng GXY, Kubit MA, Greer S, Weiss WA, Levy R, Ji HP.

Blood. 2019 Mar 7;133(10):1119-1129. doi: 10.1182/blood-2018-08-862292. Epub 2018 Dec 27.


A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis.

Hartmann FJ, Simonds EF, Bendall SC.

Sci Rep. 2018 Jul 17;8(1):10770. doi: 10.1038/s41598-018-28791-2.


GateFinder: projection-based gating strategy optimization for flow and mass cytometry.

Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP.

Bioinformatics. 2018 Dec 1;34(23):4131-4133. doi: 10.1093/bioinformatics/bty430.


Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse.

Good Z, Sarno J, Jager A, Samusik N, Aghaeepour N, Simonds EF, White L, Lacayo NJ, Fantl WJ, Fazio G, Gaipa G, Biondi A, Tibshirani R, Bendall SC, Nolan GP, Davis KL.

Nat Med. 2018 May;24(4):474-483. doi: 10.1038/nm.4505. Epub 2018 Mar 5.


A Kinase Inhibitor Targeted to mTORC1 Drives Regression in Glioblastoma.

Fan Q, Aksoy O, Wong RA, Ilkhanizadeh S, Novotny CJ, Gustafson WC, Truong AY, Cayanan G, Simonds EF, Haas-Kogan D, Phillips JJ, Nicolaides T, Okaniwa M, Shokat KM, Weiss WA.

Cancer Cell. 2017 Mar 13;31(3):424-435. doi: 10.1016/j.ccell.2017.01.014.


Pediatric high-grade glioma: biologically and clinically in need of new thinking.

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 EF, Stafford JM, Tang Y, Pfister SM, Weiss WA.

Neuro Oncol. 2017 Feb 1;19(2):153-161. doi: 10.1093/neuonc/now101. Review.


Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.

Levine JH, Simonds EF, 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.

Cell. 2015 Jul 2;162(1):184-97. doi: 10.1016/j.cell.2015.05.047. Epub 2015 Jun 18.


Drugging MYCN through an allosteric transition in Aurora kinase A.

Gustafson WC, Meyerowitz JG, Nekritz EA, Chen J, Benes C, Charron E, Simonds EF, Seeger R, Matthay KK, Hertz NT, Eilers M, Shokat KM, Weiss WA.

Cancer Cell. 2014 Sep 8;26(3):414-427. doi: 10.1016/j.ccr.2014.07.015. Epub 2014 Aug 28.


Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.

Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D.

Cell. 2014 Apr 24;157(3):714-25. doi: 10.1016/j.cell.2014.04.005.


viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.

Amir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D.

Nat Biotechnol. 2013 Jun;31(6):545-52. doi: 10.1038/nbt.2594. Epub 2013 May 19.


Normalization of mass cytometry data with bead standards.

Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC.

Cytometry A. 2013 May;83(5):483-94. doi: 10.1002/cyto.a.22271. Epub 2013 Mar 19.


Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.

Bodenmiller B, Zunder ER, Finck R, Chen TJ, Savig ES, Bruggner RV, Simonds EF, Bendall SC, Sachs K, Krutzik PO, Nolan GP.

Nat Biotechnol. 2012 Sep;30(9):858-67.


CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.

Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP.

Bioinformatics. 2012 Sep 15;28(18):2400-1. doi: 10.1093/bioinformatics/bts425. Epub 2012 Jul 10.


A platinum-based covalent viability reagent for single-cell mass cytometry.

Fienberg HG, Simonds EF, Fantl WJ, Nolan GP, Bodenmiller B.

Cytometry A. 2012 Jun;81(6):467-75. doi: 10.1002/cyto.a.22067. Epub 2012 May 10.


Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.

Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK.

Nat Biotechnol. 2011 Oct 2;29(10):886-91. doi: 10.1038/nbt.1991.


Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.

Bendall SC, Simonds EF, 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.

Science. 2011 May 6;332(6030):687-96. doi: 10.1126/science.1198704.


Alternate mechanisms of initial pattern recognition drive differential immune responses to related poxviruses.

O'Gorman WE, Sampath P, Simonds EF, Sikorski R, O'Malley M, Krutzik PO, Chen H, Panchanathan V, Chaudhri G, Karupiah G, Lewis DB, Thorne SH, Nolan GP.

Cell Host Microbe. 2010 Aug 19;8(2):174-85. doi: 10.1016/j.chom.2010.07.008.


Novel mutations in the inhibitory adaptor protein LNK drive JAK-STAT signaling in patients with myeloproliferative neoplasms.

Oh ST, Simonds EF, Jones C, Hale MB, Goltsev Y, Gibbs KD Jr, Merker JD, Zehnder JL, Nolan GP, Gotlib J.

Blood. 2010 Aug 12;116(6):988-92. doi: 10.1182/blood-2010-02-270108. Epub 2010 Apr 19.


Speeding the flow toward personalized therapy in childhood acute leukemia.

Simonds EF, Davis KL, Lacayo NJ.

Pediatr Blood Cancer. 2009 Oct;53(4):525-6. doi: 10.1002/pbc.22180. No abstract available.


The initial phase of an immune response functions to activate regulatory T cells.

O'Gorman WE, Dooms H, Thorne SH, Kuswanto WF, Simonds EF, Krutzik PO, Nolan GP, Abbas AK.

J Immunol. 2009 Jul 1;183(1):332-9. doi: 10.4049/jimmunol.0900691.


Single-cell profiling identifies aberrant STAT5 activation in myeloid malignancies with specific clinical and biologic correlates.

Kotecha N, Flores NJ, Irish JM, Simonds EF, Sakai DS, Archambeault S, Diaz-Flores E, Coram M, Shannon KM, Nolan GP, Loh ML.

Cancer Cell. 2008 Oct 7;14(4):335-43. doi: 10.1016/j.ccr.2008.08.014.

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