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Items: 1 to 50 of 58

1.

Immune monitoring using mass cytometry and related high-dimensional imaging approaches.

Hartmann FJ, Bendall SC.

Nat Rev Rheumatol. 2020 Feb;16(2):87-99. doi: 10.1038/s41584-019-0338-z. Epub 2019 Dec 31. Review.

PMID:
31892734
2.

Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution.

Karacosta LG, Anchang B, Ignatiadis N, Kimmey SC, Benson JA, Shrager JB, Tibshirani R, Bendall SC, Plevritis SK.

Nat Commun. 2019 Dec 6;10(1):5587. doi: 10.1038/s41467-019-13441-6.

3.

TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis.

Baskar R, Fienberg HG, Khair Z, Favaro P, Kimmey S, Green DR, Nolan GP, Plevritis S, Bendall SC.

Life Sci Alliance. 2019 Nov 8;2(6). pii: e201900554. doi: 10.26508/lsa.201900554. Print 2019 Dec.

4.

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure.

Keren L, Bosse M, Thompson S, Risom T, Vijayaragavan K, McCaffrey E, Marquez D, Angoshtari R, Greenwald NF, Fienberg H, Wang J, Kambham N, Kirkwood D, Nolan G, Montine TJ, Galli SJ, West R, Bendall SC, Angelo M.

Sci Adv. 2019 Oct 9;5(10):eaax5851. doi: 10.1126/sciadv.aax5851. eCollection 2019 Oct.

5.

High-Parameter Immune Profiling with CyTOF.

Sahaf B, Rahman A, Maecker HT, Bendall SC.

Methods Mol Biol. 2020;2055:351-368. doi: 10.1007/978-1-4939-9773-2_16.

PMID:
31502160
6.

The basis of cellular and regional vulnerability in Alzheimer's disease.

Mrdjen D, Fox EJ, Bukhari SA, Montine KS, Bendall SC, Montine TJ.

Acta Neuropathol. 2019 Nov;138(5):729-749. doi: 10.1007/s00401-019-02054-4. Epub 2019 Aug 7. Review.

PMID:
31392412
7.

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy.

Hartmann FJ, Babdor J, Gherardini PF, Amir ED, Jones K, Sahaf B, Marquez DM, Krutzik P, O'Donnell E, Sigal N, Maecker HT, Meyer E, Spitzer MH, Bendall SC.

Cell Rep. 2019 Jul 16;28(3):819-831.e4. doi: 10.1016/j.celrep.2019.06.049.

8.

Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function.

Yucel N, Wang YX, Mai T, Porpiglia E, Lund PJ, Markov G, Garcia BA, Bendall SC, Angelo M, Blau HM.

Cell Rep. 2019 Jun 25;27(13):3939-3955.e6. doi: 10.1016/j.celrep.2019.05.092.

9.

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.

10.

Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells.

Kimmey SC, Borges L, Baskar R, Bendall SC.

Nat Commun. 2019 Mar 12;10(1):1185. doi: 10.1038/s41467-019-09128-7.

11.

Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells.

Good Z, Borges L, Vivanco Gonzalez N, Sahaf B, Samusik N, Tibshirani R, Nolan GP, Bendall SC.

Nat Biotechnol. 2019 Mar;37(3):259-266. doi: 10.1038/s41587-019-0033-2. Epub 2019 Feb 11.

12.

A topological view of human CD34+ cell state trajectories from integrated single-cell output and proteomic data.

Knapp DJHF, Hammond CA, Wang F, Aghaeepour N, Miller PH, Beer PA, Pellacani D, VanInsberghe M, Hansen C, Bendall SC, Nolan GP, Eaves CJ.

Blood. 2019 Feb 28;133(9):927-939. doi: 10.1182/blood-2018-10-878025. Epub 2019 Jan 8.

13.

Serial transplantation reveals a critical role for endoglin in hematopoietic stem cell quiescence.

Borges L, Oliveira VKP, Baik J, Bendall SC, Perlingeiro RCR.

Blood. 2019 Feb 14;133(7):688-696. doi: 10.1182/blood-2018-09-874677. Epub 2018 Dec 28.

14.

Mass synaptometry: High-dimensional multi parametric assay for single synapses.

Gajera CR, Fernandez R, Postupna N, Montine KS, Fox EJ, Tebaykin D, Angelo M, Bendall SC, Keene CD, Montine TJ.

J Neurosci Methods. 2019 Jan 15;312:73-83. doi: 10.1016/j.jneumeth.2018.11.008. Epub 2018 Nov 20.

15.

Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry.

Han G, Spitzer MH, Bendall SC, Fantl WJ, Nolan GP.

Nat Protoc. 2018 Oct;13(10):2121-2148. doi: 10.1038/s41596-018-0016-7.

PMID:
30258176
16.

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging.

Keren L, Bosse M, Marquez D, Angoshtari R, Jain S, Varma S, Yang SR, Kurian A, Van Valen D, West R, Bendall SC, Angelo M.

Cell. 2018 Sep 6;174(6):1373-1387.e19. doi: 10.1016/j.cell.2018.08.039.

17.

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.

18.

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.

19.

DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity.

Anchang B, Davis KL, Fienberg HG, Williamson BD, Bendall SC, Karacosta LG, Tibshirani R, Nolan GP, Plevritis SK.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):E4294-E4303. doi: 10.1073/pnas.1711365115. Epub 2018 Apr 13.

20.

Publisher Correction: High-resolution myogenic lineage mapping by single-cell mass cytometry.

Porpiglia E, Samusik N, Ho ATV, Cosgrove BD, Mai T, Davis KL, Jager A, Nolan GP, Bendall SC, Fantl WJ, Blau HM.

Nat Cell Biol. 2018 Aug;20(8):990. doi: 10.1038/s41556-018-0043-1.

PMID:
29507406
21.

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.

22.

High-resolution myogenic lineage mapping by single-cell mass cytometry.

Porpiglia E, Samusik N, Ho ATV, Cosgrove BD, Mai T, Davis KL, Jager A, Nolan GP, Bendall SC, Fantl WJ, Blau HM.

Nat Cell Biol. 2017 May;19(5):558-567. doi: 10.1038/ncb3507. Epub 2017 Apr 17. Erratum in: Nat Cell Biol. 2018 Mar 5;:.

23.

Systemic Immunity Is Required for Effective Cancer Immunotherapy.

Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG.

Cell. 2017 Jan 26;168(3):487-502.e15. doi: 10.1016/j.cell.2016.12.022. Epub 2017 Jan 19.

24.

Distinct signaling programs control human hematopoietic stem cell survival and proliferation.

Knapp DJ, Hammond CA, Aghaeepour N, Miller PH, Pellacani D, Beer PA, Sachs K, Qiao W, Wang W, Humphries RK, Sauvageau G, Zandstra PW, Bendall SC, Nolan GP, Hansen C, Eaves CJ.

Blood. 2017 Jan 19;129(3):307-318. doi: 10.1182/blood-2016-09-740654. Epub 2016 Nov 8.

25.

Assessing basophil activation by using flow cytometry and mass cytometry in blood stored 24 hours before analysis.

Mukai K, Gaudenzio N, Gupta S, Vivanco N, Bendall SC, Maecker HT, Chinthrajah RS, Tsai M, Nadeau KC, Galli SJ.

J Allergy Clin Immunol. 2017 Mar;139(3):889-899.e11. doi: 10.1016/j.jaci.2016.04.060. Epub 2016 Jul 15.

26.

Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2.

Inoue S, Li WY, Tseng A, Beerman I, Elia AJ, Bendall SC, Lemonnier F, Kron KJ, Cescon DW, Hao Z, Lind EF, Takayama N, Planello AC, Shen SY, Shih AH, Larsen DM, Li Q, Snow BE, Wakeham A, Haight J, Gorrini C, Bassi C, Thu KL, Murakami K, Elford AR, Ueda T, Straley K, Yen KE, Melino G, Cimmino L, Aifantis I, Levine RL, De Carvalho DD, Lupien M, Rossi DJ, Nolan GP, Cairns RA, Mak TW.

Cancer Cell. 2016 Aug 8;30(2):337-348. doi: 10.1016/j.ccell.2016.05.018. Epub 2016 Jul 14.

27.

Visualization and cellular hierarchy inference of single-cell data using SPADE.

Anchang B, Hart TD, Bendall SC, Qiu P, Bjornson Z, Linderman M, Nolan GP, Plevritis SK.

Nat Protoc. 2016 Jul;11(7):1264-79. doi: 10.1038/nprot.2016.066. Epub 2016 Jun 16.

PMID:
27310265
28.

IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system.

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.

Science. 2015 Jul 10;349(6244):1259425. doi: 10.1126/science.1259425.

29.

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.

30.

Synthetically Modified Viral Capsids as Versatile Carriers for Use in Antibody-Based Cell Targeting.

ElSohly AM, Netirojjanakul C, Aanei IL, Jager A, Bendall SC, Farkas ME, Nolan GP, Francis MB.

Bioconjug Chem. 2015 Aug 19;26(8):1590-6. doi: 10.1021/acs.bioconjchem.5b00226. Epub 2015 Jul 6.

31.

Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus.

O'Gorman WE, Hsieh EW, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM.

J Allergy Clin Immunol. 2015 Nov;136(5):1326-36. doi: 10.1016/j.jaci.2015.04.008. Epub 2015 May 30.

32.

Single-cell mass cytometry of TCR signaling: amplification of small initial differences results in low ERK activation in NOD mice.

Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16466-71. doi: 10.1073/pnas.1419337111. Epub 2014 Oct 31.

33.

Systems biology. Conditional density-based analysis of T cell signaling in single-cell data.

Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP.

Science. 2014 Nov 28;346(6213):1250689. doi: 10.1126/science.1250689. Epub 2014 Oct 23.

34.

NRASG12V oncogene facilitates self-renewal in a murine model of acute myelogenous leukemia.

Sachs Z, LaRue RS, Nguyen HT, Sachs K, Noble KE, Mohd Hassan NA, Diaz-Flores E, Rathe SK, Sarver AL, Bendall SC, Ha NA, Diers MD, Nolan GP, Shannon KM, Largaespada DA.

Blood. 2014 Nov 20;124(22):3274-83. doi: 10.1182/blood-2013-08-521708. Epub 2014 Oct 14.

35.

Clinical recovery from surgery correlates with single-cell immune signatures.

Gaudillière B, Fragiadakis GK, Bruggner RV, Nicolau M, Finck R, Tingle M, Silva J, Ganio EA, Yeh CG, Maloney WJ, Huddleston JI, Goodman SB, Davis MM, Bendall SC, Fantl WJ, Angst MS, Nolan GP.

Sci Transl Med. 2014 Sep 24;6(255):255ra131. doi: 10.1126/scitranslmed.3009701.

36.

The Split Virus Influenza Vaccine rapidly activates immune cells through Fcγ receptors.

O'Gorman WE, Huang H, Wei YL, Davis KL, Leipold MD, Bendall SC, Kidd BA, Dekker CL, Maecker HT, Chien YH, Davis MM.

Vaccine. 2014 Oct 14;32(45):5989-97. doi: 10.1016/j.vaccine.2014.07.115. Epub 2014 Sep 6.

37.

Single-cell mass cytometry analysis of human tonsil T cell remodeling by varicella zoster virus.

Sen N, Mukherjee G, Sen A, Bendall SC, Sung P, Nolan GP, Arvin AM.

Cell Rep. 2014 Jul 24;8(2):633-45. doi: 10.1016/j.celrep.2014.06.024. Epub 2014 Jul 17.

38.

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.

39.

Multiplexed ion beam imaging of human breast tumors.

Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, Levenson RM, Lowe JB, Liu SD, Zhao S, Natkunam Y, Nolan GP.

Nat Med. 2014 Apr;20(4):436-42. doi: 10.1038/nm.3488. Epub 2014 Mar 2.

40.

Antigen-dependent integration of opposing proximal TCR-signaling cascades determines the functional fate of T lymphocytes.

Wolchinsky R, Hod-Marco M, Oved K, Shen-Orr SS, Bendall SC, Nolan GP, Reiter Y.

J Immunol. 2014 Mar 1;192(5):2109-19. doi: 10.4049/jimmunol.1301142. Epub 2014 Jan 31.

41.

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.

42.

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.

43.

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.

44.

From single cells to deep phenotypes in cancer.

Bendall SC, Nolan GP.

Nat Biotechnol. 2012 Jul 10;30(7):639-47. doi: 10.1038/nbt.2283. Review.

PMID:
22781693
45.

Single-cell mass cytometry adapted to measurements of the cell cycle.

Behbehani GK, Bendall SC, Clutter MR, Fantl WJ, Nolan GP.

Cytometry A. 2012 Jul;81(7):552-66. doi: 10.1002/cyto.a.22075. Epub 2012 Jun 12.

46.

A deep profiler's guide to cytometry.

Bendall SC, Nolan GP, Roederer M, Chattopadhyay PK.

Trends Immunol. 2012 Jul;33(7):323-32. doi: 10.1016/j.it.2012.02.010. Epub 2012 Apr 2. Review.

47.

Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes.

Newell EW, Sigal N, Bendall SC, Nolan GP, Davis MM.

Immunity. 2012 Jan 27;36(1):142-52. doi: 10.1016/j.immuni.2012.01.002. Erratum in: Immunity. 2013 Jan 24;38(1):198-9.

48.

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.

49.

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.

50.

Clonal tracking of hESCs reveals differential contribution to functional assays.

Stewart MH, Bendall SC, Levadoux-Martin M, Bhatia M.

Nat Methods. 2010 Nov;7(11):917-22. doi: 10.1038/nmeth.1519. Epub 2010 Oct 17.

PMID:
20953174

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