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Volumn 17, Issue 3-4, 2017, Pages

Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis

Author keywords

Information theoretical approaches; Mass cytometry; Single cell barcode chip; Single cell data analysis; Single cell proteomics

Indexed keywords

ANALYTIC METHOD; BIOLOGY; BIOMEDICINE; INFORMATION PROCESSING; LIMIT OF QUANTITATION; PHYSICS; POPULATION STRUCTURE; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEOMICS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; SINGLE CELL ANALYSIS; STATISTICAL ANALYSIS; ALGORITHM; ANIMAL; BIOPHYSICS; HUMAN; IMAGE PROCESSING; PROCEDURES; STATISTICS AND NUMERICAL DATA;

EID: 85012906748     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201600267     Document Type: Review
Times cited : (80)

References (98)
  • 1
    • 77952474987 scopus 로고    scopus 로고
    • Cellular heterogeneity: do differences make a difference?
    • Altschuler, S. J., Wu, L. F., Cellular heterogeneity: do differences make a difference? Cell 2010, 141, 559–563.
    • (2010) Cell , vol.141 , pp. 559-563
    • Altschuler, S.J.1    Wu, L.F.2
  • 2
    • 84959369430 scopus 로고    scopus 로고
    • Single-cell analysis tools for drug discovery and development
    • Heath, J. R., Ribas, A., Mischel, P. S., Single-cell analysis tools for drug discovery and development. Nat. Rev. Drug Discov. 2016, 15, 204–216.
    • (2016) Nat. Rev. Drug Discov. , vol.15 , pp. 204-216
    • Heath, J.R.1    Ribas, A.2    Mischel, P.S.3
  • 3
    • 84881397508 scopus 로고    scopus 로고
    • Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research
    • Wei, W., Shin, Y. S., Ma, C., Wang, J. et al., Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research. Genome Med. 2013, 5, 75.
    • (2013) Genome Med. , vol.5 , pp. 75
    • Wei, W.1    Shin, Y.S.2    Ma, C.3    Wang, J.4
  • 4
    • 84948392415 scopus 로고    scopus 로고
    • Nanotechnologies for biomedical science and translational medicine
    • Heath, J. R., Nanotechnologies for biomedical science and translational medicine. Proc. Natl. Acad. Sci. USA 2015, 112, 14436–14443.
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , pp. 14436-14443
    • Heath, J.R.1
  • 5
    • 84904355142 scopus 로고    scopus 로고
    • Microfluidics-based single-cell functional proteomics for fundamental and applied biomedical applications
    • Yu, J., Zhou, J., Sutherland, A., Wei, W. et al., Microfluidics-based single-cell functional proteomics for fundamental and applied biomedical applications. Annu. Rev. Anal. Chem. 2014, 7, 275–295.
    • (2014) Annu. Rev. Anal. Chem. , vol.7 , pp. 275-295
    • Yu, J.1    Zhou, J.2    Sutherland, A.3    Wei, W.4
  • 6
    • 84965146271 scopus 로고    scopus 로고
    • single cells, many features
    • Spitzer, M. H., Nolan, G. P., Mass cytometry: single cells, many features. Cell 2016, 165, 780–791.
    • (2016) Cell , vol.165 , pp. 780-791
    • Spitzer, M.H.1    Nolan, G.P.2    cytometry, M.3
  • 7
    • 84984972943 scopus 로고    scopus 로고
    • Emerging single-cell technologies for functional proteomics in oncology
    • Wang, J., Yang, F., Emerging single-cell technologies for functional proteomics in oncology. Expert. Rev. Proteomics 2016, 13, 805–815.
    • (2016) Expert. Rev. Proteomics , vol.13 , pp. 805-815
    • Wang, J.1    Yang, F.2
  • 8
    • 84966711505 scopus 로고    scopus 로고
    • Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots
    • Marr, C., Zhou, J. X., Huang, S., Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots. Curr. Opin. Biotechnol. 2016, 39, 207–214.
    • (2016) Curr. Opin. Biotechnol. , vol.39 , pp. 207-214
    • Marr, C.1    Zhou, J.X.2    Huang, S.3
  • 9
    • 0021020342 scopus 로고
    • A solid-phase enzyme-linked immunospot (ELISPOT) assay for enumeration of specific antibody-secreting cells
    • Czerkinsky, C. C., Nilsson, L. A., Nygren, H., Ouchterlony, O., Tarkowski, A., A solid-phase enzyme-linked immunospot (ELISPOT) assay for enumeration of specific antibody-secreting cells. J. Immunol. Methods 1983, 65, 109–121.
    • (1983) J. Immunol. Methods , vol.65 , pp. 109-121
    • Czerkinsky, C.C.1    Nilsson, L.A.2    Nygren, H.3    Ouchterlony, O.4    Tarkowski, A.5
  • 10
    • 0036792398 scopus 로고    scopus 로고
    • The history and future of the fluorescence activated cell sorter and flow cytometry: a view from Stanford
    • Herzenberg, L. A., Parks, D., Sahaf, B., Perez, O. et al., The history and future of the fluorescence activated cell sorter and flow cytometry: a view from Stanford. Clin. Chem. 2002, 48, 1819–1827.
    • (2002) Clin. Chem. , vol.48 , pp. 1819-1827
    • Herzenberg, L.A.1    Parks, D.2    Sahaf, B.3    Perez, O.4
  • 11
    • 0035126095 scopus 로고    scopus 로고
    • 11-color, 13-parameter flow cytometry: identification of human naive T cells by phenotype, function, and T-cell receptor diversity
    • De Rosa, S. C., Herzenberg, L. A., Herzenberg, L. A., Roederer, M., 11-color, 13-parameter flow cytometry: identification of human naive T cells by phenotype, function, and T-cell receptor diversity. Nat. Med. 2001, 7, 245–248.
    • (2001) Nat. Med. , vol.7 , pp. 245-248
    • De Rosa, S.C.1    Herzenberg, L.A.2    Herzenberg, L.A.3    Roederer, M.4
  • 12
    • 3543069879 scopus 로고    scopus 로고
    • Seventeen-colour flow cytometry: unravelling the immune system
    • Perfetto, S. P., Chattopadhyay, P. K., Roederer, M., Seventeen-colour flow cytometry: unravelling the immune system. Nat. Rev. Immunol. 2004, 4, 648–655.
    • (2004) Nat. Rev. Immunol. , vol.4 , pp. 648-655
    • Perfetto, S.P.1    Chattopadhyay, P.K.2    Roederer, M.3
  • 13
    • 0036173143 scopus 로고    scopus 로고
    • Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry
    • Perez, O. D., Nolan, G. P., Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nat. Biotechnol. 2002, 20, 155–162.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 155-162
    • Perez, O.D.1    Nolan, G.P.2
  • 14
    • 79955750055 scopus 로고    scopus 로고
    • Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
    • Bendall, S. C., Simonds, E. F., Qiu, P., Amir, E. A. D. et al., Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011, 332, 687–696.
    • (2011) Science , vol.332 , pp. 687-696
    • Bendall, S.C.1    Simonds, E.F.2    Qiu, P.3    Amir, E.A.D.4
  • 15
    • 33947184356 scopus 로고    scopus 로고
    • Quantitative detection of protein expression in single cells using droplet microfluidics
    • Huebner, A., Srisa-Art, M., Holt, D., Abell, C. et al., Quantitative detection of protein expression in single cells using droplet microfluidics. Chem. Commun. 2007, 43, 1218–1220.
    • (2007) Chem. Commun. , vol.43 , pp. 1218-1220
    • Huebner, A.1    Srisa-Art, M.2    Holt, D.3    Abell, C.4
  • 16
    • 84877057770 scopus 로고    scopus 로고
    • Single-cell analysis and sorting using droplet-based microfluidics
    • Mazutis, L., Gilbert, J., Ung, W. L., Weitz, D. A. et al., Single-cell analysis and sorting using droplet-based microfluidics. Nat. Protocols 2013, 8, 870–891.
    • (2013) Nat. Protocols , vol.8 , pp. 870-891
    • Mazutis, L.1    Gilbert, J.2    Ung, W.L.3    Weitz, D.A.4
  • 17
    • 84925359358 scopus 로고    scopus 로고
    • Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments
    • Tricot, S., Meyrand, M., Sammicheli, C., Elhmouzi-Younes, J. et al., Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments. Cytom Part A 2015, 87a, 357–368.
    • (2015) Cytom Part A , vol.87a , pp. 357-368
    • Tricot, S.1    Meyrand, M.2    Sammicheli, C.3    Elhmouzi-Younes, J.4
  • 18
    • 84876799270 scopus 로고    scopus 로고
    • Normalization of mass cytometry data with bead standards
    • Finck, R., Simonds, E. F., Jager, A., Krishnaswamy, S. et al., Normalization of mass cytometry data with bead standards. Cytom Part A 2013, 83a, 483–494.
    • (2013) Cytom Part A , vol.83a , pp. 483-494
    • Finck, R.1    Simonds, E.F.2    Jager, A.3    Krishnaswamy, S.4
  • 19
    • 84875902633 scopus 로고    scopus 로고
    • Quantum dot imaging platform for single-cell molecular profiling
    • Zrazhevskiy, P., Gao, X. H., Quantum dot imaging platform for single-cell molecular profiling. Nat. Commun. 2013, 4, 1619.
    • (2013) Nat. Commun. , vol.4 , pp. 1619
    • Zrazhevskiy, P.1    Gao, X.H.2
  • 20
    • 84869455584 scopus 로고    scopus 로고
    • Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells
    • Agasti, S. S., Liong, M., Peterson, V. M., Lee, H., Weissleder, R., Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells. J. Am. Chem. Soc. 2012, 134, 18499–18502.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 18499-18502
    • Agasti, S.S.1    Liong, M.2    Peterson, V.M.3    Lee, H.4    Weissleder, R.5
  • 21
    • 84893421205 scopus 로고    scopus 로고
    • Cancer cell profiling by barcoding allows multiplexed protein analysis in fine-needle aspirates
    • Ullal, A. V., Peterson, V., Agasti, S. S., Tuang, S. et al., Cancer cell profiling by barcoding allows multiplexed protein analysis in fine-needle aspirates. Sci. Transl. Med. 2014, 6, 219ra9.
    • (2014) Sci. Transl. Med. , vol.6 , pp. 219ra9
    • Ullal, A.V.1    Peterson, V.2    Agasti, S.S.3    Tuang, S.4
  • 24
    • 84856004321 scopus 로고    scopus 로고
    • Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells
    • Shi, Q. H., Qin, L. D., Wei, W., Geng, F. et al., Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proc. Natl. Acad. Sci. USA 2012, 109, 419–424.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 419-424
    • Shi, Q.H.1    Qin, L.D.2    Wei, W.3    Geng, F.4
  • 25
    • 79958122357 scopus 로고    scopus 로고
    • A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells
    • Ma, C., Fan, R., Ahmad, H., Shi, Q. H. et al., A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells. Nat. Med. 2011, 17, 738–U133.
    • (2011) Nat. Med. , vol.17 , pp. 738
    • Ma, C.1    Fan, R.2    Ahmad, H.3    Shi, Q.H.4
  • 26
    • 84926357740 scopus 로고    scopus 로고
    • Chemical methods for the simultaneous quantitation of metabolites and proteins from single cells
    • Xue, M., Wei, W., Su, Y., Kim, J. et al., Chemical methods for the simultaneous quantitation of metabolites and proteins from single cells. J. Am. Chem. Soc. 2015, 137, 4066–4069.
    • (2015) J. Am. Chem. Soc. , vol.137 , pp. 4066-4069
    • Xue, M.1    Wei, W.2    Su, Y.3    Kim, J.4
  • 27
    • 33745072443 scopus 로고    scopus 로고
    • A microengraving method for rapid selection of single cells producing antigen-specific antibodies
    • Love, J. C., Ronan, J. L., Grotenbreg, G. M., van der Veen, A. G., Ploegh, H. L., A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nat. Biotechnol. 2006, 24, 703–707.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 703-707
    • Love, J.C.1    Ronan, J.L.2    Grotenbreg, G.M.3    van der Veen, A.G.4    Ploegh, H.L.5
  • 28
    • 84870157455 scopus 로고    scopus 로고
    • Functional single-cell analysis of T-cell activation by supported lipid bilayer-tethered ligands on arrays of nanowells
    • Torres, A. J., Contento, R. L., Gordo, S., Wucherpfennig, K. W., Love, J. C., Functional single-cell analysis of T-cell activation by supported lipid bilayer-tethered ligands on arrays of nanowells. Lab Chip 2013, 13, 90–99.
    • (2013) Lab Chip , vol.13 , pp. 90-99
    • Torres, A.J.1    Contento, R.L.2    Gordo, S.3    Wucherpfennig, K.W.4    Love, J.C.5
  • 29
    • 84870891611 scopus 로고    scopus 로고
    • Quantitating cell-cell interaction functions with applications to glioblastoma multiforme cancer cells
    • Wang, J., Tham, D., Wei, W., Shin, Y. S. et al., Quantitating cell-cell interaction functions with applications to glioblastoma multiforme cancer cells. Nano Lett. 2012, 12, 6101–6106.
    • (2012) Nano Lett. , vol.12 , pp. 6101-6106
    • Wang, J.1    Tham, D.2    Wei, W.3    Shin, Y.S.4
  • 30
    • 85012893209 scopus 로고    scopus 로고
    • Single-cell, multiplexed protein detection of rare tumor cells based on a beads-on-barcode antibody microarray
    • Yang, L., Wang, Z., Deng, Y., Li, Y. et al., Single-cell, multiplexed protein detection of rare tumor cells based on a beads-on-barcode antibody microarray. Anal. Chem. 2016, 88, 11077–11083.
    • (2016) Anal. Chem. , vol.88 , pp. 11077-11083
    • Yang, L.1    Wang, Z.2    Deng, Y.3    Li, Y.4
  • 31
    • 78349260412 scopus 로고    scopus 로고
    • Chemistries for patterning robust DNA microbarcodes enable multiplex assays of cytoplasm proteins from single cancer cells
    • Shin, Y. S., Ahmad, H., Shi, Q., Kim, H. et al., Chemistries for patterning robust DNA microbarcodes enable multiplex assays of cytoplasm proteins from single cancer cells. Chemphyschem. 2010, 11, 3063–3069.
    • (2010) Chemphyschem. , vol.11 , pp. 3063-3069
    • Shin, Y.S.1    Ahmad, H.2    Shi, Q.3    Kim, H.4
  • 32
    • 84923132388 scopus 로고    scopus 로고
    • Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands
    • Lu, Y., Xue, Q., Eisele, M. R., Sulistijo, E. S. et al., Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands. Proc. Natl. Acad. Sci. USA 2015, 112, E607–E615.
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , pp. E607-E615
    • Lu, Y.1    Xue, Q.2    Eisele, M.R.3    Sulistijo, E.S.4
  • 33
    • 84877638694 scopus 로고    scopus 로고
    • Multifunctional T-cell analyses to study response and progression in adoptive cell transfer immunotherapy
    • Ma, C., Cheung, A. F., Chodon, T., Koya, R. C. et al., Multifunctional T-cell analyses to study response and progression in adoptive cell transfer immunotherapy. Cancer Discov. 2013, 3, 418–429.
    • (2013) Cancer Discov. , vol.3 , pp. 418-429
    • Ma, C.1    Cheung, A.F.2    Chodon, T.3    Koya, R.C.4
  • 34
    • 77953246142 scopus 로고    scopus 로고
    • Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations
    • Rissin, D. M., Kan, C. W., Campbell, T. G., Howes, S. C. et al., Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nat. Biotechnol. 2010, 28, 595–599.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 595-599
    • Rissin, D.M.1    Kan, C.W.2    Campbell, T.G.3    Howes, S.C.4
  • 36
    • 84930207118 scopus 로고    scopus 로고
    • Reproducibility crisis: blame it on the antibodies
    • Baker, M., Reproducibility crisis: blame it on the antibodies. Nature 2015, 521, 274–276.
    • (2015) Nature , vol.521 , pp. 274-276
    • Baker, M.1
  • 37
    • 84938419721 scopus 로고    scopus 로고
    • Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation
    • Marcon, E., Jain, H., Bhattacharya, A., Guo, H. et al., Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat. Methods 2015, 12, 725–731.
    • (2015) Nat. Methods , vol.12 , pp. 725-731
    • Marcon, E.1    Jain, H.2    Bhattacharya, A.3    Guo, H.4
  • 38
    • 79959677297 scopus 로고    scopus 로고
    • Protein signaling networks from single cell fluctuations and information theory profiling
    • Shin, Y. S., Remacle, F., Fan, R., Hwang, K. et al., Protein signaling networks from single cell fluctuations and information theory profiling. Biophys. J. 2011, 100, 2378–2386.
    • (2011) Biophys. J. , vol.100 , pp. 2378-2386
    • Shin, Y.S.1    Remacle, F.2    Fan, R.3    Hwang, K.4
  • 40
    • 80054768631 scopus 로고    scopus 로고
    • Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE
    • Qiu, P., Simonds, E. F., Bendall, S. C., Gibbs, K. D., Jr. et al., Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat. Biotechnol. 2011, 29, 886–891.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 886-891
    • Qiu, P.1    Simonds, E.F.2    Bendall, S.C.3    Gibbs, K.D.4
  • 42
    • 84968624557 scopus 로고    scopus 로고
    • Automated mapping of phenotype space with single-cell data
    • Samusik, N., Good, Z., Spitzer, M. H., Davis, K. L., Nolan, G. P., Automated mapping of phenotype space with single-cell data. Nat. Methods 2016, 13, 493–496.
    • (2016) Nat. Methods , vol.13 , pp. 493-496
    • Samusik, N.1    Good, Z.2    Spitzer, M.H.3    Davis, K.L.4    Nolan, G.P.5
  • 43
    • 84937604921 scopus 로고    scopus 로고
    • Immunology. An interactive reference framework for modeling a dynamic immune system
    • Spitzer, M. H., Gherardini, P. F., Fragiadakis, G. K., Bhattacharya, N. et al., Immunology. An interactive reference framework for modeling a dynamic immune system. Science 2015, 349, 1259425.
    • (2015) Science , vol.349 , pp. 1259425
    • Spitzer, M.H.1    Gherardini, P.F.2    Fragiadakis, G.K.3    Bhattacharya, N.4
  • 44
    • 84932198501 scopus 로고    scopus 로고
    • FlowSOM: using self-organizing maps for visualization and interpretation of cytometry data
    • Van Gassen, S., Callebaut, B., Van Helden, M. J., Lambrecht, B. N. et al., FlowSOM: using self-organizing maps for visualization and interpretation of cytometry data. Cytometry A 2015, 87, 636–645.
    • (2015) Cytometry A , vol.87 , pp. 636-645
    • Van Gassen, S.1    Callebaut, B.2    Van Helden, M.J.3    Lambrecht, B.N.4
  • 47
    • 84908388625 scopus 로고    scopus 로고
    • Clinical recovery from surgery correlates with single-cell immune signatures
    • Gaudilliere, B., Fragiadakis, G. K., Bruggner, R. V., Nicolau, M. et al., Clinical recovery from surgery correlates with single-cell immune signatures. Sci. Transl. Med. 2014, 6, 255ra131.
    • (2014) Sci. Transl. Med. , vol.6 , pp. 255ra131
    • Gaudilliere, B.1    Fragiadakis, G.K.2    Bruggner, R.V.3    Nicolau, M.4
  • 48
    • 84859994220 scopus 로고    scopus 로고
    • Computational approaches for analyzing information flow in biological networks
    • Kholodenko, B., Yaffe, M. B., Kolch, W., Computational approaches for analyzing information flow in biological networks. Sci. Signal. 2012, 5, re1.
    • (2012) Sci. Signal. , vol.5 , pp. re1
    • Kholodenko, B.1    Yaffe, M.B.2    Kolch, W.3
  • 49
    • 84962725073 scopus 로고    scopus 로고
    • Single-cell phosphoproteomics resolves adaptive signaling dynamics and informs targeted combination therapy in glioblastoma
    • Wei, W., Shin, Y. S., Xue, M., Matsutani, T. et al., Single-cell phosphoproteomics resolves adaptive signaling dynamics and informs targeted combination therapy in glioblastoma. Cancer Cell 2016, 29, 563–573.
    • (2016) Cancer Cell , vol.29 , pp. 563-573
    • Wei, W.1    Shin, Y.S.2    Xue, M.3    Matsutani, T.4
  • 50
    • 84860851412 scopus 로고    scopus 로고
    • Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks
    • Lee, M. J., Ye, A. S., Gardino, A. K., Heijink, A. M. et al., Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 2012, 149, 780–794.
    • (2012) Cell , vol.149 , pp. 780-794
    • Lee, M.J.1    Ye, A.S.2    Gardino, A.K.3    Heijink, A.M.4
  • 51
    • 84876029468 scopus 로고    scopus 로고
    • Hypoxia induces a phase transition within a kinase signaling network in cancer cells
    • Wei, W., Shi, Q. H., Remacle, F., Qin, L. D. et al., Hypoxia induces a phase transition within a kinase signaling network in cancer cells. Proc. Natl. Acad. Sci. USA 2013, 110, E1352–E1360.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. E1352-E1360
    • Wei, W.1    Shi, Q.H.2    Remacle, F.3    Qin, L.D.4
  • 52
    • 84880280631 scopus 로고    scopus 로고
    • viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
    • Amir el, A. D., Davis, K. L., Tadmor, M. D., Simonds, E. F. et al., viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat. Biotechnol. 2013, 31, 545–552.
    • (2013) Nat. Biotechnol. , vol.31 , pp. 545-552
    • Amir el, A.D.1    Davis, K.L.2    Tadmor, M.D.3    Simonds, E.F.4
  • 53
    • 0001927585 scopus 로고
    • On information and sufficiency
    • Kullback, S., Leibler, R. A., On information and sufficiency. Ann. Math. Stat. 1951, 22, 79–86.
    • (1951) Ann. Math. Stat. , vol.22 , pp. 79-86
    • Kullback, S.1    Leibler, R.A.2
  • 54
    • 84911016319 scopus 로고    scopus 로고
    • High-dimensional analysis of the murine myeloid cell system
    • Becher, B., Schlitzer, A., Chen, J., Mair, F. et al., High-dimensional analysis of the murine myeloid cell system. Nat. Immunol. 2014, 15, 1181–1189.
    • (2014) Nat. Immunol. , vol.15 , pp. 1181-1189
    • Becher, B.1    Schlitzer, A.2    Chen, J.3    Mair, F.4
  • 55
    • 84954104516 scopus 로고    scopus 로고
    • Categorical analysis of human T cell heterogeneity with one-dimensional soli-expression by nonlinear stochastic embedding
    • Cheng, Y., Wong, M. T., van der Maaten, L., Newell, E. W., Categorical analysis of human T cell heterogeneity with one-dimensional soli-expression by nonlinear stochastic embedding. J. Immunol. 2016, 196, 924–932.
    • (2016) J. Immunol. , vol.196 , pp. 924-932
    • Cheng, Y.1    Wong, M.T.2    van der Maaten, L.3    Newell, E.W.4
  • 56
    • 84891956083 scopus 로고    scopus 로고
    • Automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE)
    • Shekhar, K., Brodin, P., Davis, M. M., Chakraborty, A. K., Automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE). Proc. Natl. Acad. Sci. USA 2014, 111, 202–207.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 202-207
    • Shekhar, K.1    Brodin, P.2    Davis, M.M.3    Chakraborty, A.K.4
  • 57
    • 84934442835 scopus 로고    scopus 로고
    • Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis
    • Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L. et al., Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 2015, 162, 184–197.
    • (2015) Cell , vol.162 , pp. 184-197
    • Levine, J.H.1    Simonds, E.F.2    Bendall, S.C.3    Davis, K.L.4
  • 58
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P. et al., The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 2014, 32, 381–386.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 381-386
    • Trapnell, C.1    Cacchiarelli, D.2    Grimsby, J.3    Pokharel, P.4
  • 59
    • 84899574465 scopus 로고    scopus 로고
    • Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development
    • Bendall, S. C., Davis, K. L., Amir el, A. D., Tadmor, M. D. et al., Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 2014, 157, 714–725.
    • (2014) Cell , vol.157 , pp. 714-725
    • Bendall, S.C.1    Davis, K.L.2    Amir el, A.D.3    Tadmor, M.D.4
  • 60
    • 84924365758 scopus 로고    scopus 로고
    • Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
    • Marco, E., Karp, R. L., Guo, G., Robson, P. et al., Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc. Natl. Acad. Sci. USA 2014, 111, E5643–E5650.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. E5643-E5650
    • Marco, E.1    Karp, R.L.2    Guo, G.3    Robson, P.4
  • 61
    • 84959123422 scopus 로고    scopus 로고
    • Trajectories of cell-cycle progression from fixed cell populations
    • Gut, G., Tadmor, M. D., Pe'er, D., Pelkmans, L., Liberali, P., Trajectories of cell-cycle progression from fixed cell populations. Nat. Methods 2015, 12, 951–954.
    • (2015) Nat. Methods , vol.12 , pp. 951-954
    • Gut, G.1    Tadmor, M.D.2    Pe'er, D.3    Pelkmans, L.4    Liberali, P.5
  • 62
    • 84974587998 scopus 로고    scopus 로고
    • Wishbone identifies bifurcating developmental trajectories from single-cell data
    • Setty, M., Tadmor, M. D., Reich-Zeliger, S., Angel, O. et al., Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat. Biotechnol. 2016, 34, 637–645.
    • (2016) Nat. Biotechnol. , vol.34 , pp. 637-645
    • Setty, M.1    Tadmor, M.D.2    Reich-Zeliger, S.3    Angel, O.4
  • 63
    • 84941753288 scopus 로고    scopus 로고
    • Diffusion maps for high-dimensional single-cell analysis of differentiation data
    • Haghverdi, L., Buettner, F., Theis, F. J., Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 2015, 31, 2989–2998.
    • (2015) Bioinformatics , vol.31 , pp. 2989-2998
    • Haghverdi, L.1    Buettner, F.2    Theis, F.J.3
  • 64
    • 84942133464 scopus 로고    scopus 로고
    • Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method
    • Lin, J. R., Fallahi-Sichani, M., Sorger, P. K., Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nat. Commun. 2015, 6, 8390.
    • (2015) Nat. Commun. , vol.6 , pp. 8390
    • Lin, J.R.1    Fallahi-Sichani, M.2    Sorger, P.K.3
  • 66
    • 0242416539 scopus 로고    scopus 로고
    • Noise in eukaryotic gene expression
    • Blake, W. J., M, K. A., Cantor, C. R., Collins, J. J., Noise in eukaryotic gene expression. Nature 2003, 422, 633–637.
    • (2003) Nature , vol.422 , pp. 633-637
    • Blake, W.J.1    Cantor, C.R.2    Collins, J.J.3
  • 67
    • 84869755989 scopus 로고    scopus 로고
    • Predicting rates of cell state change caused by stochastic fluctuations using a data-driven landscape model
    • Sisan, D. R., Halter, M., Hubbard, J. B., Plant, A. L., Predicting rates of cell state change caused by stochastic fluctuations using a data-driven landscape model. Proc. Natl. Acad. Sci. USA 2012, 109, 19262–19267.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 19262-19267
    • Sisan, D.R.1    Halter, M.2    Hubbard, J.B.3    Plant, A.L.4
  • 69
    • 84960372123 scopus 로고    scopus 로고
    • Critical points in tumorigenesis: a carcinogen-initiated phase transition analyzed via single-cell proteomics
    • Poovathingal, S. K., Kravchenko-Balasha, N., Shin, Y. S., Levine, R. D., Heath, J. R., Critical points in tumorigenesis: a carcinogen-initiated phase transition analyzed via single-cell proteomics. Small 2016, 12, 1425–1431.
    • (2016) Small , vol.12 , pp. 1425-1431
    • Poovathingal, S.K.1    Kravchenko-Balasha, N.2    Shin, Y.S.3    Levine, R.D.4    Heath, J.R.5
  • 70
    • 0001479726 scopus 로고
    • Algorithm for finding the distribution of maximal entropy
    • Agmon, N., Alhassid, Y., Levine, R. D., Algorithm for finding the distribution of maximal entropy. J. Comput. Phys. 1979, 30, 250–258.
    • (1979) J. Comput. Phys. , vol.30 , pp. 250-258
    • Agmon, N.1    Alhassid, Y.2    Levine, R.D.3
  • 71
    • 84921472760 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge, UK; New York
    • Levine, R. D., Molecular Reaction Dynamics, Cambridge University Press, Cambridge, UK; New York 2005.
    • (2005) Molecular Reaction Dynamics
    • Levine, R.D.1
  • 72
    • 77953454551 scopus 로고    scopus 로고
    • Information-theoretic analysis of phenotype changes in early stages of carcinogenesis
    • Remacle, F., Kravchenko-Balasha, N., Levitzki, A., Levine, R. D., Information-theoretic analysis of phenotype changes in early stages of carcinogenesis. Proc. Natl. Acad. Sci. USA 2010, 107, 10324–10329.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 10324-10329
    • Remacle, F.1    Kravchenko-Balasha, N.2    Levitzki, A.3    Levine, R.D.4
  • 73
    • 84978150718 scopus 로고    scopus 로고
    • A thermodynamic-based interpretation of protein expression heterogeneity in different glioblastoma multiforme tumors identifies tumor-specific unbalanced processes
    • Kravchenko-Balasha, N., Johnson, H., White, F. M., Heath, J. R., Levine, R. D., A thermodynamic-based interpretation of protein expression heterogeneity in different glioblastoma multiforme tumors identifies tumor-specific unbalanced processes. J. Phys. Chem. B 2016, 120, 5990–5997.
    • (2016) J. Phys. Chem. B , vol.120 , pp. 5990-5997
    • Kravchenko-Balasha, N.1    Johnson, H.2    White, F.M.3    Heath, J.R.4    Levine, R.D.5
  • 74
    • 84906987240 scopus 로고    scopus 로고
    • Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition
    • Zadran, S., Arumugam, R., Herschman, H., Phelps, M. E., Levine, R. D., Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition. Proc. Natl. Acad. Sci. USA 2014, 111, 13235–13240.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 13235-13240
    • Zadran, S.1    Arumugam, R.2    Herschman, H.3    Phelps, M.E.4    Levine, R.D.5
  • 75
    • 84969776902 scopus 로고    scopus 로고
    • Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement
    • Kravchenko-Balasha, N., Shin, Y. S., Sutherland, A., Levine, R. D., Heath, J. R., Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement. Proc. Natl. Acad. Sci. USA 2016, 113, 5520–5525.
    • (2016) Proc. Natl. Acad. Sci. USA , vol.113 , pp. 5520-5525
    • Kravchenko-Balasha, N.1    Shin, Y.S.2    Sutherland, A.3    Levine, R.D.4    Heath, J.R.5
  • 77
    • 84899645410 scopus 로고    scopus 로고
    • Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions
    • Kravchenko-Balasha, N., Wang, J., Remacle, F., Levine, R. D., Heath, J. R., Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions. Proc. Natl. Acad. Sci USA 2014, 111, 6521–6526.
    • (2014) Proc. Natl. Acad. Sci USA , vol.111 , pp. 6521-6526
    • Kravchenko-Balasha, N.1    Wang, J.2    Remacle, F.3    Levine, R.D.4    Heath, J.R.5
  • 78
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: stochastic gene expression and its consequences
    • Raj, A., van Oudenaarden, A., Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 2008, 135, 216–226.
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    van Oudenaarden, A.2
  • 79
    • 84900990155 scopus 로고    scopus 로고
    • Environmental sensing, information transfer, and cellular decision-making
    • Bowsher, C. G., Swain, P. S., Environmental sensing, information transfer, and cellular decision-making. Curr. Opin. Biotechnol. 2014, 28, 149–155.
    • (2014) Curr. Opin. Biotechnol. , vol.28 , pp. 149-155
    • Bowsher, C.G.1    Swain, P.S.2
  • 80
    • 0032641874 scopus 로고    scopus 로고
    • Estimation of the information by an adaptive partitioning of the observation space
    • Darbellay, G. A., Vajda, I., Estimation of the information by an adaptive partitioning of the observation space. Ieee T Inform. Theory 1999, 45, 1315–1321.
    • (1999) Ieee T Inform. Theory , vol.45 , pp. 1315-1321
    • Darbellay, G.A.1    Vajda, I.2
  • 82
    • 84879435511 scopus 로고    scopus 로고
    • hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests
    • Jang, I. S., Margolin, A., Califano, A., hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus 2013, 3, 20130011.
    • (2013) Interface Focus , vol.3 , pp. 20130011
    • Jang, I.S.1    Margolin, A.2    Califano, A.3
  • 83
    • 84914127300 scopus 로고    scopus 로고
    • Conditional density-based analysis of T cell signaling in single-cell data
    • Krishnaswamy, S., Spitzer, M. H., Mingueneau, M., Bendall, S. C. et al., Conditional density-based analysis of T cell signaling in single-cell data. Science 2014, 346, 1250689.
    • (2014) Science , vol.346 , pp. 1250689
    • Krishnaswamy, S.1    Spitzer, M.H.2    Mingueneau, M.3    Bendall, S.C.4
  • 85
    • 67650095196 scopus 로고    scopus 로고
    • Elite and stochastic models for induced pluripotent stem cell generation
    • Yamanaka, S., Elite and stochastic models for induced pluripotent stem cell generation. Nature 2009, 460, 49–52.
    • (2009) Nature , vol.460 , pp. 49-52
    • Yamanaka, S.1
  • 86
    • 77952914558 scopus 로고    scopus 로고
    • The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation
    • Wang, J., Xu, L., Wang, E., Huang, S., The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophys. J. 2010, 99, 29–39.
    • (2010) Biophys. J. , vol.99 , pp. 29-39
    • Wang, J.1    Xu, L.2    Wang, E.3    Huang, S.4
  • 88
    • 79953230529 scopus 로고    scopus 로고
    • Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation
    • Tian, R. J., Wang, S. A., Elisma, F., Li, L. et al., Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation. Mol. Cell Proteomics 2011, 10, M110.000679.
    • (2011) Mol. Cell Proteomics , vol.10 , pp. 000679
    • Tian, R.J.1    Wang, S.A.2    Elisma, F.3    Li, L.4
  • 89
    • 80054681742 scopus 로고    scopus 로고
    • Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry
    • Thakur, D., Rejtar, T., Wang, D. D., Bones, J. et al., Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J. Chromatogr. A 2011, 1218, 8168–8174.
    • (2011) J. Chromatogr. A , vol.1218 , pp. 8168-8174
    • Thakur, D.1    Rejtar, T.2    Wang, D.D.3    Bones, J.4
  • 90
    • 84943196371 scopus 로고    scopus 로고
    • Single-cell codetection of metabolic activity, intracellular functional proteins, and genetic mutations from rare circulating tumor cells
    • Zhang, Y., Tang, Y., Sun, S., Wang, Z. H. et al., Single-cell codetection of metabolic activity, intracellular functional proteins, and genetic mutations from rare circulating tumor cells. Anal. Chem. 2015, 87, 9761–9768.
    • (2015) Anal. Chem. , vol.87 , pp. 9761-9768
    • Zhang, Y.1    Tang, Y.2    Sun, S.3    Wang, Z.H.4
  • 91
    • 84991821805 scopus 로고    scopus 로고
    • Assay of genome-wide transcriptome and secreted proteins on the same single immune cells by microfluidics and RNA sequencing
    • George, J., Wang, J., Assay of genome-wide transcriptome and secreted proteins on the same single immune cells by microfluidics and RNA sequencing. Anal. Chem. 2016, 88, 10309–10315.
    • (2016) Anal. Chem. , vol.88 , pp. 10309-10315
    • George, J.1    Wang, J.2
  • 92
    • 84959248377 scopus 로고    scopus 로고
    • Highly multiplexed simultaneous detection of RNAs and proteins in single cells
    • Frei, A. P., Bava, F. A., Zunder, E. R., Hsieh, E. W. Y. et al., Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat. Methods 2016, 13, 269–275.
    • (2016) Nat. Methods , vol.13 , pp. 269-275
    • Frei, A.P.1    Bava, F.A.2    Zunder, E.R.3    Hsieh, E.W.Y.4
  • 93
    • 84962564367 scopus 로고    scopus 로고
    • Digital quantification of proteins and mRNA in single mammalian cells
    • Albayrak, C., Jordi, C. A., Zechner, C., Lin, J. et al., Digital quantification of proteins and mRNA in single mammalian cells. Mol. Cell 2016, 61, 914–924.
    • (2016) Mol. Cell , vol.61 , pp. 914-924
    • Albayrak, C.1    Jordi, C.A.2    Zechner, C.3    Lin, J.4
  • 94
    • 84960400481 scopus 로고    scopus 로고
    • Supramolecular probes for assessing glutamine uptake enable semi-quantitative metabolic models in single cells
    • Xue, M., Wei, W., Su, Y. P., Johnson, D., Heath, J. R., Supramolecular probes for assessing glutamine uptake enable semi-quantitative metabolic models in single cells. J. Am. Chem. Soc. 2016, 138, 3085–3093.
    • (2016) J. Am. Chem. Soc. , vol.138 , pp. 3085-3093
    • Xue, M.1    Wei, W.2    Su, Y.P.3    Johnson, D.4    Heath, J.R.5
  • 95
    • 84898402897 scopus 로고    scopus 로고
    • Multiplexed ion beam imaging of human breast tumors
    • Angelo, M., Bendall, S. C., Finck, R., Hale, M. B. et al., Multiplexed ion beam imaging of human breast tumors. Nat. Med. 2014, 20, 436–442.
    • (2014) Nat. Med. , vol.20 , pp. 436-442
    • Angelo, M.1    Bendall, S.C.2    Finck, R.3    Hale, M.B.4
  • 96
    • 84897954497 scopus 로고    scopus 로고
    • Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
    • Giesen, C., Wang, H. A. O., Schapiro, D., Zivanovic, N. et al., Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat. Methods 2014, 11, 417–422.
    • (2014) Nat. Methods , vol.11 , pp. 417-422
    • Giesen, C.1    Wang, H.A.O.2    Schapiro, D.3    Zivanovic, N.4
  • 97
    • 84897452794 scopus 로고    scopus 로고
    • Single-cell in situ RNA profiling by sequential hybridization
    • Lubeck, E., Coskun, A. F., Zhiyentayev, T., Ahmad, M., Cai, L., Single-cell in situ RNA profiling by sequential hybridization. Nat. Methods 2014, 11, 360–361.
    • (2014) Nat. Methods , vol.11 , pp. 360-361
    • Lubeck, E.1    Coskun, A.F.2    Zhiyentayev, T.3    Ahmad, M.4    Cai, L.5
  • 98
    • 84963626928 scopus 로고    scopus 로고
    • Expansion microscopy with conventional antibodies and fluorescent proteins
    • Chozinski, T. J., Halpern, A. R., Okawa, H., Kim, H. J. et al., Expansion microscopy with conventional antibodies and fluorescent proteins. Nat. Methods 2016, 13, 485–488.
    • (2016) Nat. Methods , vol.13 , pp. 485-488
    • Chozinski, T.J.1    Halpern, A.R.2    Okawa, H.3    Kim, H.J.4


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