-
1
-
-
77952474987
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
22
-
-
84903616029
-
Single-cell western blotting
-
Hughes, A. J., Spelke, D. P., Xu, Z., Kang, C. C. et al., Single-cell western blotting. Nat. Methods 2014, 11, 749–755.
-
(2014)
Nat. Methods
, vol.11
, pp. 749-755
-
-
Hughes, A.J.1
Spelke, D.P.2
Xu, Z.3
Kang, C.C.4
-
23
-
-
84979888019
-
Single cell-resolution western blotting
-
Kang, C. C., Yamauchi, K. A., Vlassakis, J., Sinkala, E. et al., Single cell-resolution western blotting. Nat. Protoc. 2016, 11, 1508–1530.
-
(2016)
Nat. Protoc.
, vol.11
, pp. 1508-1530
-
-
Kang, C.C.1
Yamauchi, K.A.2
Vlassakis, J.3
Sinkala, E.4
-
24
-
-
84856004321
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
35
-
-
84959547980
-
Protein counting in single cancer cells
-
Schubert, S. M., Walter, S. R., Manesse, M., Walt, D. R., Protein counting in single cancer cells. Anal. Chem. 2016, 88, 2952–2957.
-
(2016)
Anal. Chem.
, vol.88
, pp. 2952-2957
-
-
Schubert, S.M.1
Walter, S.R.2
Manesse, M.3
Walt, D.R.4
-
36
-
-
84930207118
-
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
-
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
-
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
-
39
-
-
74949118948
-
Publishing flow cytometry data
-
Alvarez, D. F., Helm, K., Degregori, J., Roederer, M., Majka, S., Publishing flow cytometry data. Am. J. Physiol. Lung Cell Mol. Physiol. 2010, 298, L127–L130.
-
(2010)
Am. J. Physiol. Lung Cell Mol. Physiol.
, vol.298
, pp. L127-L130
-
-
Alvarez, D.F.1
Helm, K.2
Degregori, J.3
Roederer, M.4
Majka, S.5
-
40
-
-
80054768631
-
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
-
41
-
-
84903703398
-
Automated identification of stratifying signatures in cellular subpopulations
-
Bruggner, R. V., Bodenmiller, B., Dill, D. L., Tibshirani, R. J., Nolan, G. P., Automated identification of stratifying signatures in cellular subpopulations. Proc. Natl. Acad. Sci. USA 2014, 111, E2770–E2777.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. E2770-E2777
-
-
Bruggner, R.V.1
Bodenmiller, B.2
Dill, D.L.3
Tibshirani, R.J.4
Nolan, G.P.5
-
42
-
-
84968624557
-
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
-
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
-
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
-
45
-
-
0003430544
-
-
John Wiley & Sons, Inc
-
Kaufman, L., Rousseeuw, P. J., Finding Groups in Data, John Wiley & Sons, Inc. 2008, pp. 126–163.
-
(2008)
Finding Groups in Data
, pp. 126-163
-
-
Kaufman, L.1
Rousseeuw, P.J.2
-
46
-
-
84872198906
-
A gene ontology inferred from molecular networks
-
Dutkowski, J., Kramer, M., Surma, M. A., Balakrishnan, R. et al., A gene ontology inferred from molecular networks. Nat. Biotechnol. 2013, 31, 38–45.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 38-45
-
-
Dutkowski, J.1
Kramer, M.2
Surma, M.A.3
Balakrishnan, R.4
-
47
-
-
84908388625
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
65
-
-
33646540711
-
Predicting stochastic gene expression dynamics in single cells
-
Mettetal, J. T., Muzzey, D., Pedraza, J. M., Ozbudak, E. M., van Oudenaarden, A., Predicting stochastic gene expression dynamics in single cells. Proc. Natl. Acad. Sci. USA 2006, 103, 7304–7309.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 7304-7309
-
-
Mettetal, J.T.1
Muzzey, D.2
Pedraza, J.M.3
Ozbudak, E.M.4
van Oudenaarden, A.5
-
66
-
-
0242416539
-
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
-
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
-
68
-
-
84948406395
-
Entropy, ergodicity, and stem cell multipotency
-
Ridden, S. J., Chang, H. H., Zygalakis, K. C., MacArthur, B. D., Entropy, ergodicity, and stem cell multipotency. Phys. Rev. Lett. 2015, 115, 208103.
-
(2015)
Phys. Rev. Lett.
, vol.115
, pp. 208103
-
-
Ridden, S.J.1
Chang, H.H.2
Zygalakis, K.C.3
MacArthur, B.D.4
-
69
-
-
84960372123
-
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
-
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
-
-
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
-
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
-
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
-
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
-
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
-
76
-
-
84858695934
-
On a fundamental structure of gene networks in living cells
-
Kravchenko-Balasha, N., Levitzki, A., Goldstein, A., Rotter, V. et al., On a fundamental structure of gene networks in living cells. Proc. Natl. Acad. Sci. USA 2012, 109, 4702–4707.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 4702-4707
-
-
Kravchenko-Balasha, N.1
Levitzki, A.2
Goldstein, A.3
Rotter, V.4
-
77
-
-
84899645410
-
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
-
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
-
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
-
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
-
81
-
-
33750353888
-
Reverse engineering cellular networks
-
Margolin, A. A., Wang, K., Lim, W. K., Kustagi, M. et al., Reverse engineering cellular networks. Nat. Protoc. 2006, 1, 662–671.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 662-671
-
-
Margolin, A.A.1
Wang, K.2
Lim, W.K.3
Kustagi, M.4
-
82
-
-
84879435511
-
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
-
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
-
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
-
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
-
87
-
-
84948406395
-
Entropy, ergodicity, and stem cell multipotency
-
Ridden, S. J., Chang, H. H., Zygalakis, K. C., MacArthur, B. D., Entropy, ergodicity, and stem cell multipotency. Phys. Rev. Lett. 2015, 115, 208103.
-
(2015)
Phys. Rev. Lett.
, vol.115
, pp. 208103
-
-
Ridden, S.J.1
Chang, H.H.2
Zygalakis, K.C.3
MacArthur, B.D.4
-
88
-
-
79953230529
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|