-
1
-
-
3843126332
-
RNA dynamics in live Escherichia coli cells
-
doi:10.1073/pnas.0404443101
-
Golding I, Cox EC. 2004 RNA dynamics in live Escherichia coli cells. Proc. Natl Acad. Sci. USA 101, 11 310-11 315. (doi:10.1073/pnas.0404443101)
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 11310-11315
-
-
Golding, I.1
Cox, E.C.2
-
2
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
doi:10.1371/journal.pbio. 0040309
-
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. 2006 Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309. (doi:10.1371/journal.pbio. 0040309)
-
(2006)
PLoS Biol.
, vol.4
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
3
-
-
33745220278
-
Singlecell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
doi:10.1038/nature04785
-
Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. 2006 Singlecell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846. (doi:10.1038/nature04785)
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.S.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
DeRisi, J.L.6
Weissman, J.S.7
-
4
-
-
48249156189
-
Quantification of mRNA in single cells and modelling of RT-qPCR induced noise
-
doi:10.1186/1471-2199-9-63
-
Bengtsson M, Hemberg M, Rorsman P, Ståhlberg A. 2008 Quantification of mRNA in single cells and modelling of RT-qPCR induced noise. BMC Mol. Biol. 9, 63. (doi:10.1186/1471-2199-9-63)
-
(2008)
BMC Mol. Biol.
, vol.9
, pp. 63
-
-
Bengtsson, M.1
Hemberg, M.2
Rorsman, P.3
Ståhlberg, A.4
-
5
-
-
84866139606
-
Fractional proliferation: A method to deconvolve cell population dynamics from single-cell data
-
doi:10.1038/nmeth.2138
-
Tyson DR, Garbett SP, Frick PL, Quaranta V. 2012 Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data. Nat. Methods 9, 923-928. (doi:10.1038/nmeth.2138)
-
(2012)
Nat. Methods
, vol.9
, pp. 923-928
-
-
Tyson, D.R.1
Garbett, S.P.2
Frick, P.L.3
Quaranta, V.4
-
6
-
-
33845616177
-
Phenotypic consequences of promoter-mediated transcriptional noise
-
doi:10.1016/j.molcel.2006.11.003
-
Blake WJ et al. 2006 Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell 24, 853-865. (doi:10.1016/j.molcel.2006.11.003)
-
(2006)
Mol. Cell
, vol.24
, pp. 853-865
-
-
Blake, W.J.1
-
7
-
-
57349097152
-
Dynamic proteomics of individual cancer cells in response to a drug
-
doi:10.1126/science.1160165
-
Cohen AA et al. 2008 Dynamic proteomics of individual cancer cells in response to a drug. Science 322, 1511-1516. (doi:10.1126/science.1160165)
-
(2008)
Science
, vol.322
, pp. 1511-1516
-
-
Cohen, A.A.1
-
8
-
-
84861133687
-
Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptormediated apoptosis
-
doi:10.1371/journal.pcbi.1002482
-
Gaudet S, Spencer SL, Chen WW, Sorger PK. 2012 Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptormediated apoptosis. PLoS Comput. Biol. 8, e1002482. (doi:10.1371/ journal.pcbi.1002482)
-
(2012)
PLoS Comput. Biol.
, vol.8
-
-
Gaudet, S.1
Spencer, S.L.2
Chen, W.W.3
Sorger, P.K.4
-
9
-
-
56249130793
-
Analytical distributions for stochastic gene expression
-
doi:10.1073/pnas.0803850105
-
Shahrezaei V, Swain PS. 2008 Analytical distributions for stochastic gene expression. Proc. Natl Acad. Sci. USA 105, 17 256-17 261. (doi:10.1073/pnas. 0803850105)
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 17256-17261
-
-
Shahrezaei, V.1
Swain, P.S.2
-
10
-
-
80053054440
-
Origins of stochastic intracellular processes and consequences for cell-tocell variability and cellular survival strategies
-
Schwabe A, Dobrzýnski M, Rybakova K, Verschure P, Bruggeman FJ. 2011 Origins of stochastic intracellular processes and consequences for cell-tocell variability and cellular survival strategies. Methods Enzymol. 500, 597-625.
-
(2011)
Methods Enzymol.
, vol.500
, pp. 597-625
-
-
Schwabe, A.1
Dobrzýnski, M.2
Rybakova, K.3
Verschure, P.4
Bruggeman, F.J.5
-
11
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
doi:10.1126/science.1119623
-
Yu J, Xiao J, Ren X, Lao K, Xie XS. 2006 Probing gene expression in live cells, one protein molecule at a time. Science 311, 1600-1603. (doi:10.1126/science.1119623)
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
-
12
-
-
0242416539
-
Noise in eukaryotic gene expression
-
doi:10.1038/nature01546
-
Blake WJ, Kærn M, Cantor CR, Collins JJ. 2003 Noise in eukaryotic gene expression. Nature 422, 633-637. (doi:10.1038/nature01546)
-
(2003)
Nature
, vol.422
, pp. 633-637
-
-
Blake, W.J.1
Kærn, M.2
Cantor, C.R.3
Collins, J.J.4
-
13
-
-
17144456808
-
Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
-
doi:10.1093/emboj/20.10.2528
-
Becskei A, Séraphin B, Serrano L. 2001 Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20, 2528-2535. (doi:10.1093/emboj/20.10.2528)
-
(2001)
EMBO J.
, vol.20
, pp. 2528-2535
-
-
Becskei, A.1
Séraphin, B.2
Serrano, L.3
-
14
-
-
33644524741
-
Cell-signalling dynamics in time and space
-
doi:10.1038/nrm1838
-
Kholodenko BN. 2006 Cell-signalling dynamics in time and space. Nat. Rev. Mol. Cell Biol. 7, 165-176. (doi:10.1038/nrm1838)
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 165-176
-
-
Kholodenko, B.N.1
-
15
-
-
79959650941
-
Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells
-
doi:10.1038/nrc3081
-
Tyson JJ, Baumann WT, Chen C, Verdugo A, Tavassoly I, Wang Y, Weiner LM, Clarke R. 2011 Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nat. Rev. Cancer 11,523-532. (doi:10.1038/nrc3081)
-
(2011)
Nat. Rev. Cancer
, vol.11
, pp. 523-532
-
-
Tyson, J.J.1
Baumann, W.T.2
Chen, C.3
Verdugo, A.4
Tavassoly, I.5
Wang, Y.6
Weiner, L.M.7
Clarke, R.8
-
16
-
-
84867115539
-
Crosstalk and signaling switches in mitogenactivated protein kinase cascades
-
doi:10.3389/fphys.2012.00355
-
Fey D, Croucher DR, Kolch W, Kholodenko BN. 2012 Crosstalk and signaling switches in mitogenactivated protein kinase cascades. Front. Physiol. 3, 355. (doi:10.3389/fphys.2012.00355)
-
(2012)
Front. Physiol.
, vol.3
, pp. 355
-
-
Fey, D.1
Croucher, D.R.2
Kolch, W.3
Kholodenko, B.N.4
-
17
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
doi:10.1038/35002131
-
Collins JJ, Gardner TS, Cantor CR. 2000 Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342. (doi:10.1038/35002131)
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Collins, J.J.1
Gardner, T.S.2
Cantor, C.R.3
-
18
-
-
14044265753
-
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations
-
doi:10.1073/pnas.0406841102
-
Samoilov M, Plyasunov S, Arkin AP. 2005 Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc. Natl Acad. Sci. USA 102, 2310-2315. (doi:10.1073/pnas. 0406841102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 2310-2315
-
-
Samoilov, M.1
Plyasunov, S.2
Arkin, A.P.3
-
19
-
-
78149242181
-
Noisy-threshold control of cell death
-
doi:10.1186/1752-0509-4-152
-
Vilar JMG. 2010 Noisy-threshold control of cell death. BMC Syst. Biol. 4, 152. (doi:10.1186/1752-0509-4-152)
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 152
-
-
Vilar, J.M.G.1
-
20
-
-
84865298239
-
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise
-
doi:10.1186/1752-0509-6-109
-
Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN. 2012 Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. BMC Syst. Biol. 6, 109. (doi:10.1186/1752-0509-6-109)
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 109
-
-
Birtwistle, M.R.1
Rauch, J.2
Kiyatkin, A.3
Aksamitiene, E.4
Dobrzyński, M.5
Hoek, J.B.6
Kolch, W.7
Ogunnaike, B.A.8
Kholodenko, B.N.9
-
21
-
-
84867850712
-
Bimodal protein distributions in heterogeneous oscillating systems
-
Computational methods in systems biology (eds D Gilbert, M Heiner), Berlin, Germany: Springer
-
Dobrzyński M, Fey D, Nguyen LK, Kholodenko BN. 2012 Bimodal protein distributions in heterogeneous oscillating systems. In Computational methods in systems biology (eds D Gilbert, M Heiner), Lecture Notes in Computer Science, pp. 17-28. Berlin, Germany: Springer.
-
(2012)
Lecture Notes in Computer Science
, pp. 17-28
-
-
Dobrzyński, M.1
Fey, D.2
Nguyen, L.K.3
Kholodenko, B.N.4
-
22
-
-
0029790351
-
Ultrasensitivity in the mitogen-activated protein kinase cascade
-
doi:10.1073/pnas.93.19.10078
-
Huang CY, Ferrell JE. 1996 Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl Acad. Sci. USA 93, 10 078-10 083. (doi:10.1073/pnas.93.19.10078)
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 10078-10083
-
-
Huang, C.Y.1
Ferrell, J.E.2
-
23
-
-
84856264773
-
A two-dimensional ERK-AKT signaling code for an NGF-triggered cell-fate decision
-
doi:10.1016/j.molcel.2011.11.023
-
Chen J-Y, Lin J-R, Cimprich KA, Meyer T. 2012 A two-dimensional ERK-AKT signaling code for an NGF-triggered cell-fate decision. Mol. Cell 45, 196-209. (doi:10.1016/j.molcel.2011.11.023)
-
(2012)
Mol. Cell
, vol.45
, pp. 196-209
-
-
Chen, J.-Y.1
Lin, J.-R.2
Cimprich, K.A.3
Meyer, T.4
-
24
-
-
16344387146
-
Stochastic simulations of the origins and implications of long-tailed distributions in gene expression
-
doi:10.1073/pnas.0406415102
-
Krishna S, Banerjee B, Ramakrishnan TV, Shivashankar GV. 2005 Stochastic simulations of the origins and implications of long-tailed distributions in gene expression. Proc. Natl Acad. Sci. USA 102, 4771-4776. (doi:10.1073/pnas. 0406415102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4771-4776
-
-
Krishna, S.1
Banerjee, B.2
Ramakrishnan, T.V.3
Shivashankar, G.V.4
-
25
-
-
68549085470
-
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems
-
doi:10.1093/bioinformatics/btp360
-
Lu C, King RD. 2009 An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems. Bioinformatics 25, 2020-2027. (doi:10.1093/bioinformatics/btp360)
-
(2009)
Bioinformatics
, vol.25
, pp. 2020-2027
-
-
Lu, C.1
King, R.D.2
-
26
-
-
84867365249
-
Mammalian protein expression noise: Scaling principles and the implications for knockdown experiments
-
doi:10.1039/c2mb25168j
-
Birtwistle MR, von Kriegsheim A, Dobrzyński M, Kholodenko BN, Kolch W. 2012 Mammalian protein expression noise: scaling principles and the implications for knockdown experiments. Mol. Biosyst. 8, 3068-3076. (doi:10.1039/c2mb25168j)
-
(2012)
Mol. Biosyst.
, vol.8
, pp. 3068-3076
-
-
Birtwistle, M.R.1
Von Kriegsheim, A.2
Dobrzyński, M.3
Kholodenko, B.N.4
Kolch, W.5
-
27
-
-
19544379881
-
Stochasticity in gene expression: From theories to phenotypes
-
doi:10.1038/nrg1615
-
Kærn M, Elston TC, Blake WJ, Collins JJ. 2005 Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6, 451-464. (doi:10.1038/nrg1615)
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 451-464
-
-
Kærn, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
28
-
-
50449096238
-
Information flow and optimization in transcriptional regulation
-
doi:10.1073/pnas.0806077105
-
Tkacik G, Callan CG, Bialek W. 2008 Information flow and optimization in transcriptional regulation. Proc. Natl Acad. Sci. USA 105, 12 265-12 270. (doi:10.1073/pnas.0806077105)
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 12265-12270
-
-
Tkacik, G.1
Callan, C.G.2
Bialek, W.3
-
29
-
-
66149144779
-
A stochastic spectral analysis of transcriptional regulatory cascades
-
doi:10.1073/pnas.0811999106
-
Walczak AM, Mugler A, Wiggins CH. 2009 A stochastic spectral analysis of transcriptional regulatory cascades. Proc. Natl Acad. Sci. USA 106, 6529-6534. (doi:10.1073/pnas.0811999106)
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 6529-6534
-
-
Walczak, A.M.1
Mugler, A.2
Wiggins, C.H.3
-
30
-
-
78650644119
-
Bimodal gene expression in noncooperative regulatory systems
-
doi:10.1073/pnas.1008965107
-
Ochab-Marcinek A, Tabaka M. 2010 Bimodal gene expression in noncooperative regulatory systems. Proc. Natl Acad. Sci. USA 107, 22 096-22 101. (doi:10.1073/pnas.1008965107)
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 22096-22101
-
-
Ochab-Marcinek, A.1
Tabaka, M.2
-
31
-
-
34249663979
-
Information maximization in face processing
-
doi:10.1016/j.neucom.2006.02.025
-
Bartlett MS. 2007 Information maximization in face processing. Neurocomputing 70, 2204-2217. (doi:10.1016/j.neucom.2006.02.025)
-
(2007)
Neurocomputing
, vol.70
, pp. 2204-2217
-
-
Bartlett, M.S.1
-
32
-
-
0019620028
-
A simple coding procedure enhances a neuron's information capacity
-
Laughlin S. 1981 A simple coding procedure enhances a neuron's information capacity. Z. Naturforsch., C, Biosci. 36, 910-912.
-
(1981)
Z. Naturforsch., C, Biosci.
, vol.36
, pp. 910-912
-
-
Laughlin, S.1
-
33
-
-
75749090855
-
Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues
-
doi:10.1073/pnas.0908647107
-
Lipshtat A, Jayaraman G, He JC, Iyengar R. 2010 Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues. Proc. Natl Acad. Sci. USA 107, 1247-1252. (doi:10.1073/pnas.0908647107)
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 1247-1252
-
-
Lipshtat, A.1
Jayaraman, G.2
He, J.C.3
Iyengar, R.4
-
34
-
-
34249885757
-
Engineering synthetic signaling proteins with ultra-sensitive input/output control
-
doi:10.1038/nbt1308
-
Dueber JE, Mirsky EA, Lim WA. 2007 Engineering synthetic signaling proteins with ultra-sensitive input/output control. Nat. Biotechnol. 25, 660-662. (doi:10.1038/nbt1308)
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 660-662
-
-
Dueber, J.E.1
Mirsky, E.A.2
Lim, W.A.3
-
35
-
-
0006470992
-
Entropy, relative entropy and mutual information
-
New York, NY: John Wiley & Sons
-
Cover TM, Thomas JA. 1991 Entropy, relative entropy and mutual information. In Elements of information theory, pp. 12-49. New York, NY: John Wiley & Sons.
-
(1991)
Elements of Information Theory
, pp. 12-49
-
-
Cover, T.M.1
Thomas, J.A.2
-
36
-
-
84856739946
-
Hypoxia-inducible factors in physiology and medicine
-
doi:10.1016/j.cell.2012.01.021
-
Semenza GL. 2012 Hypoxia-inducible factors in physiology and medicine. Cell 148, 399-408. (doi:10.1016/j.cell.2012.01.021)
-
(2012)
Cell
, vol.148
, pp. 399-408
-
-
Semenza, G.L.1
-
38
-
-
0035834409
-
A conserved family of prolyl-4-hydroxylases that modify HIF
-
doi:10.1126/science.1066373
-
Bruick RK, McKnight SL. 2001 A conserved family of prolyl-4-hydroxylases that modify HIF. Science 294, 1337-1340. (doi:10.1126/science.1066373)
-
(2001)
Science
, vol.294
, pp. 1337-1340
-
-
Bruick, R.K.1
McKnight, S.L.2
-
39
-
-
0035903468
-
Independent function of two destruction domains in hypoxia-inducible factoralpha chains activated by prolyl hydroxylation
-
doi:10.1093/emboj/20.18.5197
-
Masson N, Willam C, Maxwell PH, Pugh CW, Ratcliffe PJ. 2001 Independent function of two destruction domains in hypoxia-inducible factoralpha chains activated by prolyl hydroxylation. EMBO J. 20, 5197-5206. (doi:10.1093/emboj/20. 18.5197)
-
(2001)
EMBO J.
, vol.20
, pp. 5197-5206
-
-
Masson, N.1
Willam, C.2
Maxwell, P.H.3
Pugh, C.W.4
Ratcliffe, P.J.5
-
40
-
-
70449624093
-
Reactivating HIF prolyl hydroxylases under hypoxia results in metabolic catastrophe and cell death
-
doi:10.1038/onc.2009.250
-
Tennant DA et al. 2009 Reactivating HIF prolyl hydroxylases under hypoxia results in metabolic catastrophe and cell death. Oncogene 28, 4009-4021. (doi:10.1038/onc.2009.250)
-
(2009)
Oncogene
, vol.28
, pp. 4009-4021
-
-
Tennant, D.A.1
-
41
-
-
17944375360
-
C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation
-
doi:10.1016/S0092-8674(01)00507-4
-
Epstein AC et al. 2001 C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell 107, 43-54. (doi:10.1016/S0092-8674(01)00507-4)
-
(2001)
Cell
, vol.107
, pp. 43-54
-
-
Epstein, A.C.1
-
42
-
-
84877917354
-
A dynamic model of the hypoxia-inducible factor 1α(HIF-1α) network
-
doi:10.1242/jcs.119974
-
Nguyen LK et al. 2013 A dynamic model of the hypoxia-inducible factor 1α(HIF-1α) network. J. Cell Sci. 126, 1454-1463. (doi:10.1242/jcs.119974)
-
(2013)
J. Cell Sci.
, vol.126
, pp. 1454-1463
-
-
Nguyen, L.K.1
-
43
-
-
0016355478
-
A new look at the statistical model identification
-
doi:10.1109/TAC.1974.1100705
-
Akaike H. 1974 A new look at the statistical model identification. IEEE Trans. Autom. Control 19, 716-723. (doi:10.1109/TAC.1974.1100705)
-
(1974)
IEEE Trans. Autom. Control
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
44
-
-
50149090966
-
Variability and robustness in T cell activation from regulated heterogeneity in protein levels
-
doi:10.1126/science.1158013
-
Feinerman O, Veiga J, Dorfman JR, Germain RN, Altan-Bonnet G. 2008 Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science 321, 1081-1084. (doi:10.1126/science.1158013)
-
(2008)
Science
, vol.321
, pp. 1081-1084
-
-
Feinerman, O.1
Veiga, J.2
Dorfman, J.R.3
Germain, R.N.4
Altan-Bonnet, G.5
-
45
-
-
70549093092
-
Non-genetic cell-to-cell variability and the consequences for pharmacology
-
doi:10.1016/j.cbpa.2009.09.015
-
Niepel M, Spencer SL, Sorger PK. 2009 Non-genetic cell-to-cell variability and the consequences for pharmacology. Curr. Opin. Chem. Biol. 13, 556-561. (doi:10.1016/j.cbpa.2009.09.015)
-
(2009)
Curr. Opin. Chem. Biol.
, vol.13
, pp. 556-561
-
-
Niepel, M.1
Spencer, S.L.2
Sorger, P.K.3
-
46
-
-
66249136447
-
Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis
-
doi:10.1038/nature08012
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Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK. 2009 Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 459, 428-432. (doi:10.1038/nature08012)
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(2009)
Nature
, vol.459
, pp. 428-432
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Spencer, S.L.1
Gaudet, S.2
Albeck, J.G.3
Burke, J.M.4
Sorger, P.K.5
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