-
1
-
-
28844441230
-
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis
-
doi:10.1126/science.1116598
-
Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K., Lauffenburger, D. A. & Yaffe, M. B. 2005 A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653. (doi:10.1126/science.1116598)
-
(2005)
Science
, vol.310
, pp. 1646-1653
-
-
Janes, K.A.1
Albeck, J.G.2
Gaudet, S.3
Sorger, P.K.4
Lauffenburger, D.A.5
Yaffe, M.B.6
-
2
-
-
49549116189
-
Quantitative phosphoproteomic analysis of signaling network dynamics
-
doi:10.1016/j.copbio.2008.06.006
-
White, F. M. 2008 Quantitative phosphoproteomic analysis of signaling network dynamics. Curr. Opin. Biotechnol. 19, 404-409. (doi:10.1016/j.copbio. 2008.06.006)
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 404-409
-
-
White, F.M.1
-
3
-
-
72149093283
-
A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation
-
doi:10.1074/mcp.M800307-MCP200
-
Nguyen, V. et al. 2009 A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Mol. Cell Proteomics 8, 2418-2431. (doi:10.1074/mcp.M800307-MCP200)
-
(2009)
Mol. Cell Proteomics
, vol.8
, pp. 2418-2431
-
-
Nguyen, V.1
-
4
-
-
33750351769
-
Data-driven modelling of signal-transduction networks
-
doi:10.1038/nrm2041
-
Janes, K. A. & Yaffe, M. B. 2006 Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell. Biol. 7, 820-828. (doi:10.1038/nrm2041)
-
(2006)
Nat. Rev. Mol. Cell. Biol.
, vol.7
, pp. 820-828
-
-
Janes, K.A.1
Yaffe, M.B.2
-
5
-
-
65349179556
-
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin- induced signaling
-
doi:10.1371/journal.pcbi.1000340
-
Aldridge, B. B., Saez-Rodriguez, J., Muhlich, J. L., Sorger, P. K. & Lauffenburger, D. A. 2009 Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput. Biol. 5, e1000340. (doi:10.1371/journal.pcbi.1000340)
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Aldridge, B.B.1
Saez-Rodriguez, J.2
Muhlich, J.L.3
Sorger, P.K.4
Lauffenburger, D.A.5
-
6
-
-
0000325341
-
On lines and planes of closest fit to systems of points in space
-
Pearson, K. 1901 On lines and planes of closest fit to systems of points in space. Philos. Mag. 2, 559-572.
-
(1901)
Philos. Mag.
, vol.2
, pp. 559-572
-
-
Pearson, K.1
-
7
-
-
58149421595
-
Analysis of a complex of statistical variables into principal components
-
doi:10.1037/h0070888
-
Hotelling, H. 1933 Analysis of a complex of statistical variables into principal components. J. Educ. Psychol. 24, 498-520. (doi:10.1037/h0070888)
-
(1933)
J. Educ. Psychol.
, vol.24
, pp. 498-520
-
-
Hotelling, H.1
-
8
-
-
27644496624
-
A compendium of signals and responses triggered by prodeath and prosurvival cytokines
-
doi:10.1074/mcp.M500158-MCP200
-
Gaudet, S., Janes, K. A., Albeck, J. G., Pace, E. A., Lauffenburger, D. A. & Sorger, P. K. 2005 A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol. Cell. Proteomics 4, 1569-1590. (doi:10.1074/mcp.M500158-MCP200)
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1569-1590
-
-
Gaudet, S.1
Janes, K.A.2
Albeck, J.G.3
Pace, E.A.4
Lauffenburger, D.A.5
Sorger, P.K.6
-
9
-
-
4544381664
-
Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data
-
doi:10.1089/1066527041887258
-
Janes, K. A., Kelly, J. R., Gaudet, S., Albeck, J. G., Sorger, P. K. & Lauffenburger, D. A. 2004 Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J. Comput. Biol. 11, 544-561. (doi:10.1089/1066527041887258)
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 544-561
-
-
Janes, K.A.1
Kelly, J.R.2
Gaudet, S.3
Albeck, J.G.4
Sorger, P.K.5
Lauffenburger, D.A.6
-
10
-
-
53749085729
-
Cytokine-induced signaling networks prioritize dynamic range over signal strength
-
doi:10.1016/j.cell.2008.08.034
-
Janes, K. A., Reinhardt, H. C. & Yaffe, M. B. 2008 Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 135, 343-354. (doi:10.1016/j.cell.2008.08.034)
-
(2008)
Cell
, vol.135
, pp. 343-354
-
-
Janes, K.A.1
Reinhardt, H.C.2
Yaffe, M.B.3
-
11
-
-
34547623194
-
Common effector processing mediates cell-specific responses to stimuli
-
doi:10.1038/nature06001
-
Miller-Jensen, K., Janes, K. A., Brugge, J. S. & Lauffenburger, D. A. 2007 Common effector processing mediates cell-specific responses to stimuli. Nature 448, 604-608. (doi:10.1038/nature06001)
-
(2007)
Nature
, vol.448
, pp. 604-608
-
-
Miller-Jensen, K.1
Janes, K.A.2
Brugge, J.S.3
Lauffenburger, D.A.4
-
12
-
-
33750696663
-
Effects of HER2 overexpression on cell signaling networks governing proliferation and migration
-
doi:10.1038/msb4100094
-
Wolf-Yadlin, A., Kumar, N., Zhang, Y., Hautaniemi, S., Zaman, M., Kim, H. D., Grantcharova, V., Lauffenburger, D. A. & White, F. M. 2006 Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol. Syst. Biol. 2, 54. (doi:10.1038/msb4100094)
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 54
-
-
Wolf-Yadlin, A.1
Kumar, N.2
Zhang, Y.3
Hautaniemi, S.4
Zaman, M.5
Kim, H.D.6
Grantcharova, V.7
Lauffenburger, D.A.8
White, F.M.9
-
13
-
-
0004270403
-
-
3rd edn. Oxford, UK: Pergamon Press
-
Landau, L. D. & Lifshits, E. M. 1976 Mechanics, vol. 1, 3rd edn. Oxford, UK: Pergamon Press.
-
(1976)
Mechanics
, vol.1
-
-
Landau, L.D.1
Lifshits, E.M.2
-
14
-
-
37649025842
-
A mathematical tool for exploring the dynamics of biological networks
-
doi:10.1073/pnas.0709955104
-
Barbano, P. E., Spivak, M., Flajolet, M., Nairn, A. C., Greengard, P. & Greengard, L. 2007 A mathematical tool for exploring the dynamics of biological networks. Proc. Natl Acad. Sci. USA 104, 19 169-19 174. (doi:10.1073/pnas.0709955104)
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 19169-19174
-
-
Barbano, P.E.1
Spivak, M.2
Flajolet, M.3
Nairn, A.C.4
Greengard, P.5
Greengard, L.6
-
15
-
-
52949144952
-
Top-down analysis of temporal hierarchy in biochemical reaction networks
-
doi:10.1371/journal.pcbi.1000177
-
Jamshidi, N. & Palsson, B. O. 2008 Top-down analysis of temporal hierarchy in biochemical reaction networks. PLoS Comput. Biol. 4, e1000177. (doi:10.1371/journal.pcbi.1000177)
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Jamshidi, N.1
Palsson, B.O.2
-
16
-
-
50649101988
-
From the determination of complex reaction mechanisms to systems biology
-
doi:10.1146/annurev.biochem.77.102507.115132
-
Ross, J. 2008 From the determination of complex reaction mechanisms to systems biology. Annu. Rev. Biochem. 77, 479-494. (doi:10.1146/annurev.biochem. 77.102507.115132)
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 479-494
-
-
Ross, J.1
-
19
-
-
67650360968
-
Unlimited multistability in multisite phosphorylation systems
-
doi:10.1038/nature08102
-
Thomson, M. & Gunawardena, J. 2009 Unlimited multistability in multisite phosphorylation systems. Nature 460, 274-277. (doi:10.1038/ nature08102)
-
(2009)
Nature
, vol.460
, pp. 274-277
-
-
Thomson, M.1
Gunawardena, J.2
-
21
-
-
62049085839
-
Modern multivariate statistical techniques regression, classification, and manifold learning
-
New York, NY: Springer
-
Izenman, A. J. 2008 Modern multivariate statistical techniques regression, classification, and manifold learning. In Springer texts in statistics, vol. xxv. New York, NY: Springer.
-
(2008)
Springer Texts in Statistics
, vol.25
-
-
Izenman, A.J.1
-
22
-
-
0033570090
-
Quantification of short term signaling by the epidermal growth factor receptor
-
doi:10.1074/jbc.274.42.30169
-
Kholodenko, B. N., Demin, O. V., Moehren, G. & Hoek, J. B. 1999 Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274, 30 169-30 181. (doi:10.1074/jbc.274.42.30169)
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 30169-30181
-
-
Kholodenko, B.N.1
Demin, O.V.2
Moehren, G.3
Hoek, J.B.4
-
23
-
-
10244219918
-
BIONETGEN: Software for rule-based modeling of signal transduction based on the interactions of molecular domains
-
doi:10.1093/bioinformatics/bth378
-
Blinov, M. L., Faeder, J. R., Goldstein, B. & Hlavacek, W. S. 2004 BIONETGEN: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. (doi:10.1093/bioinformatics/bth378)
-
(2004)
Bioinformatics
, vol.20
, pp. 3289-3291
-
-
Blinov, M.L.1
Faeder, J.R.2
Goldstein, B.3
Hlavacek, W.S.4
-
24
-
-
32044469862
-
A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity
-
doi:10.1016/j.biosystems.2005.06.014
-
Blinov, M. L., Faeder, J. R., Goldstein, B. & Hlavacek, W. S. 2006 A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems 83, 136-151. (doi:10.1016/j.biosystems.2005.06.014)
-
(2006)
Biosystems
, vol.83
, pp. 136-151
-
-
Blinov, M.L.1
Faeder, J.R.2
Goldstein, B.3
Hlavacek, W.S.4
-
25
-
-
72949108077
-
Pairing computation with experimentation: A powerful coupling for understanding T cell signalling
-
doi:10.1038/nri2688
-
Chakraborty, A. K. & Das, J. 2010 Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat. Rev. Immunol. 10, 59-71. (doi:10.1038/nri2688)
-
(2010)
Nat. Rev. Immunol.
, vol.10
, pp. 59-71
-
-
Chakraborty, A.K.1
Das, J.2
-
26
-
-
58249092059
-
Digital signaling and hysteresis characterize Ras activation in lymphoid cells
-
doi:10.1016/j.cell.2008.11.051
-
Das, J., Ho, M., Zikherman, J., Govern, C., Yang, M., Weiss, A., Chakraborty, A. K. & Roose, J. P. 2009 Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell 136, 337-351. (doi:10.1016/j.cell.2008.11.051)
-
(2009)
Cell
, vol.136
, pp. 337-351
-
-
Das, J.1
Ho, M.2
Zikherman, J.3
Govern, C.4
Yang, M.5
Weiss, A.6
Chakraborty, A.K.7
Roose, J.P.8
-
27
-
-
0036532226
-
Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability
-
doi:10.1016/s0955-0674(02)00314-9
-
Ferrell Jr, J. E. 2002 Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol. 14, 140-148. (doi:10.1016/s0955-0674(02)00314-9)
-
(2002)
Curr. Opin. Cell Biol.
, vol.14
, pp. 140-148
-
-
Ferrell Jr., J.E.1
-
28
-
-
0003490410
-
-
Reading, MA: Addison-Wesley Publications
-
Strogatz, S. H. 1994 Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering. Reading, MA: Addison-Wesley Publications.
-
(1994)
Nonlinear Dynamics and Chaos: with Applications to Physics, Biology, Chemistry, and Engineering
-
-
Strogatz, S.H.1
-
29
-
-
0037044575
-
The IκB-NF-κB signaling module: Temporal control and selective gene activation
-
doi:10.1126/science.1071914
-
Hoffmann, A., Levchenko, A., Scott, M. L. & Baltimore, D. 2002 The IκB-NF-κB signaling module: temporal control and selective gene activation. Science 298, 1241-1245. (doi:10.1126/science.1071914)
-
(2002)
Science
, vol.298
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
30
-
-
7444254365
-
Oscillations in NF-κB signaling control the dynamics of gene expression
-
doi:10.1126/science.1099962
-
Nelson, D. E. et al. 2004 Oscillations in NF-κB signaling control the dynamics of gene expression. Science 306, 704-708. (doi:10.1126/science. 1099962)
-
(2004)
Science
, vol.306
, pp. 704-708
-
-
Nelson, D.E.1
-
31
-
-
34249857117
-
Oscillation patterns in negative loops
-
doi:10.1073/pnas.0610759104
-
Pigolotti, S., Krishna, S. & Jensen, M. H. 2007 Oscillation patterns in negative loops. Proc. Natl Acad. Sci. USA 104, 6533-6537. (doi:10.1073/pnas.0610759104)
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 6533-6537
-
-
Pigolotti, S.1
Krishna, S.2
Jensen, M.H.3
-
33
-
-
0034704222
-
Nonlinear dimensionality reduction by locally linear embedding
-
doi:10.1126/science.290.5500.2323
-
Roweis, S. T. & Saul, L. K. 2000 Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323-2326. (doi:10.1126/science.290. 5500.2323)
-
(2000)
Science
, vol.290
, pp. 2323-2326
-
-
Roweis, S.T.1
Saul, L.K.2
-
34
-
-
77949289122
-
Clusters from higher order correlations
-
doi:10.1016/j.physleta.2010.02.021
-
Schulman, L. S. 2010 Clusters from higher order correlations. Phys. Lett. A 374, 1625-1630. (doi:10.1016/j.physleta.2010.02.021)
-
(2010)
Phys. Lett. A
, vol.374
, pp. 1625-1630
-
-
Schulman, L.S.1
|