-
1
-
-
33750314698
-
Collecting, andorganizing systematic sets of protein data
-
Albeck, J. G., MacBeath, G., White, F. M., Sorger, P. K., Lauffenburger, D. A. and Gaudet, S. (2006). Collecting and organizing systematic sets of protein data. Nat. Rev. Mol. Cell Biol. 7, 803-812.
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 803-812
-
-
Albeck, J.G.1
MacBeath, G.2
White, F.M.3
Sorger, P.K.4
Lauffenburger, D.A.Q.5
Gaudet, S.6
-
2
-
-
84883829346
-
Modeling a snap-action, variable-delay switch controlling extrinsic cell death
-
Albeck, J. G., Burke, J. M., Spencer, S. L., Lauffenburger, D. A. and Sorger, P. K. (2008). Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol. 6, 2831-2852.
-
(2008)
PLoS Biol.
, vol.6
, pp. 2831-2852
-
-
Albeck, J.G.1
Burke, J.M.2
Spencer, S.L.3
Lauffenburger, D.A.4
Sorger, P.K.5
-
3
-
-
33750533388
-
Physicochemical modelling of cell signalling pathways
-
Aldridge, B. B., Burke, J. M., Lauffenburger, D. A. and Sorger, P. K. (2006). Physicochemical modelling of cell signalling pathways. Nat. Cell Biol. 8, 1195-1203.
-
(2006)
Nat. Cell Biol.
, vol.8
, pp. 1195-1203
-
-
Aldridge, B.B.1
Burke, J.M.2
Lauffenburger, D.A.3
Sorger, P.K.4
-
4
-
-
65349179556
-
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling
-
Aldridge, B. B., Saez-Rodriguez, J., Muhlich, J. L., Sorger, P. K. and Lauffenburger, D. A. (2009). Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLOS Comput. Biol. 5, e1000340.
-
(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
-
5
-
-
27844541328
-
Modeling T cell antigen discrimination based on feedback control of digital ERK responses
-
Altan-Bonnet, G. and Germain, R. N. (2005). Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biol. 3, e356.
-
(2005)
PLoS Biol.
, vol.3
-
-
Altan-Bonnet, G.1
Germain, R.N.2
-
6
-
-
34047174559
-
A module of negative feedback regulators defines growth factor signaling
-
Amit, I., Citri, A., Shay, T., Lu, Y., Katz, M., Zhang, F., Tarcic, G., Siwak, D., Lahad, J., Jacob-Hirsch, J. et al. (2007). A module of negative feedback regulators defines growth factor signaling. Nat. Genet. 39, 503-512.
-
(2007)
Nat. Genet.
, vol.39
, pp. 503-512
-
-
Amit, I.1
Citri, A.2
Shay, T.3
Lu, Y.4
Katz, M.5
Zhang, F.6
Tarcic, G.7
Siwak, D.8
Lahad, J.9
Jacob-Hirsch, J.10
-
7
-
-
33751217466
-
Tumor morphology, andphenotypic evolution driven by selective pressure from the microenvironment
-
Anderson, A. R., Weaver, A. M., Cummings, P. T. and Quaranta, V. (2006). Tumor morphology, andphenotypic evolution driven by selective pressure from the microenvironment. Cell 127, 905-915.
-
(2006)
Cell
, vol.127
, pp. 905-915
-
-
Anderson, A.R.1
Weaver, A.M.2
Cummings, P.T.3
Quaranta, V.4
-
8
-
-
35748935235
-
Proteins, drug targets, andthe mechanisms they control: the simple truth about complex networks
-
Araujo, R. P., Liotta, L. A. and Petricoin, E. F. (2007). Proteins, drug targets, andthe mechanisms they control: the simple truth about complex networks. Nat. Rev. Drug Discov. 6, 871-880.
-
(2007)
Nat. Rev. Drug Discov.
, vol.6
, pp. 871-880
-
-
Araujo, R.P.1
Liotta, L.A.2
Petricoin, E.F.3
-
9
-
-
79952643760
-
Network news: innovations in 21st century systems biology
-
Arkin, A. P. and Schaffer, D. V. (2011). Network news: innovations in 21st century systems biology. Cell 144, 844-849.
-
(2011)
Cell
, vol.144
, pp. 844-849
-
-
Arkin, A.P.1
Schaffer, D.V.2
-
10
-
-
84868376130
-
Multiscale models of cell signaling
-
Bajikar, S. S. and Janes, K. A. (2012). Multiscale models of cell signaling. Ann. Biomed. Eng. 40, 2319-2327.
-
(2012)
Ann. Biomed. Eng.
, vol.40
, pp. 2319-2327
-
-
Bajikar, S.S.1
Janes, K.A.2
-
11
-
-
84862523863
-
Sequence analysis of mutations, andtranslocations across breast cancer subtypes
-
Banerji, S., Cibulskis, K., Rangel-Escareno, C., Brown, K. K., Carter, S. L., Frederick, A. M., Lawrence, M. S., Sivachenko, A. Y., Sougnez, C., Zou, L. et al. (2012). Sequence analysis of mutations, andtranslocations across breast cancer subtypes. Nature 486, 405-409.
-
(2012)
Nature
, vol.486
, pp. 405-409
-
-
Banerji, S.1
Cibulskis, K.2
Rangel-Escareno, C.3
Brown, K.K.4
Carter, S.L.5
Frederick, A.M.6
Lawrence, M.S.7
Sivachenko, A.Y.8
Sougnez, C.9
Zou, L.10
-
12
-
-
0344551102
-
Stochastic model of autocrine, andparacrine signals in cell culture assays
-
Batsilas, L., Berezhkovskii, A. M. and Shvartsman, S. Y. (2003). Stochastic model of autocrine, andparacrine signals in cell culture assays. Biophys. J. 85, 3659-3665.
-
(2003)
Biophys. J.
, vol.85
, pp. 3659-3665
-
-
Batsilas, L.1
Berezhkovskii, A.M.2
Shvartsman, S.Y.3
-
13
-
-
4544246088
-
Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis
-
Bentele, M., Lavrik, I., Ulrich, M., Stösser, S., Heermann, D. W., Kalthoff, H., Krammer, P. H. and Eils, R. (2004). Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J. Cell Biol. 166, 839-851.
-
(2004)
J. Cell Biol.
, vol.166
, pp. 839-851
-
-
Bentele, M.1
Lavrik, I.2
Ulrich, M.3
Stösser, S.4
Heermann, D.W.5
Kalthoff, H.6
Krammer, P.H.7
Eils, R.8
-
14
-
-
80051680291
-
A continuum model for tumour suppression
-
Berger, A. H., Knudson, A. G. and Pandolfi, P. P. (2011). A continuum model for tumour suppression. Nature 476, 163-169.
-
(2011)
Nature
, vol.476
, pp. 163-169
-
-
Berger, A.H.1
Knudson, A.G.2
Pandolfi, P.P.3
-
15
-
-
84862318594
-
Cross-talk between receptor tyrosine kinase, andtumor necrosis factor-alpha signaling networks regulates apoptosis but not proliferation
-
M111013292
-
Beyer, E. M. and MacBeath, G. (2012). Cross-talk between receptor tyrosine kinase, andtumor necrosis factor-alpha signaling networks regulates apoptosis but not proliferation. Mol. Cell Proteomics 11, M111.013292.
-
(2012)
Mol. Cell Proteomics
, vol.11
-
-
Beyer, E.M.1
MacBeath, G.2
-
16
-
-
0842266708
-
Introductory science, andmathematics education for 21st-Century biologists
-
Bialek, W. and Botstein, D. (2004). Introductory science, andmathematics education for 21st-Century biologists. Science 303, 788-790.
-
(2004)
Science
, vol.303
, pp. 788-790
-
-
Bialek, W.1
Botstein, D.2
-
17
-
-
27144517984
-
Interlinked fast, andslow positive feedback loops drive reliable cell decisions
-
Brandman, O., Ferrell, J. E., Jr, Li, R. and Meyer, T. (2005). Interlinked fast, andslow positive feedback loops drive reliable cell decisions. Science 310, 496-498.
-
(2005)
Science
, vol.310
, pp. 496-498
-
-
Brandman, O.1
Ferrell Jr., J.E.2
Li, R.3
Meyer, T.4
-
18
-
-
78650647490
-
A comprehensive map of the mTOR signaling network
-
Caron, E., Ghosh, S., Matsuoka, Y., Ashton-Beaucage, D., Therrien, M., Lemieux, S., Perreault, C., Roux, P. P. and Kitano, H. (2010). A comprehensive map of the mTOR signaling network. Mol. Syst. Biol. 6, 453.
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 453
-
-
Caron, E.1
Ghosh, S.2
Matsuoka, Y.3
Ashton-Beaucage, D.4
Therrien, M.5
Lemieux, S.6
Perreault, C.7
Roux, P.P.8
Kitano, H.9
-
19
-
-
78651458656
-
AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression, andactivity
-
Chandarlapaty, S., Sawai, A., Scaltriti, M., Rodrik-Outmezguine, V., Grbovic-Huezo, O., Serra, V., Majumder, P. K., Baselga, J. and Rosen, N. (2011). AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression, andactivity. Cancer Cell 19, 58-71.
-
(2011)
Cancer Cell
, vol.19
, pp. 58-71
-
-
Chandarlapaty, S.1
Sawai, A.2
Scaltriti, M.3
Rodrik-Outmezguine, V.4
Grbovic-Huezo, O.5
Serra, V.6
Majumder, P.K.7
Baselga, J.8
Rosen, N.9
-
20
-
-
77954522738
-
Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli
-
Chatterjee, M. S., Purvis, J. E., Brass, L. F. and Diamond, S. L. (2010). Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli. Nat. Biotechnol. 28, 727-732.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 727-732
-
-
Chatterjee, M.S.1
Purvis, J.E.2
Brass, L.F.3
Diamond, S.L.4
-
21
-
-
84867581908
-
Designing synthetic regulatory networks capable of self-organizing cell polarization
-
Chau, A. H., Walter, J. M., Gerardin, J., Tang, C. and Lim, W. A. (2012). Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell 151, 320-332.
-
(2012)
Cell
, vol.151
, pp. 320-332
-
-
Chau, A.H.1
Walter, J.M.2
Gerardin, J.3
Tang, C.4
Lim, W.A.5
-
22
-
-
23244460597
-
Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis
-
Chen, Z., Trotman, L. C., Shaffer, D., Lin, H. K., Dotan, Z. A., Niki, M., Koutcher, J. A., Scher, H. I., Ludwig, T., Gerald, W. et al. (2005). Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis. Nature 436, 725-730.
-
(2005)
Nature
, vol.436
, pp. 725-730
-
-
Chen, Z.1
Trotman, L.C.2
Shaffer, D.3
Lin, H.K.4
Dotan, Z.A.5
Niki, M.6
Koutcher, J.A.7
Scher, H.I.8
Ludwig, T.9
Gerald, W.10
-
23
-
-
58549083142
-
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
-
Chen, W. W., Schoeberl, B., Jasper, P. J., Niepel, M., Nielsen, U. B., Lauffenburger, D. A. and Sorger, P. K. (2009). Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol. Syst. Biol. 5, 239.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 239
-
-
Chen, W.W.1
Schoeberl, B.2
Jasper, P.J.3
Niepel, M.4
Nielsen, U.B.5
Lauffenburger, D.A.6
Sorger, P.K.7
-
24
-
-
79952173562
-
The specificity of innate immune responses is enforced by repression of interferon response elements by NF-kB p50
-
Cheng, C. S., Feldman, K. E., Lee, J., Verma, S., Huang, D. B., Huynh, K., Chang, M., Ponomarenko, J. V., Sun, S. C., Benedict, C. A. et al. (2011). The specificity of innate immune responses is enforced by repression of interferon response elements by NF-kB p50. Sci. Signal. 4, ra11.
-
(2011)
Sci. Signal.
, vol.4
-
-
Cheng, C.S.1
Feldman, K.E.2
Lee, J.3
Verma, S.4
Huang, D.B.5
Huynh, K.6
Chang, M.7
Ponomarenko, J.V.8
Sun, S.C.9
Benedict, C.A.10
-
25
-
-
80054841161
-
Information transduction capacity of noisy biochemical signaling networks
-
Cheong, R., Rhee, A., Wang, C. J., Nemenman, I. and Levchenko, A. (2011). Information transduction capacity of noisy biochemical signaling networks. Science 334, 354-358.
-
(2011)
Science
, vol.334
, pp. 354-358
-
-
Cheong, R.1
Rhee, A.2
Wang, C.J.3
Nemenman, I.4
Levchenko, A.5
-
26
-
-
71149092283
-
Dynamics, andvariability of ERK2 response to EGF in individual living cells
-
Cohen-Saidon, C., Cohen, A. A., Sigal, A., Liron, Y. and Alon, U. (2009). Dynamics, andvariability of ERK2 response to EGF in individual living cells. Mol. Cell 36, 885-893.
-
(2009)
Mol. Cell
, vol.36
, pp. 885-893
-
-
Cohen-Saidon, C.1
Cohen, A.A.2
Sigal, A.3
Liron, Y.4
Alon, U.5
-
27
-
-
47149092247
-
An inducible autocrine cascade regulates rat hepatocyte proliferation, andapoptosis responses to tumor necrosis factor-alpha
-
Cosgrove, B. D., Cheng, C., Pritchard, J. R., Stolz, D. B., Lauffenburger, D. A. and Griffith, L. G. (2008). An inducible autocrine cascade regulates rat hepatocyte proliferation, andapoptosis responses to tumor necrosis factor-alpha. Hepatology 48, 276-288.
-
(2008)
Hepatology
, vol.48
, pp. 276-288
-
-
Cosgrove, B.D.1
Cheng, C.2
Pritchard, J.R.3
Stolz, D.B.4
Lauffenburger, D.A.5
Griffith, L.G.6
-
28
-
-
77953593640
-
Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation
-
Cosgrove, B. D., Alexopoulos, L. G., Hang, T. C., Hendriks, B. S., Sorger, P. K., Griffith, L. G. and Lauffenburger, D. A. (2010). Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol. Biosyst. 6, 1195-1206.
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 1195-1206
-
-
Cosgrove, B.D.1
Alexopoulos, L.G.2
Hang, T.C.3
Hendriks, B.S.4
Sorger, P.K.5
Griffith, L.G.6
Lauffenburger, D.A.7
-
29
-
-
24944586285
-
Achieving stability of lipopolysaccharide-induced NF-kappaB activation
-
Covert, M. W., Leung, T. H., Gaston, J. E. and Baltimore, D. (2005). Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Science 309, 1854-1857.
-
(2005)
Science
, vol.309
, pp. 1854-1857
-
-
Covert, M.W.1
Leung, T.H.2
Gaston, J.E.3
Baltimore, D.4
-
30
-
-
33744744785
-
Understanding bistability in complex enzyme-driven reaction networks
-
Craciun, G., Tang, Y. and Feinberg, M. (2006). Understanding bistability in complex enzyme-driven reaction networks. Proc. Natl. Acad. Sci. USA 103, 8697-8702.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 8697-8702
-
-
Craciun, G.1
Tang, Y.2
Feinberg, M.3
-
31
-
-
0034942833
-
Quantitative analysis of the EGF receptor autocrine system reveals cryptic regulation of cell response by ligand capture
-
DeWitt, A. E., Dong, J. Y., Wiley, H. S. and Lauffenburger, D. A. (2001). Quantitative analysis of the EGF receptor autocrine system reveals cryptic regulation of cell response by ligand capture. J. Cell Sci. 114, 2301-2313.
-
(2001)
J. Cell Sci.
, vol.114
, pp. 2301-2313
-
-
DeWitt, A.E.1
Dong, J.Y.2
Wiley, H.S.3
Lauffenburger, D.A.4
-
32
-
-
33749506763
-
From in vivo to in silico biology, andback
-
Di Ventura, B., Lemerle, C., Michalodimitrakis, K. and Serrano, L. (2006). From in vivo to in silico biology, andback. Nature 443, 527-533.
-
(2006)
Nature
, vol.443
, pp. 527-533
-
-
Di Ventura, B.1
Lemerle, C.2
Michalodimitrakis, K.3
Serrano, L.4
-
33
-
-
84859765844
-
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer
-
Duncan, J. S., Whittle, M. C., Nakamura, K., Abell, A. N., Midland, A. A., Zawistowski, J. S., Johnson, N. L., Granger, D. A., Jordan, N. V., Darr, D. B. et al. (2012). Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer. Cell 149, 307-321.
-
(2012)
Cell
, vol.149
, pp. 307-321
-
-
Duncan, J.S.1
Whittle, M.C.2
Nakamura, K.3
Abell, A.N.4
Midland, A.A.5
Zawistowski, J.S.6
Johnson, N.L.7
Granger, D.A.8
Jordan, N.V.9
Darr, D.B.10
-
34
-
-
56749102636
-
Regulatory activity revealed by dynamic correlations in gene expression noise
-
Dunlop, M. J., Cox, R. S., 3rd, Levine, J. H., Murray, R. M. and Elowitz, M. B. (2008). Regulatory activity revealed by dynamic correlations in gene expression noise. Nat. Genet. 40, 1493-1498.
-
(2008)
Nat. Genet.
, vol.40
, pp. 1493-1498
-
-
Dunlop, M.J.1
Cox, R.S.2
Levine, J.H.3
Murray, R.M.4
Elowitz, M.B.5
-
35
-
-
84865094962
-
Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations
-
Dworkin, M., Mukherjee, S., Jayaprakash, C. and Das, J. (2012). Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations. J. R. Soc. Interface 9, 1824-1835.
-
(2012)
J. R. Soc. Interface
, vol.9
, pp. 1824-1835
-
-
Dworkin, M.1
Mukherjee, S.2
Jayaprakash, C.3
Das, J.4
-
36
-
-
84862584058
-
Whole-genome analysis informs breast cancer response to aromatase inhibition
-
Ellis, M. J., Ding, L., Shen, D., Luo, J., Suman, V. J., Wallis, J. W., Van Tine, B. A., Hoog, J., Goiffon, R. J., Goldstein, T. C. et al. (2012). Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486, 353-360.
-
(2012)
Nature
, vol.486
, pp. 353-360
-
-
Ellis, M.J.1
Ding, L.2
Shen, D.3
Luo, J.4
Suman, V.J.5
Wallis, J.W.6
Van Tine, B.A.7
Hoog, J.8
Goiffon, R.J.9
Goldstein, T.C.10
-
37
-
-
0035905782
-
Modelling cellular behaviour
-
Endy, D. and Brent, R. (2001). Modelling cellular behaviour. Nature 409, 391-395.
-
(2001)
Nature
, vol.409
, pp. 391-395
-
-
Endy, D.1
Brent, R.2
-
38
-
-
0023531427
-
Chemical-reaction network structure, andthe stability of complex isothermal reactors.1. The deficiency-zero, anddeficiency-one theorems.
-
Feinberg, M. (1987). Chemical-reaction network structure, andthe stability of complex isothermal reactors. 1. The deficiency-zero, anddeficiency-one theorems. Chem. Eng. Sci. 42, 2229-2268.
-
(1987)
Chem. Eng. Sci.
, vol.42
, pp. 2229-2268
-
-
Feinberg, M.1
-
39
-
-
0023842283
-
Chemical-reaction network structure, andthe stability of complex isothermal reactors. 2. Multiple steady-states for networks of deficiency one.
-
Feinberg, M. (1988). Chemical-reaction network structure, andthe stability of complex isothermal reactors. 2. Multiple steady-states for networks of deficiency one. Chem. Eng. Sci. 43, 1-25.
-
(1988)
Chem. Eng. Sci.
, vol.43
, pp. 1-25
-
-
Feinberg, M.1
-
40
-
-
50149090966
-
Variability, androbustness in T cell activation from regulated heterogeneity in protein levels
-
Feinerman, O., Veiga, J., Dorfman, J. R., Germain, R. N. and Altan-Bonnet, G. (2008). Variability, androbustness in T cell activation from regulated heterogeneity in protein levels. Science 321, 1081-1084.
-
(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
-
41
-
-
71149086936
-
Signaling motifs, andWeber's law
-
Ferrell, J. E., Jr (2009). Signaling motifs, andWeber's law. Mol. Cell 36, 724-727.
-
(2009)
Mol. Cell
, vol.36
, pp. 724-727
-
-
Ferrell, J.E.Jr.1
-
42
-
-
79957573284
-
Strong negative feedback from Erk to Raf confers robustness to MAPK signalling
-
Fritsche-Guenther, R., Witzel, F., Sieber, A., Herr, R., Schmidt, N., Braun, S., Brummer, T., Sers, C. and Blüthgen, N. (2011). Strong negative feedback from Erk to Raf confers robustness to MAPK signalling. Mol. Syst. Biol. 7, 489.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 489
-
-
Fritsche-Guenther, R.1
Witzel, F.2
Sieber, A.3
Herr, R.4
Schmidt, N.5
Braun, S.6
Brummer, T.7
Sers, C.8
Blüthgen, N.9
-
43
-
-
78049316294
-
Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection
-
Garmaroudi, F. S., Marchant, D., Si, X., Khalili, A., Bashashati, A., Wong, B. W., Tabet, A., Ng, R. T., Murphy, K., Luo, H. et al. (2010). Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc. Natl. Acad. Sci. USA 107, 17053-17058.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 17053-17058
-
-
Garmaroudi, F.S.1
Marchant, D.2
Si, X.3
Khalili, A.4
Bashashati, A.5
Wong, B.W.6
Tabet, A.7
Ng, R.T.8
Murphy, K.9
Luo, H.10
-
44
-
-
11144325691
-
Partial least-squares regression -a tutorial
-
Geladi, P. and Kowalski, B. R. (1986). Partial least-squares regression -a tutorial. Anal. Chim. Acta 185, 1-17.
-
(1986)
Anal. Chim. Acta
, vol.185
, pp. 1-17
-
-
Geladi, P.1
Kowalski, B.R.2
-
45
-
-
77649101892
-
Protein dynamics in drug combinations: a linear superposition of individual-drug responses
-
Geva-Zatorsky, N., Dekel, E., Cohen, A. A., Danon, T., Cohen, L. and Alon, U. (2010). Protein dynamics in drug combinations: a linear superposition of individual-drug responses. Cell 140, 643-651.
-
(2010)
Cell
, vol.140
, pp. 643-651
-
-
Geva-Zatorsky, N.1
Dekel, E.2
Cohen, A.A.3
Danon, T.4
Cohen, L.5
Alon, U.6
-
46
-
-
80052749408
-
Compensatory pathways induced by MEK inhibition are effective drug targets for combination therapy against castration-resistant prostate cancer
-
Gioeli, D., Wunderlich, W., Sebolt-Leopold, J., Bekiranov, S., Wulfkuhle, J. D., Petricoin, E. F., 3rd, Conaway, M. and Weber, M. J. (2011). Compensatory pathways induced by MEK inhibition are effective drug targets for combination therapy against castration-resistant prostate cancer. Mol. Cancer Ther. 10, 1581-1590.
-
(2011)
Mol. Cancer Ther.
, vol.10
, pp. 1581-1590
-
-
Gioeli, D.1
Wunderlich, W.2
Sebolt-Leopold, J.3
Bekiranov, S.4
Wulfkuhle, J.D.5
Petricoin, E.F.6
Conaway, M.7
Weber, M.J.8
-
47
-
-
71149092489
-
Evidence that fold-change,, andnot absolute level, of beta-catenin dictates Wnt signaling
-
Goentoro, L. and Kirschner, M. W. (2009). Evidence that fold-change,, andnot absolute level, of beta-catenin dictates Wnt signaling. Mol. Cell 36, 872-884.
-
(2009)
Mol. Cell
, vol.36
, pp. 872-884
-
-
Goentoro, L.1
Kirschner, M.W.2
-
48
-
-
71149099313
-
The incoherent feedforward loop can provide fold-change detection in gene regulation
-
Goentoro, L., Shoval, O., Kirschner, M. W. and Alon, U. (2009). The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol. Cell 36, 894-899.
-
(2009)
Mol. Cell
, vol.36
, pp. 894-899
-
-
Goentoro, L.1
Shoval, O.2
Kirschner, M.W.3
Alon, U.4
-
49
-
-
58549118075
-
Linear combinations of docking affinities explain quantitative differences in RTK signaling
-
Gordus, A., Krall, J. A., Beyer, E. M., Kaushansky, A., Wolf-Yadlin, A., Sevecka, M., Chang, B. H., Rush, J. and MacBeath, G. (2009). Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol. Syst. Biol. 5, 235.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 235
-
-
Gordus, A.1
Krall, J.A.2
Beyer, E.M.3
Kaushansky, A.4
Wolf-Yadlin, A.5
Sevecka, M.6
Chang, B.H.7
Rush, J.8
MacBeath, G.9
-
50
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
Gutenkunst, R. N., Waterfall, J. J., Casey, F. P., Brown, K. S., Myers, C. R. and Sethna, J. P. (2007). Universally sloppy parameter sensitivities in systems biology models. PLOS Comput. Biol. 3, 1871-1878.
-
(2007)
PLOS Comput. Biol.
, vol.3
, pp. 1871-1878
-
-
Gutenkunst, R.N.1
Waterfall, J.J.2
Casey, F.P.3
Brown, K.S.4
Myers, C.R.5
Sethna, J.P.6
-
51
-
-
84866872269
-
Parameter-free model discrimination criterion based on steady-state coplanarity
-
Harrington, H. A., Ho, K. L., Thorne, T. and Stumpf, M. P. (2012). Parameter-free model discrimination criterion based on steady-state coplanarity. Proc. Natl. Acad. Sci. USA 109, 15746-15751.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 15746-15751
-
-
Harrington, H.A.1
Ho, K.L.2
Thorne, T.3
Stumpf, M.P.4
-
52
-
-
77949685981
-
RAF inhibitors prime wild-type RAF to activate the MAPK pathway, andenhance growth
-
Hatzivassiliou, G., Song, K., Yen, I., Brandhuber, B. J. Anderson, D. J., Alvarado, R., Ludlam, M. J., Stokoe, D., Gloor, S. L., Vigers, G. et al. (2010). RAF inhibitors prime wild-type RAF to activate the MAPK pathway, andenhance growth. Nature 464, 431-435.
-
(2010)
Nature
, vol.464
, pp. 431-435
-
-
Hatzivassiliou, G.1
Song, K.2
Yen, I.3
Brandhuber, B.J.4
Anderson, D.J.5
Alvarado, R.6
Ludlam, M.J.7
Stokoe, D.8
Gloor, S.L.9
Vigers, G.10
-
53
-
-
80755141377
-
Ensuring congruency in multiscale modeling: towards linking agent based, andcontinuum biomechanical models of arterial adaptation
-
Hayenga, H. N., Thorne, B. C., Peirce, S. M. and Humphrey, J. D. (2011). Ensuring congruency in multiscale modeling: towards linking agent based, andcontinuum biomechanical models of arterial adaptation. Ann. Biomed. Eng. 39, 2669-2682.
-
(2011)
Ann. Biomed. Eng.
, vol.39
, pp. 2669-2682
-
-
Hayenga, H.N.1
Thorne, B.C.2
Peirce, S.M.3
Humphrey, J.D.4
-
54
-
-
0037044575
-
The IkappaBNF-kappaB signaling module: temporal control, andselective gene activation
-
Hoffmann, A., Levchenko, A., Scott, M. L. and Baltimore, D. (2002). The IkappaBNF-kappaB signaling module: temporal control, andselective gene activation. Science 298, 1241-1245.
-
(2002)
Science
, vol.298
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
55
-
-
70350517075
-
Deciphering signaling outcomes from a system of complex networks
-
Hsueh, R. C., Natarajan, M., Fraser, I., Pond, B., Liu, J., Mumby, S., Han, H., Jiang, L. I., Simon, M. I., Taussig, R. et al. (2009). Deciphering signaling outcomes from a system of complex networks. Sci. Signal. 2, ra22.
-
(2009)
Sci. Signal.
, vol.2
-
-
Hsueh, R.C.1
Natarajan, M.2
Fraser, I.3
Pond, B.4
Liu, J.5
Mumby, S.6
Han, H.7
Jiang, L.I.8
Simon, M.I.9
Taussig, R.10
-
56
-
-
0029790351
-
Ultrasensitivity in the mitogen-activated protein kinase cascade
-
Huang, C. Y. and Ferrell, J. E., Jr (1996). Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. USA 93, 10078-10083.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 10078-10083
-
-
Huang, C.Y.1
Ferrell, J.E.Jr.2
-
57
-
-
70350452746
-
Integrating proteomic, transcriptional,, andinteractome data reveals hidden components of signaling, andregulatory networks
-
Huang, S. S. and Fraenkel, E. (2009). Integrating proteomic, transcriptional,, andinteractome data reveals hidden components of signaling, andregulatory networks. Sci. Signal. 2, ra40.
-
(2009)
Sci. Signal.
, vol.2
-
-
Huang, S.S.1
Fraenkel, E.2
-
58
-
-
3242683662
-
Single cell profiling of potentiated phospho-protein networks in cancer cells
-
Irish, J. M., Hovland, R., Krutzik, P. O., Perez, O. D., Bruserud, O., Gjertsen, B. T. and Nolan, G. P. (2004). Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118, 217-228.
-
(2004)
Cell
, vol.118
, pp. 217-228
-
-
Irish, J.M.1
Hovland, R.2
Krutzik, P.O.3
Perez, O.D.4
Bruserud, O.5
Gjertsen, B.T.6
Nolan, G.P.7
-
59
-
-
33644833555
-
Mapping normal, andcancer cell signalling networks: towards single-cell proteomics
-
Irish, J. M., Kotecha, N. and Nolan, G. P. (2006). Mapping normal, andcancer cell signalling networks: towards single-cell proteomics. Nat. Rev. Cancer 6, 146-155.
-
(2006)
Nat. Rev. Cancer
, vol.6
, pp. 146-155
-
-
Irish, J.M.1
Kotecha, N.2
Nolan, G.P.3
-
60
-
-
77954522737
-
Paring down signaling complexity
-
Janes, K. A. (2010). Paring down signaling complexity. Nat. Biotechnol. 28, 681-682.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 681-682
-
-
Janes, K.A.1
-
61
-
-
80055108192
-
RUNX1, andits understudied role in breast cancer
-
Janes, K. A. (2011). RUNX1, andits understudied role in breast cancer. Cell Cycle 10, 3461-3465.
-
(2011)
Cell Cycle
, vol.10
, pp. 3461-3465
-
-
Janes, K.A.1
-
62
-
-
32044471825
-
A biological approach to computational models of proteomic networks
-
Janes, K. A. and Lauffenburger, D. A. (2006). A biological approach to computational models of proteomic networks. Curr. Opin. Chem. Biol. 10, 73-80.
-
(2006)
Curr. Opin. Chem. Biol.
, vol.10
, pp. 73-80
-
-
Janes, K.A.1
Lauffenburger, D.A.2
-
63
-
-
33750351769
-
Data-driven modelling of signal-transduction networks
-
Janes, K. A. and Yaffe, M. B. (2006). Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell Biol. 7, 820-828.
-
(2006)
Nat. Rev. Mol. Cell Biol.
, vol.7
, pp. 820-828
-
-
Janes, K.A.1
Yaffe, M.B.2
-
64
-
-
28844441230
-
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis
-
Janes, K. A., Albeck, J. G., Gaudet, S., Sorger, P. K., Lauffenburger, D. A. and Yaffe, M. B. (2005). A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 310, 1646-1653.
-
(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
-
65
-
-
33646036758
-
The response of human epithelial cells to TNF involves an inducible autocrine cascade
-
Janes, K. A., Gaudet, S., Albeck, J. G., Nielsen, U. B., Lauffenburger, D. A. and Sorger, P. K. (2006). The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell 124, 1225-1239.
-
(2006)
Cell
, vol.124
, pp. 1225-1239
-
-
Janes, K.A.1
Gaudet, S.2
Albeck, J.G.3
Nielsen, U.B.4
Lauffenburger, D.A.5
Sorger, P.K.6
-
66
-
-
53749085729
-
Cytokine-induced signaling networks prioritize dynamic range over signal strength
-
Janes, K. A., Reinhardt, H. C. and Yaffe, M. B. (2008). Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 135, 343-354.
-
(2008)
Cell
, vol.135
, pp. 343-354
-
-
Janes, K.A.1
Reinhardt, H.C.2
Yaffe, M.B.3
-
67
-
-
77951643590
-
Identifying single-cell molecular programs by stochastic profiling
-
Janes, K. A.,Wang,C. C., Holmberg, K. J., Cabral, K. andBrugge, J. S. (2010). Identifying single-cell molecular programs by stochastic profiling. Nat. Methods 7, 311-317.
-
(2010)
Nat. Methods
, vol.7
, pp. 311-317
-
-
Janes, K.A.1
Wang, C.2
Holmberg, K.J.3
Cabral, K.4
Brugge, J.S.5
-
68
-
-
84864944169
-
Modeling the latent dimensions of multivariate signaling datasets
-
Jensen, K. J. and Janes, K. A. (2012). Modeling the latent dimensions of multivariate signaling datasets. Phys. Biol. 9, 045004.
-
(2012)
Phys. Biol.
, vol.9
, pp. 045004
-
-
Jensen, K.J.1
Janes, K.A.2
-
69
-
-
84872513387
-
An ERK-p38 subnetwork coordinates host cell apoptosis, andnecrosis during coxsackievirus B3 infection
-
Jensen, K. J., Garmaroudi, F. S., Zhang, J., Lin, J., Boroomand, S., Zhang, M., Luo, Z., Yang, D., Luo, H., McManus, B. M. et al. (2013). An ERK-p38 subnetwork coordinates host cell apoptosis, andnecrosis during coxsackievirus B3 infection. Cell Host Microbe 13, 67-76.
-
(2013)
Cell Host Microbe
, vol.13
, pp. 67-76
-
-
Jensen, K.J.1
Garmaroudi, F.S.2
Zhang, J.3
Lin, J.4
Boroomand, S.5
Zhang, M.6
Luo, Z.7
Yang, D.8
Luo, H.9
McManus, B.M.10
-
70
-
-
57049151271
-
Fluctuations of intracellular forces during cell protrusion
-
Ji, L., Lim, J. and Danuser, G. (2008). Fluctuations of intracellular forces during cell protrusion. Nat. Cell Biol. 10, 1393-1400.
-
(2008)
Nat. Cell Biol.
, vol.10
, pp. 1393-1400
-
-
Ji, L.1
Lim, J.2
Danuser, G.3
-
71
-
-
72149101924
-
Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells
-
Jørgensen, C., Sherman, A., Chen, G. I., Pasculescu, A., Poliakov, A., Hsiung, M., Larsen, B., Wilkinson, D. G., Linding, R. and Pawson, T. (2009). Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326, 1502-1509.
-
(2009)
Science
, vol.326
, pp. 1502-1509
-
-
Jørgensen, C.1
Sherman, A.2
Chen, G.I.3
Pasculescu, A.4
Poliakov, A.5
Hsiung, M.6
Larsen, B.7
Wilkinson, D.G.8
Linding, R.9
Pawson, T.10
-
72
-
-
77953562059
-
Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context
-
Joslin, E. J., Shankaran, H., Opresko, L. K., Bollinger, N., Lauffenburger, D. A. and Wiley, H. S. (2010). Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context. Mol. Biosyst. 6, 1293-1306.
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 1293-1306
-
-
Joslin, E.J.1
Shankaran, H.2
Opresko, L.K.3
Bollinger, N.4
Lauffenburger, D.A.5
Wiley, H.S.6
-
73
-
-
34247127891
-
Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response
-
Kemp, M. L., Wille, L., Lewis, C. L., Nicholson, L. B. and Lauffenburger, D. A. (2007). Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response. J. Immunol. 178, 4984-4992.
-
(2007)
J. Immunol.
, vol.178
, pp. 4984-4992
-
-
Kemp, M.L.1
Wille, L.2
Lewis, C.L.3
Nicholson, L.B.4
Lauffenburger, D.A.5
-
74
-
-
68749116324
-
Cell-cell interaction networks regulate blood stem, andprogenitor cell fate
-
Kirouac, D. C., Madlambayan, G. J., Yu, M., Sykes, E. A., Ito, C. and Zandstra, P. W. (2009). Cell-cell interaction networks regulate blood stem, andprogenitor cell fate. Mol. Syst. Biol. 5, 293.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 293
-
-
Kirouac, D.C.1
Madlambayan, G.J.2
Yu, M.3
Sykes, E.A.4
Ito, C.5
Zandstra, P.W.6
-
75
-
-
84862167967
-
Creating, andanalyzing pathway, andprotein interaction compendia for modelling signal transduction networks
-
Kirouac, D. C., Saez-Rodriguez, J., Swantek, J., Burke, J. M., Lauffenburger, D. A. and Sorger, P. K. (2012). Creating, andanalyzing pathway, andprotein interaction compendia for modelling signal transduction networks. BMC Syst. Biol. 6, 29.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 29
-
-
Kirouac, D.C.1
Saez-Rodriguez, J.2
Swantek, J.3
Burke, J.M.4
Lauffenburger, D.A.5
Sorger, P.K.6
-
76
-
-
80052211582
-
Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling, anddrug binding
-
Kleiman, L. B., Maiwald, T., Conzelmann, H., Lauffenburger, D. A. and Sorger, P. K. (2011). Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling, anddrug binding. Mol. Cell 43, 723-737.
-
(2011)
Mol. Cell
, vol.43
, pp. 723-737
-
-
Kleiman, L.B.1
Maiwald, T.2
Conzelmann, H.3
Lauffenburger, D.A.4
Sorger, P.K.5
-
77
-
-
34948840834
-
Ensemble modeling for analysis of cell signaling dynamics
-
Kuepfer, L., Peter, M., Sauer, U. and Stelling, J. (2007). Ensemble modeling for analysis of cell signaling dynamics. Nat. Biotechnol. 25, 1001-1006.
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 1001-1006
-
-
Kuepfer, L.1
Peter, M.2
Sauer, U.3
Stelling, J.4
-
78
-
-
36849091481
-
Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response
-
Kumar, D., Srikanth, R., Ahlfors, H., Lahesmaa, R. and Rao, K. V. (2007a). Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol. Syst. Biol. 3, 150.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 150
-
-
Kumar, D.1
Srikanth, R.2
Ahlfors, H.3
Lahesmaa, R.4
Rao, K.V.5
-
79
-
-
33846554088
-
Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data
-
Kumar, N., Wolf-Yadlin, A., White, F. M. and Lauffenburger, D. A. (2007b). Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLOS Comput. Biol. 3, e4.
-
(2007)
PLOS Comput. Biol.
, vol.3
-
-
Kumar, N.1
Wolf-Yadlin, A.2
White, F.M.3
Lauffenburger, D.A.4
-
80
-
-
0036080430
-
Do morphogen gradients arise by diffusion?
-
Lander, A. D., Nie, Q. and Wan, F. Y. (2002). Do morphogen gradients arise by diffusion? Dev. Cell 2, 785-796.
-
(2002)
Dev. Cell
, vol.2
, pp. 785-796
-
-
Lander, A.D.1
Nie, Q.2
Wan, F.Y.3
-
81
-
-
79953102845
-
In vivo systems analysis identifies spatial, andtemporal aspects of the modulation of TNF-a-induced apoptosis, andproliferation by MAPKs
-
Lau, K. S., Juchheim, A. M., Cavaliere, K. R., Philips, S. R., Lauffenburger, D. A. and Haigis, K. M. (2011). In vivo systems analysis identifies spatial, andtemporal aspects of the modulation of TNF-a-induced apoptosis, andproliferation by MAPKs. Sci. Signal. 4, ra16.
-
(2011)
Sci. Signal.
, vol.4
-
-
Lau, K.S.1
Juchheim, A.M.2
Cavaliere, K.R.3
Philips, S.R.4
Lauffenburger, D.A.5
Haigis, K.M.6
-
82
-
-
84866706825
-
Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-a-induced apoptosis in the intestinal epithelium
-
Lau, K. S., Cortez-Retamozo, V., Philips, S. R., Pittet, M. J., Lauffenburger, D. A. and Haigis, K. M. (2012). Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-a-induced apoptosis in the intestinal epithelium. PLoS Biol. 10, e1001393.
-
(2012)
PLoS Biol.
, vol.10
-
-
Lau, K.S.1
Cortez-Retamozo, V.2
Philips, S.R.3
Pittet, M.J.4
Lauffenburger, D.A.5
Haigis, K.M.6
-
83
-
-
4243067196
-
The roles of APC, andAxin derived from experimental, andtheoretical analysis of the Wnt pathway
-
Lee, E., Salic, A., Krüger, R., Heinrich, R. and Kirschner, M. W. (2003). The roles of APC, andAxin derived from experimental, andtheoretical analysis of the Wnt pathway. PLoS Biol. 1, e10.
-
(2003)
PLoS Biol.
, vol.1
-
-
Lee, E.1
Salic, A.2
Krüger, R.3
Heinrich, R.4
Kirschner, M.W.5
-
84
-
-
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., Sorger, P. K., MacBeath, G. and Yaffe, M. B. (2012). Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 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
Sorger, P.K.5
MacBeath, G.6
Yaffe, M.B.7
-
85
-
-
0001641514
-
Mutations of bacteria from virus sensitivity to virus resistance
-
Luria, S. E. and Delbrück, M. (1943). Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28, 491-511.
-
(1943)
Genetics
, vol.28
, pp. 491-511
-
-
Luria, S.E.1
Delbrück, M.2
-
86
-
-
68749118345
-
Defining network topologies that can achieve biochemical adaptation
-
Ma, W., Trusina, A., El-Samad, H., Lim, W. A. and Tang, C. (2009). Defining network topologies that can achieve biochemical adaptation. Cell 138, 760-773.
-
(2009)
Cell
, vol.138
, pp. 760-773
-
-
Ma, W.1
Trusina, A.2
El-Samad, H.3
Lim, W.A.4
Tang, C.5
-
87
-
-
69949185998
-
Coordination of Rho GTPase activities during cell protrusion
-
Machacek, M., Hodgson, L., Welch, C., Elliott, H., Pertz, O., Nalbant, P., Abell, A., Johnson, G. L., Hahn, K. M. and Danuser, G. (2009). Coordination of Rho GTPase activities during cell protrusion. Nature 461, 99-103.
-
(2009)
Nature
, vol.461
, pp. 99-103
-
-
Machacek, M.1
Hodgson, L.2
Welch, C.3
Elliott, H.4
Pertz, O.5
Nalbant, P.6
Abell, A.7
Johnson, G.L.8
Hahn, K.M.9
Danuser, G.10
-
88
-
-
77954586080
-
A quantitative model of transcriptional regulation reveals the influence of binding location on expression
-
MacIsaac, K. D., Lo, K. A., Gordon, W., Motola, S., Mazor, T. and Fraenkel, E. (2010). A quantitative model of transcriptional regulation reveals the influence of binding location on expression. PLOS Comput. Biol. 6, e1000773.
-
(2010)
PLOS Comput. Biol.
, vol.6
-
-
MacIsaac, K.D.1
Lo, K.A.2
Gordon, W.3
Motola, S.4
Mazor, T.5
Fraenkel, E.6
-
89
-
-
0142027814
-
Structure, andfunction of the feed-forward loop network motif
-
Mangan, S. and Alon, U. (2003). Structure, andfunction of the feed-forward loop network motif. Proc. Natl. Acad. Sci. USA 100, 11980-11985.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
90
-
-
33750300100
-
Adenoviral vector saturates Akt pro-survival signaling, andblocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis
-
Miller-Jensen, K., Janes, K. A., Wong, Y. L., Griffith, L. G. and Lauffenburger, D. A. (2006). Adenoviral vector saturates Akt pro-survival signaling, andblocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis. J. Cell Sci. 119, 3788-3798.
-
(2006)
J. Cell Sci.
, vol.119
, pp. 3788-3798
-
-
Miller-Jensen, K.1
Janes, K.A.2
Wong, Y.L.3
Griffith, L.G.4
Lauffenburger, D.A.5
-
91
-
-
34547623194
-
Common effector processing mediates cell-specific responses to stimuli
-
Miller-Jensen, K., Janes, K. A., Brugge, J. S. and Lauffenburger, D. A. (2007). Common effector processing mediates cell-specific responses to stimuli. Nature 448, 604-608.
-
(2007)
Nature
, vol.448
, pp. 604-608
-
-
Miller-Jensen, K.1
Janes, K.A.2
Brugge, J.S.3
Lauffenburger, D.A.4
-
92
-
-
0037174670
-
Network motifs: simple building blocks of complex networks
-
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. and Alon, U. (2002). Network motifs: simple building blocks of complex networks. Science 298, 824-827.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
93
-
-
79953668247
-
Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli
-
Morris, M. K., Saez-Rodriguez, J., Clarke, D. C., Sorger, P. K. and Lauffenburger, D. A. (2011). Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLOS Comput. Biol. 7, e1001099.
-
(2011)
PLOS Comput. Biol.
, vol.7
-
-
Morris, M.K.1
Saez-Rodriguez, J.2
Clarke, D.C.3
Sorger, P.K.4
Lauffenburger, D.A.5
-
94
-
-
77952902183
-
Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics
-
Nakakuki, T., Birtwistle, M. R., Saeki, Y., Yumoto, N., Ide, K., Nagashima, T., Brusch, L., Ogunnaike, B. A., Okada-Hatakeyama, M. and Kholodenko, B. N. (2010). Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell 141, 884-896.
-
(2010)
Cell
, vol.141
, pp. 884-896
-
-
Nakakuki, T.1
Birtwistle, M.R.2
Saeki, Y.3
Yumoto, N.4
Ide, K.5
Nagashima, T.6
Brusch, L.7
Ogunnaike, B.A.8
Okada-Hatakeyama, M.9
Kholodenko, B.N.10
-
95
-
-
33744809296
-
A global analysis of cross-talk in a mammalian cellular signalling network
-
Natarajan, M., Lin, K. M., Hsueh, R. C., Sternweis, P. C. and Ranganathan, R. (2006). A global analysis of cross-talk in a mammalian cellular signalling network. Nat. Cell Biol. 8, 571-580.
-
(2006)
Nat. Cell Biol.
, vol.8
, pp. 571-580
-
-
Natarajan, M.1
Lin, K.M.2
Hsueh, R.C.3
Sternweis, P.C.4
Ranganathan, R.5
-
96
-
-
77649259720
-
Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen
-
Nir, O., Bakal, C., Perrimon, N. and Berger, B. (2010). Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. Genome Res. 20, 372-380.
-
(2010)
Genome Res.
, vol.20
, pp. 372-380
-
-
Nir, O.1
Bakal, C.2
Perrimon, N.3
Berger, B.4
-
97
-
-
73149122136
-
Applications of genomescale metabolic reconstructions
-
Oberhardt, M. A., Palsson, B. O. and Papin, J. A. (2009). Applications of genomescale metabolic reconstructions. Mol. Syst. Biol. 5, 320.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 320
-
-
Oberhardt, M.A.1
Palsson, B.O.2
Papin, J.A.3
-
98
-
-
33745463739
-
A comprehensive map of the toll-like receptor signaling network
-
Oda, K. and Kitano, H. (2006). A comprehensive map of the toll-like receptor signaling network. Mol. Syst. Biol. 2, 2006.0015.
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Oda, K.1
Kitano, H.2
-
99
-
-
33746889808
-
A comprehensive pathway map of epidermal growth factor receptor signaling
-
20050010.
-
Oda, K., Matsuoka, Y., Funahashi, A. and Kitano, H. (2005). A comprehensive pathway map of epidermal growth factor receptor signaling. Mol. Syst. Biol. 1, 2005.0010.
-
(2005)
Mol. Syst. Biol.
, vol.1
-
-
Oda, K.1
Matsuoka, Y.2
Funahashi, A.3
Kitano, H.4
-
100
-
-
13444278821
-
Reconstruction of cellular signalling networks, andanalysis of their properties
-
Papin, J. A., Hunter, T., Palsson, B. O. and Subramaniam, S. (2005). Reconstruction of cellular signalling networks, andanalysis of their properties. Nat. Rev. Mol. Cell Biol. 6, 99-111.
-
(2005)
Nat. Rev. Mol. Cell Biol.
, vol.6
, pp. 99-111
-
-
Papin, J.A.1
Hunter, T.2
Palsson, B.O.3
Subramaniam, S.4
-
101
-
-
77949732073
-
RAF inhibitors transactivate RAF dimers, andERK signalling in cells with wild-type BRAF
-
Poulikakos, P. I., Zhang, C., Bollag, G., Shokat, K. M. and Rosen, N. (2010). RAF inhibitors transactivate RAF dimers, andERK signalling in cells with wild-type BRAF. Nature 464, 427-430.
-
(2010)
Nature
, vol.464
, pp. 427-430
-
-
Poulikakos, P.I.1
Zhang, C.2
Bollag, G.3
Shokat, K.M.4
Rosen, N.5
-
102
-
-
4143070653
-
What's in a picture? The temptation of image manipulation
-
Rossner, M. and Yamada, K. M. (2004). What's in a picture? The temptation of image manipulation. J. Cell Biol. 166, 11-15.
-
(2004)
J. Cell Biol.
, vol.166
, pp. 11-15
-
-
Rossner, M.1
Yamada, K.M.2
-
103
-
-
71449120701
-
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
-
Saez-Rodriguez, J., Alexopoulos, L. G., Epperlein, J., Samaga, R., Lauffenburger, D. A., Klamt, S. and Sorger, P. K. (2009). Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol. Syst. Biol. 5, 331.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 331
-
-
Saez-Rodriguez, J.1
Alexopoulos, L.G.2
Epperlein, J.3
Samaga, R.4
Lauffenburger, D.A.5
Klamt, S.6
Sorger, P.K.7
-
104
-
-
80051692878
-
Comparing signaling networks between normal, andtransformed hepatocytes using discrete logical models
-
Saez-Rodriguez, J., Alexopoulos, L. G., Zhang, M., Morris, M. K., Lauffenburger, D. A. and Sorger, P. K. (2011). Comparing signaling networks between normal, andtransformed hepatocytes using discrete logical models. Cancer Res. 71, 5400-5411.
-
(2011)
Cancer Res.
, vol.71
, pp. 5400-5411
-
-
Saez-Rodriguez, J.1
Alexopoulos, L.G.2
Zhang, M.3
Morris, M.K.4
Lauffenburger, D.A.5
Sorger, P.K.6
-
105
-
-
33847355217
-
Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
-
Santos, S. D., Verveer, P. J. and Bastiaens, P. I. (2007). Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat. Cell Biol. 9, 324-330.
-
(2007)
Nat. Cell Biol.
, vol.9
, pp. 324-330
-
-
Santos, S.D.1
Verveer, P.J.2
Bastiaens, P.I.3
-
106
-
-
17344362384
-
Prediction, andvalidation of the distinct dynamics of transient, andsustained ERK activation
-
Sasagawa, S., Ozaki, Y., Fujita, K. and Kuroda, S. (2005). Prediction, andvalidation of the distinct dynamics of transient, andsustained ERK activation. Nat. Cell Biol. 7, 365-373.
-
(2005)
Nat. Cell Biol.
, vol.7
, pp. 365-373
-
-
Sasagawa, S.1
Ozaki, Y.2
Fujita, K.3
Kuroda, S.4
-
107
-
-
0036212767
-
Computational modeling of the dynamics of the MAP kinase cascade activated by surface, andinternalized EGF receptors
-
Schoeberl, B., Eichler-Jonsson, C., Gilles, E. D. and Müller, G. (2002). Computational modeling of the dynamics of the MAP kinase cascade activated by surface, andinternalized EGF receptors. Nat. Biotechnol. 20, 370-375.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 370-375
-
-
Schoeberl, B.1
Eichler-Jonsson, C.2
Gilles, E.D.3
Müller, G.4
-
108
-
-
69849115198
-
Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis
-
Schoeberl, B., Pace, E. A., Fitzgerald, J. B., Harms, B. D., Xu, L., Nie, L., Linggi, B., Kalra, A., Paragas, V., Bukhalid, R. et al. (2009). Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci. Signal. 2, ra31.
-
(2009)
Sci. Signal.
, vol.2
-
-
Schoeberl, B.1
Pace, E.A.2
Fitzgerald, J.B.3
Harms, B.D.4
Xu, L.5
Nie, L.6
Linggi, B.7
Kalra, A.8
Paragas, V.9
Bukhalid, R.10
-
109
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U. and Gaul, U. (2008). Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451, 535-540.
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
110
-
-
79959859399
-
Robust network topologies for generating switch-like cellular responses
-
Shah, N. A. and Sarkar, C. A. (2011). Robust network topologies for generating switch-like cellular responses. PLOS Comput. Biol. 7, e1002085.
-
(2011)
PLOS Comput. Biol.
, vol.7
-
-
Shah, N.A.1
Sarkar, C.A.2
-
111
-
-
84862002321
-
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
-
Sharon, E., Kalma, Y., Sharp, A., Raveh-Sadka, T., Levo, M., Zeevi, D., Keren, L., Yakhini, Z., Weinberger, A. and Segal, E. (2012). Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat. Biotechnol. 30, 521-530.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 521-530
-
-
Sharon, E.1
Kalma, Y.2
Sharp, A.3
Raveh-Sadka, T.4
Levo, M.5
Zeevi, D.6
Keren, L.7
Yakhini, Z.8
Weinberger, A.9
Segal, E.10
-
112
-
-
0036080555
-
Autocrine loops with positive feedback enable context-dependent cell signaling
-
Shvartsman, S. Y., Hagan, M. P., Yacoub, A., Dent, P., Wiley, H. S. and Lauffenburger, D. A. (2002a). Autocrine loops with positive feedback enable context-dependent cell signaling. Am. J. Physiol. Cell Physiol. 282, C545-C559.
-
(2002)
Am. J. Physiol. Cell Physiol.
, vol.282
-
-
Shvartsman, S.Y.1
Hagan, M.P.2
Yacoub, A.3
Dent, P.4
Wiley, H.S.5
Lauffenburger, D.A.6
-
113
-
-
0036333324
-
Modeling, andcomputational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis
-
Shvartsman, S. Y., Muratov, C. B. and Lauffenburger, D. A. (2002b). Modeling, andcomputational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis. Development 129, 2577-2589.
-
(2002)
Development
, vol.129
, pp. 2577-2589
-
-
Shvartsman, S.Y.1
Muratov, C.B.2
Lauffenburger, D.A.3
-
114
-
-
0037127047
-
Systems analysis of Ran transport
-
Smith, A. E., Slepchenko, B. M., Schaff, J. C., Loew, L. M. and Macara, I. G. (2002). Systems analysis of Ran transport. Science 295, 488-491.
-
(2002)
Science
, vol.295
, pp. 488-491
-
-
Smith, A.E.1
Slepchenko, B.M.2
Schaff, J.C.3
Loew, L.M.4
Macara, I.G.5
-
115
-
-
0035751937
-
Assessing TP53 status in human tumours to evaluate clinical outcome
-
Soussi, T. and Béroud, C. (2001). Assessing TP53 status in human tumours to evaluate clinical outcome. Nat. Rev. Cancer 1, 233-240.
-
(2001)
Nat. Rev. Cancer
, vol.1
, pp. 233-240
-
-
Soussi, T.1
Béroud, C.2
-
116
-
-
84857437687
-
Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae
-
Stewart-Ornstein, J., Weissman, J. S. and El-Samad, H. (2012). Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Mol. Cell 45, 483-493.
-
(2012)
Mol. Cell
, vol.45
, pp. 483-493
-
-
Stewart-Ornstein, J.1
Weissman, J.S.2
El-Samad, H.3
-
117
-
-
84863011640
-
Combined experimental, andcomputational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis, andG1/S arrest after genotoxic stress
-
Tentner, A. R., Lee, M. J., Ostheimer, G. J., Samson, L. D., Lauffenburger, D. A. and Yaffe, M. B. (2012). Combined experimental, andcomputational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis, andG1/S arrest after genotoxic stress. Mol. Syst. Biol. 8, 568.
-
(2012)
Mol. Syst. Biol.
, vol.8
, pp. 568
-
-
Tentner, A.R.1
Lee, M.J.2
Ostheimer, G.J.3
Samson, L.D.4
Lauffenburger, D.A.5
Yaffe, M.B.6
-
118
-
-
79957884622
-
Protein kinase A governs a RhoA-RhoGDI protrusion-retraction pacemaker in migrating cells
-
Tkachenko, E., Sabouri-Ghomi, M., Pertz, O., Kim, C., Gutierrez, E., Machacek, M., Groisman, A., Danuser, G. and Ginsberg, M. H. (2011). Protein kinase A governs a RhoA-RhoGDI protrusion-retraction pacemaker in migrating cells. Nat. Cell Biol. 13, 660-667.
-
(2011)
Nat. Cell Biol.
, vol.13
, pp. 660-667
-
-
Tkachenko, E.1
Sabouri-Ghomi, M.2
Pertz, O.3
Kim, C.4
Gutierrez, E.5
Machacek, M.6
Groisman, A.7
Danuser, G.8
Ginsberg, M.H.9
-
119
-
-
84859167118
-
Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling
-
Toyoshima, Y., Kakuda, H., Fujita, K. A., Uda, S. and Kuroda, S. (2012). Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling. Nat. Commun 3, 743.
-
(2012)
Nat. Commun
, vol.3
, pp. 743
-
-
Toyoshima, Y.1
Kakuda, H.2
Fujita, K.A.3
Uda, S.4
Kuroda, S.5
-
120
-
-
46849090495
-
Robust, tunable biological oscillations from interlinked positive, andnegative feedback loops
-
Tsai, T. Y., Choi, Y. S., Ma, W., Pomerening, J. R., Tang, C. and Ferrell, J. E., Jr (2008). Robust, tunable biological oscillations from interlinked positive, andnegative feedback loops. Science 321, 126-129.
-
(2008)
Science
, vol.321
, pp. 126-129
-
-
Tsai, T.Y.1
Choi, Y.S.2
Ma, W.3
Pomerening, J.R.4
Tang, C.5
Ferrell, J.E.Jr.6
-
121
-
-
80052511352
-
What's wrong with correlative experiments?
-
Vilela, M. and Danuser, G. (2011). What's wrong with correlative experiments?. Nat. Cell Biol. 13, 1011.
-
(2011)
Nat. Cell Biol.
, vol.13
, pp. 1011
-
-
Vilela, M.1
Danuser, G.2
-
122
-
-
80053645783
-
Intersection of FOXO-, andRUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis, andtumor progression
-
Wang, L., Brugge, J. S. and Janes, K. A. (2011). Intersection of FOXO-, andRUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis, andtumor progression. Proc. Natl. Acad. Sci. USA 108, E803-E812.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
-
-
Wang, L.1
Brugge, J.S.2
Janes, K.A.3
-
123
-
-
24944489952
-
Stimulus specificity of gene expression programs determined by temporal control of IKK activity
-
Werner, S. L., Barken, D. and Hoffmann, A. (2005). Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science 309, 1857-1861.
-
(2005)
Science
, vol.309
, pp. 1857-1861
-
-
Werner, S.L.1
Barken, D.2
Hoffmann, A.3
|