-
1
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
(doi:10.1016/S0955-0674(03)00017-6)
-
Tyson JJ, Chen KC, Novak B. 2003 Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221-231. (doi:10.1016/S0955-0674(03)00017-6)
-
(2003)
Curr. Opin. Cell Biol.
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
2
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
(doi:10.1038/nrg2102)
-
Alon U. 2007 Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461. (doi:10.1038/nrg2102)
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
3
-
-
54249137797
-
Feedback loops shape cellular signals in space and time
-
(doi:10.1126/science.1160617)
-
Brandman O, Meyer T. 2008 Feedback loops shape cellular signals in space and time. Science 322, 390-395. (doi:10.1126/science.1160617)
-
(2008)
Science
, vol.322
, pp. 390-395
-
-
Brandman, O.1
Meyer, T.2
-
4
-
-
77952918610
-
Simplified models of biological networks
-
(doi:10.1146/annurev.biophys.093008.131241)
-
Sneppen K, Krishna S, Semsey S. 2010 Simplified models of biological networks. Annu. Rev. Biophys. 39, 43-59. (doi:10.1146/annurev.biophys.093008. 131241)
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 43-59
-
-
Sneppen, K.1
Krishna, S.2
Semsey, S.3
-
5
-
-
77951681944
-
Functional motifs in biochemical reaction networks
-
(doi:10.1146/annurev. physchem.012809.103457)
-
Tyson JJ, Novak B. 2010 Functional motifs in biochemical reaction networks. Annu. Rev. Phys. Chem. 61, 219-240. (doi:10.1146/annurev. physchem.012809.103457)
-
(2010)
Annu. Rev. Phys. Chem.
, vol.61
, pp. 219-240
-
-
Tyson, J.J.1
Novak, B.2
-
6
-
-
0031559933
-
Quantification of information transfer via cellular signal transduction pathways
-
(doi:10.1016/S0014-5793(97)01018-1)
-
Kholodenko BN, Hoek JB, Westerhoff HV, Brown GC. 1997 Quantification of information transfer via cellular signal transduction pathways. FEBS Lett. 414, 430-434. (doi:10.1016/S0014-5793(97)01018-1)
-
(1997)
FEBS Lett.
, vol.414
, pp. 430-434
-
-
Kholodenko, B.N.1
Hoek, J.B.2
Westerhoff, H.V.3
Brown, G.C.4
-
7
-
-
23844525556
-
Quantitative analysis of ultrasensitive responses
-
(doi:10.1111/j.1742-4658.2005.04818.x)
-
Legewie S, Bluthgen N, Herzel H. 2005 Quantitative analysis of ultrasensitive responses. FEBS J. 272, 4071-4079. (doi:10.1111/j.1742-4658.2005. 04818.x)
-
(2005)
FEBS J.
, vol.272
, pp. 4071-4079
-
-
Legewie, S.1
Bluthgen, N.2
Herzel, H.3
-
8
-
-
0020171028
-
Sensitivity amplification in biochemical systems
-
(doi:10.1017/S0033583500003449)
-
Goldbeter A, Koshland Jr DE. 1982 Sensitivity amplification in biochemical systems. Q. Rev. Biophys. 15, 555-591. (doi:10.1017/ S0033583500003449)
-
(1982)
Q. Rev. Biophys.
, vol.15
, pp. 555-591
-
-
Goldbeter, A.1
Koshland Jr., D.E.2
-
9
-
-
0019996706
-
Amplification and adaptation in regulatory and sensory systems
-
(doi:10.1126/science.7089556)
-
Koshland Jr DE, Goldbeter A, Stock JB. 1982 Amplification and adaptation in regulatory and sensory systems. Science 217, 220-225. (doi:10. 1126/science.7089556)
-
(1982)
Science
, vol.217
, pp. 220-225
-
-
Koshland Jr., D.E.1
Goldbeter, A.2
Stock, J.B.3
-
10
-
-
71149086936
-
Signaling motifs and weber's law
-
(doi:10.1016/j.molcel. 2009.11.032)
-
Ferrell Jr JE. 2009 Signaling motifs and Weber's law. Mol. Cell. 36, 724-727. (doi:10.1016/j.molcel. 2009.11.032)
-
(2009)
Mol. Cell.
, vol.36
, pp. 724-727
-
-
Ferrell Jr., J.E.1
-
11
-
-
71149092283
-
Dynamics and variability of ERK2 response to EGF in individual living cells
-
(doi:10.1016/j.molcel.2009.11.025)
-
Cohen-Saidon C, Cohen AA, Sigal A, Liron Y, Alon U. 2009 Dynamics and variability of ERK2 response to EGF in individual living cells. Mol. Cell. 36, 885-893. (doi:10.1016/j.molcel.2009.11.025)
-
(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
-
12
-
-
71149092489
-
Evidence that fold-change, and not absolute level, of b-catenin dictates wnt signaling
-
(doi:10.1016/j.molcel.2009.11.017)
-
Goentoro L, Kirschner MW. 2009 Evidence that fold-change, and not absolute level, of b-catenin dictates Wnt signaling. Mol. Cell. 36, 872-884. (doi:10.1016/j.molcel.2009.11.017)
-
(2009)
Mol. Cell.
, vol.36
, pp. 872-884
-
-
Goentoro, L.1
Kirschner, M.W.2
-
13
-
-
0036532226
-
Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability
-
(doi:10.1016/S0955-0674(02)00314-9)
-
Ferrell Jr JE. 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
-
14
-
-
34047239539
-
Dose response relationship in anti-stress gene regulatory networks
-
(doi:10.1371/journal. pcbi.0030024)
-
Zhang Q, Andersen ME. 2007 Dose response relationship in anti-stress gene regulatory networks. PLoS Comput. Biol. 3, e24. (doi:10.1371/journal. pcbi.0030024)
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Zhang, Q.1
Andersen, M.E.2
-
15
-
-
0037079015
-
Computational approaches to cellular rhythms
-
(doi:10.1038/nature01259)
-
Goldbeter A. 2002 Computational approaches to cellular rhythms. Nature 420, 238-245. (doi:10. 1038/nature01259)
-
(2002)
Nature
, vol.420
, pp. 238-245
-
-
Goldbeter, A.1
-
16
-
-
3242729569
-
Quantitative analysis of signaling networks
-
(doi:10.1016/j.pbiomolbio.2004.03.002)
-
Sauro HM, Kholodenko BN. 2004 Quantitative analysis of signaling networks. Prog. Biophys. Mol. Biol. 86, 5-43. (doi:10.1016/j.pbiomolbio.2004.03. 002)
-
(2004)
Prog. Biophys. Mol. Biol.
, vol.86
, pp. 5-43
-
-
Sauro, H.M.1
Kholodenko, B.N.2
-
19
-
-
0015103748
-
Concepts relating the behavior of biochemical systems to their underlying molecular properties
-
(doi:10.1016/S0003-9861(71)80021-8)
-
Savageau MA. 1971 Concepts relating the behavior of biochemical systems to their underlying molecular properties. Arch. Biochem. Biophys. 145, 612-621. (doi:10.1016/S0003-9861(71)80021-8)
-
(1971)
Arch. Biochem. Biophys.
, vol.145
, pp. 612-621
-
-
Savageau, M.A.1
-
21
-
-
0001424903
-
An amplified sensitivity arising from covalent modification in biological systems
-
(doi:10.1073/pnas.78.11.6840)
-
Goldbeter A, Koshland Jr DE. 1981 An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl Acad. Sci. USA 78, 6840-6844. (doi:10.1073/pnas.78.11.6840)
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 6840-6844
-
-
Goldbeter, A.1
Koshland Jr., D.E.2
-
22
-
-
0001145764
-
The combinations of haemoglobin with oxygen and with carbon monoxide
-
Hill AV. 1913 The combinations of haemoglobin with oxygen and with carbon monoxide. I. Biochem. J. 7, 471-480.
-
(1913)
I. Biochem. J.
, vol.7
, pp. 471-480
-
-
Hill, A.V.1
-
24
-
-
0030445778
-
Tripping the switch fantastic: How a protein kinase cascade can convert graded inputs into switch-like outputs
-
(doi:10.1016/S0968-0004(96)20026-X)
-
Ferrell Jr JE. 1996 Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem. Sci. 21, 460-466. (doi:10.1016/S0968-0004(96)20026-X)
-
(1996)
Trends Biochem. Sci.
, vol.21
, pp. 460-466
-
-
Ferrell Jr., J.E.1
-
25
-
-
77953992568
-
Ultrasensitive response motifs in biochemical networks
-
(eds K Krishnan, ME Andersen) Hoboken, NJ: John Wiley & Sons
-
Zhang Q, Bhattacharya S, Woods CG, Andersen ME. 2010 Ultrasensitive response motifs in biochemical networks. In Quantitative modeling in toxicology (eds K Krishnan, ME Andersen), pp. 199-217. Hoboken, NJ: John Wiley & Sons.
-
(2010)
Quantitative Modeling in Toxicology
, pp. 199-217
-
-
Zhang, Q.1
Bhattacharya, S.2
Woods, C.G.3
Andersen, M.E.4
-
27
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
(doi:10.1021/bi00865a047)
-
Koshland Jr DE, Nemethy G, Filmer D. 1966 Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365-385. (doi:10.1021/bi00865a047)
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland Jr., D.E.1
Nemethy, G.2
Filmer, D.3
-
28
-
-
0001314221
-
The hemoglobin system. VI. The oxygen dissociation curve of hemoglobin
-
Adair GS. 1925 The hemoglobin system. VI. The oxygen dissociation curve of hemoglobin. J. Biol. Chem. 63, 529-545.
-
(1925)
J. Biol. Chem.
, vol.63
, pp. 529-545
-
-
Adair, G.S.1
-
29
-
-
0021111555
-
Probable involvement of both intrachain cAMP binding sites in activation of protein kinase
-
Robinson-Steiner AM, Corbin JD. 1983 Probable involvement of both intrachain cAMP binding sites in activation of protein kinase. J. Biol. Chem. 258, 1032-1040.
-
(1983)
J. Biol. Chem.
, vol.258
, pp. 1032-1040
-
-
Robinson-Steiner, A.M.1
Corbin, J.D.2
-
30
-
-
0023835874
-
Tyrosine-371 contributes to the positive cooperativity between the two cAMP binding sites in the regulatory subunit of cAMP-dependent protein kinase I
-
(doi:10.1021/bi00405a026)
-
Bubis J, Saraswat LD, Taylor SS. 1988 Tyrosine-371 contributes to the positive cooperativity between the two cAMP binding sites in the regulatory subunit of cAMP-dependent protein kinase I. Biochemistry 27, 1570-1576. (doi:10.1021/bi00405a026)
-
(1988)
Biochemistry
, vol.27
, pp. 1570-1576
-
-
Bubis, J.1
Saraswat, L.D.2
Taylor, S.S.3
-
31
-
-
0028844346
-
Conformational changes and calcium binding by calretinin and its recombinant fragments containing different sets of EF hand motifs
-
(doi:10.1021/bi00047a001)
-
Kuznicki J, Strauss KI, Jacobowitz DM. 1995 Conformational changes and calcium binding by calretinin and its recombinant fragments containing different sets of EF hand motifs. Biochemistry 34, 15 389-15 394. (doi:10.1021/ bi00047a001)
-
(1995)
Biochemistry
, vol.34
, pp. 15389-15394
-
-
Kuznicki, J.1
Strauss, K.I.2
Jacobowitz, D.M.3
-
33
-
-
0018967724
-
Positive cooperative binding of calcium to bovine brain calmodulin
-
(doi:10.1021/bi00557a009)
-
Crouch TH, Klee CB. 1980 Positive cooperative binding of calcium to bovine brain calmodulin. Biochemistry 19, 3692-3698. (doi:10.1021/bi00557a009)
-
(1980)
Biochemistry
, vol.19
, pp. 3692-3698
-
-
Crouch, T.H.1
Klee, C.B.2
-
34
-
-
46349104159
-
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: A structural systems biology approach
-
(doi:10.1186/1752-0509-2-48)
-
Valeyev NV, Bates DG, Heslop-Harrison P, Postlethwaite I, Kotov NV. 2008 Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach. BMC Syst. Biol. 2, 48. (doi:10.1186/1752- 0509-2-48)
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 48
-
-
Valeyev, N.V.1
Bates, D.G.2
Heslop-Harrison, P.3
Postlethwaite, I.4
Kotov, N.V.5
-
35
-
-
0037154273
-
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the drosophila genome
-
(doi:10.1073/pnas.231608898)
-
Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. 2002 Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA 99, 757-762. (doi:10.1073/pnas.231608898)
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 757-762
-
-
Berman, B.P.1
Nibu, Y.2
Pfeiffer, B.D.3
Tomancak, P.4
Celniker, S.E.5
Levine, M.6
Rubin, G.M.7
Eisen, M.B.8
-
36
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in drosophila segmentation
-
(doi:10.1038/nature06496)
-
Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. 2008 Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451, 535-540. (doi:10.1038/nature06496)
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Raveh-Sadka, T.2
Schroeder, M.3
Unnerstall, U.4
Gaul, U.5
-
37
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
(doi:10.1101/gr.104471.109)
-
Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. 2010 Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res. 20, 565-577. (doi:10.1101/gr.104471.109)
-
(2010)
Genome Res.
, vol.20
, pp. 565-577
-
-
Gotea, V.1
Visel, A.2
Westlund, J.M.3
Nobrega, M.A.4
Pennacchio, L.A.5
Ovcharenko, I.6
-
38
-
-
0032979987
-
Cooperative binding of heat shock factor to the yeast HSP82 promoter in vivo and in vitro
-
Erkine AM, Magrogan SF, Sekinger EA, Gross DS. 1999 Cooperative binding of heat shock factor to the yeast HSP82 promoter in vivo and in vitro. Mol. Cell. Biol. 19, 1627-1639.
-
(1999)
Mol. Cell. Biol.
, vol.19
, pp. 1627-1639
-
-
Erkine, A.M.1
Magrogan, S.F.2
Sekinger, E.A.3
Gross, D.S.4
-
39
-
-
0007208716
-
Interactions between DNA-bound repressors govern regulation by the lambda phage repressor
-
(doi:10.1073/pnas.76.10.5061)
-
Johnson AD, Meyer BJ, Ptashne M. 1979 Interactions between DNA-bound repressors govern regulation by the lambda phage repressor. Proc. Natl Acad. Sci. USA 76, 5061-5065. (doi:10.1073/pnas.76.10.5061)
-
(1979)
Proc. Natl Acad. Sci. USA
, vol.76
, pp. 5061-5065
-
-
Johnson, A.D.1
Meyer, B.J.2
Ptashne, M.3
-
40
-
-
0023677769
-
A gradient of bicoid protein in drosophila embryos
-
(doi:10.1016/0092-8674(88)90182-1)
-
Driever W, Nusslein-Volhard C. 1988 A gradient of bicoid protein in Drosophila embryos. Cell 54, 83-93. (doi:10.1016/0092-8674(88)90182-1)
-
(1988)
Cell
, vol.54
, pp. 83-93
-
-
Driever, W.1
Nusslein-Volhard, C.2
-
41
-
-
0023679744
-
The bicoid protein determines position in the drosophila embryo in a concentration-dependent manner
-
(doi:10.1016/0092-8674(88)90183-3)
-
Driever W, Nusslein-Volhard C. 1988 The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell 54, 95-104. (doi:10.1016/0092-8674(88)90183-3)
-
(1988)
Cell
, vol.54
, pp. 95-104
-
-
Driever, W.1
Nusslein-Volhard, C.2
-
42
-
-
34447099234
-
Probing the limits to positional information
-
(doi:10.1016/j.cell.2007.05.025)
-
Gregor T, Tank DW, Wieschaus EF, Bialek W. 2007 Probing the limits to positional information. Cell 130, 153-164. (doi:10.1016/j.cell.2007.05.025)
-
(2007)
Cell
, vol.130
, pp. 153-164
-
-
Gregor, T.1
Tank, D.W.2
Wieschaus, E.F.3
Bialek, W.4
-
43
-
-
0032531831
-
Cooperative DNA-binding by bicoid provides a mechanism for threshold-dependent gene activation in the drosophila embryo
-
(doi:10.1093/emboj/17.20.5998)
-
Burz DS, Rivera-Pomar R, Jackle H, Hanes SD. 1998 Cooperative DNA-binding by Bicoid provides a mechanism for threshold-dependent gene activation in the Drosophila embryo. EMBO J. 17, 5998-6009. (doi:10.1093/emboj/17.20.5998)
-
(1998)
EMBO J.
, vol.17
, pp. 5998-6009
-
-
Burz, D.S.1
Rivera-Pomar, R.2
Jackle, H.3
Hanes, S.D.4
-
44
-
-
0027938515
-
Cooperative binding of heat shock transcription factor to the hsp70 promoter in vivo and in vitro
-
Amin J, Fernandez M, Ananthan J, Lis JT, Voellmy R. 1994 Cooperative binding of heat shock transcription factor to the Hsp70 promoter in vivo and in vitro. J. Biol. Chem. 269, 4804-4811.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 4804-4811
-
-
Amin, J.1
Fernandez, M.2
Ananthan, J.3
Lis, J.T.4
Voellmy, R.5
-
45
-
-
0025965278
-
Cooperative binding of drosophila heat shock factor to arrays of a conserved 5 bp unit
-
(doi:10.1016/0092-8674(91)90242-Q)
-
Xiao H, Perisic O, Lis JT. 1991 Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit. Cell 64, 585-593. (doi:10.1016/0092-8674(91)90242-Q)
-
(1991)
Cell
, vol.64
, pp. 585-593
-
-
Xiao, H.1
Perisic, O.2
Lis, J.T.3
-
46
-
-
0141733263
-
Kinetic analysis of platelet-derived growth factor receptor/ phosphoinositide 3-kinase/Akt signaling in fibroblasts
-
(doi:10.1074/jbc.M304968200)
-
Park CS, Schneider IC, Haugh JM. 2003 Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts. J. Biol. Chem. 278, 37 064-37 072. (doi:10.1074/jbc.M304968200)
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 37064-37072
-
-
Park, C.S.1
Schneider, I.C.2
Haugh, J.M.3
-
47
-
-
77955627615
-
Structural basis for negative cooperativity in growth factor binding to an EGF receptor
-
(doi:10.1016/j.cell.2010.07.015)
-
Alvarado D, Klein DE, Lemmon MA. 2010 Structural basis for negative cooperativity in growth factor binding to an EGF receptor. Cell 142, 568-579. (doi:10.1016/j.cell.2010.07.015)
-
(2010)
Cell
, vol.142
, pp. 568-579
-
-
Alvarado, D.1
Klein, D.E.2
Lemmon, M.A.3
-
48
-
-
0024604096
-
The purified activated glucocorticoid receptor is a homodimer
-
Wrange O, Eriksson P, Perlmann T. 1989 The purified activated glucocorticoid receptor is a homodimer. J. Biol. Chem. 264, 5253-5259.
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 5253-5259
-
-
Wrange, O.1
Eriksson, P.2
Perlmann, T.3
-
49
-
-
0023808861
-
The estrogen receptor binds tightly to its responsive element as a ligand-induced homodimer
-
(doi:10.1016/0092-8674(88)90017-7)
-
Kumar V, Chambon P. 1988 The estrogen receptor binds tightly to its responsive element as a ligand-induced homodimer. Cell 55, 145-156. (doi:10. 1016/0092-8674(88)90017-7)
-
(1988)
Cell
, vol.55
, pp. 145-156
-
-
Kumar, V.1
Chambon, P.2
-
50
-
-
0030822421
-
Dimerizing the estrogen receptor DNA binding domain enhances binding to estrogen response elements
-
(doi:10.1074/jbc.272.44.27949)
-
Kuntz MA, Shapiro DJ. 1997 Dimerizing the estrogen receptor DNA binding domain enhances binding to estrogen response elements. J. Biol. Chem. 272, 27 949-27 956. (doi:10.1074/jbc.272.44.27949)
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 27949-27956
-
-
Kuntz, M.A.1
Shapiro, D.J.2
-
51
-
-
85047678506
-
Binding of [3H]progesterone to the human progesterone receptor: Differences between individual and mixed isoforms
-
(doi:10.1210/en.137.6.2339)
-
Carbajo P, Christensen K, Edwards DP, Skafar DF. 1996 Binding of [3H]progesterone to the human progesterone receptor: differences between individual and mixed isoforms. Endocrinology 137, 2339-2346. (doi:10.1210/en.137.6.2339)
-
(1996)
Endocrinology
, vol.137
, pp. 2339-2346
-
-
Carbajo, P.1
Christensen, K.2
Edwards, D.P.3
Skafar, D.F.4
-
52
-
-
0019815828
-
Positive cooperativity of the estrogen receptor
-
(doi:10.1073/pnas. 78.8.4926)
-
Notides AC, Lerner N, Hamilton DE. 1981 Positive cooperativity of the estrogen receptor. Proc. Natl Acad. Sci. USA 78, 4926-4930. (doi:10.1073/pnas. 78.8.4926)
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 4926-4930
-
-
Notides, A.C.1
Lerner, N.2
Hamilton, D.E.3
-
53
-
-
0036294669
-
Dimerization is required for phosphorylation and DNA binding of TonEBP/NFAT5
-
(doi:10.1016/S0006-291X(02)00572-7)
-
Lee SD, Woo SK, Kwon HM. 2002 Dimerization is required for phosphorylation and DNA binding of TonEBP/NFAT5. Biochem. Biophys. Res. Commun. 294, 968-975. (doi:10.1016/S0006-291X(02)00572-7)
-
(2002)
Biochem. Biophys. Res. Commun.
, vol.294
, pp. 968-975
-
-
Lee, S.D.1
Woo, S.K.2
Kwon, H.M.3
-
54
-
-
0028349904
-
Interferon activation of the transcription factor stat91 involves dimerization through SH2-phosphotyrosyl peptide interactions
-
(doi:10.1016/0092-8674(94)90357-3)
-
Shuai K, Horvath CM, Huang LH, Qureshi SA, Cowburn D, Darnell Jr JE. 1994 Interferon activation of the transcription factor Stat91 involves dimerization through SH2-phosphotyrosyl peptide interactions. Cell 76, 821-828. (doi:10.1016/0092-8674(94)90357-3)
-
(1994)
Cell
, vol.76
, pp. 821-828
-
-
Shuai, K.1
Horvath, C.M.2
Huang, L.H.3
Qureshi, S.A.4
Cowburn, D.5
Darnell Jr., J.E.6
-
55
-
-
0023771685
-
C-jun dimerizes with itself and with c-fos, forming complexes of different DNA binding affinities
-
(doi:10.1016/0092-8674(88)90147-X)
-
Halazonetis TD, Georgopoulos K, Greenberg ME, Leder P. 1988 c-Jun dimerizes with itself and with c-Fos, forming complexes of different DNA binding affinities. Cell 55, 917-924. (doi:10.1016/0092-8674(88)90147-X)
-
(1988)
Cell
, vol.55
, pp. 917-924
-
-
Halazonetis, T.D.1
Georgopoulos, K.2
Greenberg, M.E.3
Leder, P.4
-
56
-
-
0030941744
-
MyoD-E12 heterodimers and MyoD-myod homodimers are equally stable
-
(doi:10.1021/bi970262m)
-
Maleki SJ, Royer CA, Hurlburt BK. 1997 MyoD-E12 heterodimers and MyoD-MyoD homodimers are equally stable. Biochemistry 36, 6762-6767. (doi:10.1021/bi970262m)
-
(1997)
Biochemistry
, vol.36
, pp. 6762-6767
-
-
Maleki, S.J.1
Royer, C.A.2
Hurlburt, B.K.3
-
57
-
-
0033546171
-
Modulation of human heat shock factor trimerization by the linker domain
-
(doi:10.1074/jbc.274.24.17219)
-
Liu PC, Thiele DJ. 1999 Modulation of human heat shock factor trimerization by the linker domain. J. Biol. Chem. 274, 17 219-17 225. (doi:10.1074/jbc.274.24.17219)
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 17219-17225
-
-
Liu, P.C.1
Thiele, D.J.2
-
58
-
-
58149460239
-
The oligomerization of OxyR in escherichia coli
-
(doi:10.1002/pro.241)
-
Knapp GS, Tsai JW, Hu JC. 2009 The oligomerization of OxyR in Escherichia coli. Protein Sci. 18, 101-107. (doi:10.1002/pro.241)
-
(2009)
Protein Sci.
, vol.18
, pp. 101-107
-
-
Knapp, G.S.1
Tsai, J.W.2
Hu, J.C.3
-
59
-
-
33750486164
-
The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity
-
(doi:10.1038/sj.emboj.7601382)
-
Okorokov AL, Sherman MB, Plisson C, Grinkevich V, Sigmundsson K, Selivanova G, Milner J, Orlova EV. 2006 The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity. EMBO J. 25, 5191-5200. (doi:10.1038/sj. emboj.7601382)
-
(2006)
EMBO J.
, vol.25
, pp. 5191-5200
-
-
Okorokov, A.L.1
Sherman, M.B.2
Plisson, C.3
Grinkevich, V.4
Sigmundsson, K.5
Selivanova, G.6
Milner, J.7
Orlova, E.V.8
-
60
-
-
77649272110
-
A systems biology perspective on nrf2-mediated antioxidant response
-
(doi:10.1016/j.taap.2009.08.018)
-
Zhang Q, Pi J, Woods CG, Andersen ME. 2010 A systems biology perspective on Nrf2-mediated antioxidant response. Toxicol. Appl. Pharmacol. 244, 84-97. (doi:10.1016/j.taap.2009.08.018)
-
(2010)
Toxicol. Appl. Pharmacol.
, vol.244
, pp. 84-97
-
-
Zhang, Q.1
Pi, J.2
Woods, C.G.3
Andersen, M.E.4
-
61
-
-
0028169847
-
Purification and immunoelectron microscopic localization of cellular glutathione peroxidase in rat hepatocytes: Quantitative analysis by postembedding method
-
(doi:10.1007/BF00268898)
-
Asayama K, Yokota S, Dobashi K, Hayashibe H, Kawaoi A, Nakazawa S. 1994 Purification and immunoelectron microscopic localization of cellular glutathione peroxidase in rat hepatocytes: quantitative analysis by postembedding method. Histochemistry 102, 213-219. (doi:10.1007/BF00268898)
-
(1994)
Histochemistry
, vol.102
, pp. 213-219
-
-
Asayama, K.1
Yokota, S.2
Dobashi, K.3
Hayashibe, H.4
Kawaoi, A.5
Nakazawa, S.6
-
62
-
-
0009424743
-
Catalase: A tetrameric enzyme with four tightly bound molecules of NADPH
-
(doi:10.1073/pnas.81.14.4343)
-
Kirkman HN, Gaetani GF. 1984 Catalase: a tetrameric enzyme with four tightly bound molecules of NADPH. Proc. Natl Acad. Sci. USA 81, 4343-4347. (doi:10.1073/pnas.81.14.4343)
-
(1984)
Proc. Natl Acad. Sci. USA
, vol.81
, pp. 4343-4347
-
-
Kirkman, H.N.1
Gaetani, G.F.2
-
63
-
-
0018906818
-
Isolation and characterization of metallothionein dimers
-
(doi:10.1016/0006-2952(80)90540-7)
-
Suzuki KT, Yamamura M. 1980 Isolation and characterization of metallothionein dimers. Biochem. Pharmacol. 29, 689-692. (doi:10.1016/0006- 2952(80)90540-7)
-
(1980)
Biochem. Pharmacol.
, vol.29
, pp. 689-692
-
-
Suzuki, K.T.1
Yamamura, M.2
-
64
-
-
0035914346
-
Oligomerization of human gadd45a protein
-
(doi:10.1074/jbc. M105115200)
-
Kovalsky O, Lung FD, Roller PP, Fornace Jr AJ. 2001 Oligomerization of human Gadd45a protein. J. Biol. Chem. 276, 39 330-39 339. (doi:10.1074/jbc. M105115200)
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 39330-39339
-
-
Kovalsky, O.1
Lung, F.D.2
Roller, P.P.3
Fornace Jr., A.J.4
-
65
-
-
44349132633
-
The crystal structure and dimerization interface of GADD45g
-
(doi:10.1073/pnas.0800086105)
-
Schrag JD, Jiralerspong S, Banville M, Jaramillo ML, O'Connor-McCourt MD. 2008 The crystal structure and dimerization interface of GADD45g. Proc. Natl Acad. Sci. USA 105, 6566-6571. (doi:10.1073/pnas. 0800086105)
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 6566-6571
-
-
Schrag, J.D.1
Jiralerspong, S.2
Banville, M.3
Jaramillo, M.L.4
O'Connor-McCourt, M.D.5
-
66
-
-
83455171075
-
A source of ultrasensitivity in the glutamine response of the bicyclic cascade system controlling glutamine synthetase adenylylation state and activity in escherichia coli
-
(doi:10.1021/bi201410x)
-
Jiang P, Ninfa AJ. 2011 A source of ultrasensitivity in the glutamine response of the bicyclic cascade system controlling glutamine synthetase adenylylation state and activity in Escherichia coli. Biochemistry 50, 10 929-10 940. (doi:10.1021/bi201410x)
-
(2011)
Biochemistry
, vol.50
, pp. 10929-10940
-
-
Jiang, P.1
Ninfa, A.J.2
-
67
-
-
66249102308
-
Multisite protein phosphorylation-from molecular mechanisms to kinetic models
-
(doi:10.1111/j.1742-4658.2009.07027.x)
-
Salazar C, Hofer T. 2009 Multisite protein phosphorylation-from molecular mechanisms to kinetic models. FEBS J. 276, 3177-3198. (doi:10. 1111/j.1742-4658.2009.07027.x)
-
(2009)
FEBS J.
, vol.276
, pp. 3177-3198
-
-
Salazar, C.1
Hofer, T.2
-
68
-
-
26844571282
-
Multisite protein phosphorylation makes a good threshold but can be a poor switch
-
(doi:10.1073/pnas.0507322102)
-
Gunawardena J. 2005 Multisite protein phosphorylation makes a good threshold but can be a poor switch. Proc. Natl Acad. Sci. USA 102, 14 617-14 622. (doi:10.1073/pnas.0507322102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 14617-14622
-
-
Gunawardena, J.1
-
69
-
-
0030746219
-
Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase
-
(doi:10.1074/jbc.272.30.19008)
-
Ferrell Jr JE, Bhatt RR. 1997 Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J. Biol. Chem. 272, 19 008-19 016. (doi:10.1074/jbc.272.30.19008)
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 19008-19016
-
-
Ferrell Jr., J.E.1
Bhatt, R.R.2
-
70
-
-
0030972112
-
The activating dual phosphorylation of MAPK by MEK is nonprocessive
-
(doi:10.1021/bi970535d)
-
Burack WR, Sturgill TW. 1997 The activating dual phosphorylation of MAPK by MEK is nonprocessive. Biochemistry 36, 5929-5933. (doi:10.1021/bi970535d)
-
(1997)
Biochemistry
, vol.36
, pp. 5929-5933
-
-
Burack, W.R.1
Sturgill, T.W.2
-
71
-
-
0029790351
-
Ultrasensitivity in the mitogen-activated protein kinase cascade
-
(doi:10.1073/pnas.93.19.10078)
-
Huang CY, Ferrell Jr 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 Jr., J.E.2
-
72
-
-
0035943595
-
The mechanism of dephosphorylation of extracellular signal-regulated kinase 2 by mitogen-activated protein kinase phosphatase 3
-
(doi:10.1074/jbc.M103369200)
-
Zhao Y, Zhang ZY. 2001 The mechanism of dephosphorylation of extracellular signal-regulated kinase 2 by mitogen-activated protein kinase phosphatase 3. J. Biol. Chem. 276, 32 382-32 391. (doi:10.1074/jbc.M103369200)
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 32382-32391
-
-
Zhao, Y.1
Zhang, Z.Y.2
-
73
-
-
0035969559
-
Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication
-
(doi:10.1038/35107009)
-
Nash P, Tang X, Orlicky S, Chen Q, Gertler FB, Mendenhall MD, Sicheri F, Pawson T, Tyers M. 2001 Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414, 514-521. (doi:10.1038/35107009)
-
(2001)
Nature
, vol.414
, pp. 514-521
-
-
Nash, P.1
Tang, X.2
Orlicky, S.3
Chen, Q.4
Gertler, F.B.5
Mendenhall, M.D.6
Sicheri, F.7
Pawson, T.8
Tyers, M.9
-
74
-
-
82555205273
-
Cascades of multisite phosphorylation control sic1 destruction at the onset of S phase
-
(doi:10.1038/nature10560)
-
Koivomagi M, Valk E, Venta R, Iofik A, Lepiku M, Balog ER, Rubin SM, Morgan DO, Loog M. 2011 Cascades of multisite phosphorylation control Sic1 destruction at the onset of S phase. Nature 480, 128-131. (doi:10.1038/ nature10560)
-
(2011)
Nature
, vol.480
, pp. 128-131
-
-
Koivomagi, M.1
Valk, E.2
Venta, R.3
Iofik, A.4
Lepiku, M.5
Balog, E.R.6
Rubin, S.M.7
Morgan, D.O.8
Loog, M.9
-
75
-
-
0036498527
-
A phosphorylation-driven ubiquitination switch for cell-cycle control
-
(doi:10.1016/S0962-8924(01)02238-3)
-
Harper JW. 2002 A phosphorylation-driven ubiquitination switch for cell-cycle control. Trends Cell. Biol. 12, 104-107. (doi:10.1016/S0962-8924(01) 02238-3)
-
(2002)
Trends Cell. Biol.
, vol.12
, pp. 104-107
-
-
Harper, J.W.1
-
76
-
-
0035966288
-
Multisite phosphorylation and the countdown to S phase
-
(doi:10.1016/S0092-8674(01)00620-1)
-
Deshaies RJ, Ferrell Jr JE. 2001 Multisite phosphorylation and the countdown to S phase. Cell 107, 819-822. (doi:10.1016/S0092-8674(01)00620-1)
-
(2001)
Cell
, vol.107
, pp. 819-822
-
-
Deshaies, R.J.1
Ferrell Jr., J.E.2
-
77
-
-
0033634846
-
Concerted dephosphorylation of the transcription factor NFAT1 induces a conformational switch that regulates transcriptional activity
-
(doi:10.1016/S1097-2765(00)00053-8)
-
Okamura H et al. 2000 Concerted dephosphorylation of the transcription factor NFAT1 induces a conformational switch that regulates transcriptional activity. Mol. Cell 6, 539-550. (doi:10.1016/S1097-2765(00)00053-8)
-
(2000)
Mol. Cell
, vol.6
, pp. 539-550
-
-
Okamura, H.1
-
78
-
-
0037436383
-
Allosteric regulation of the transcription factor NFAT1 by multiple phosphorylation sites: A mathematical analysis
-
(doi:10.1016/S0022-2836(03)00085-8)
-
Salazar C, Hofer T. 2003 Allosteric regulation of the transcription factor NFAT1 by multiple phosphorylation sites: a mathematical analysis. J. Mol. Biol. 327, 31-45. (doi:10.1016/S0022-2836(03)00085-8)
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 31-45
-
-
Salazar, C.1
Hofer, T.2
-
79
-
-
0032580202
-
Calcium oscillations increase the efficiency and specificity of gene expression
-
(doi:10.1038/31960)
-
Dolmetsch RE, Xu K, Lewis RS. 1998 Calcium oscillations increase the efficiency and specificity of gene expression. Nature 392, 933-936. (doi:10. 1038/31960)
-
(1998)
Nature
, vol.392
, pp. 933-936
-
-
Dolmetsch, R.E.1
Xu, K.2
Lewis, R.S.3
-
80
-
-
79251534050
-
Ultrasensitivity in the regulation of cdc25c by cdk1
-
(doi:10.1016/j.molcel.2011.01.012)
-
Trunnell NB, Poon AC, Kim SY, Ferrell Jr JE. 2011 Ultrasensitivity in the regulation of Cdc25C by Cdk1. Mol. Cell 41, 263-274. (doi:10.1016/j.molcel. 2011. 01.012)
-
(2011)
Mol. Cell
, vol.41
, pp. 263-274
-
-
Trunnell, N.B.1
Poon, A.C.2
Kim, S.Y.3
Ferrell Jr., J.E.4
-
81
-
-
77951639384
-
A combination of multisite phosphorylation and substrate sequestration produces switchlike responses
-
(doi:10.1016/j.bpj.2009.12.4307)
-
Liu X, Bardwell L, Nie Q. 2010 A combination of multisite phosphorylation and substrate sequestration produces switchlike responses. Biophys. J. 98, 1396-1407. (doi:10.1016/j.bpj.2009.12.4307)
-
(2010)
Biophys. J.
, vol.98
, pp. 1396-1407
-
-
Liu, X.1
Bardwell, L.2
Nie, Q.3
-
82
-
-
79953897645
-
Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins
-
(doi:10.1016/j.bpj.2011.01.060)
-
Dushek O, van der Merwe PA, Shahrezaei V. 2011 Ultrasensitivity in multisite phosphorylation of membrane-anchored proteins. Biophys. J. 100, 1189-1197. (doi:10.1016/j.bpj.2011.01.060)
-
(2011)
Biophys. J.
, vol.100
, pp. 1189-1197
-
-
Dushek, O.1
Van Der Merwe, P.A.2
Shahrezaei, V.3
-
83
-
-
33846820252
-
Versatile regulation of multisite protein phosphorylation by the order of phosphate processing and protein-protein interactions
-
(doi:10.1111/j.1742-4658.2007.05653.x)
-
Salazar C, Hofer T. 2007 Versatile regulation of multisite protein phosphorylation by the order of phosphate processing and protein-protein interactions. FEBS J. 274, 1046-1061. (doi:10.1111/j.1742-4658.2007.05653.x)
-
(2007)
FEBS J.
, vol.274
, pp. 1046-1061
-
-
Salazar, C.1
Hofer, T.2
-
84
-
-
82955222826
-
The interplay of double phosphorylation and scaffolding in MAPK pathways
-
(doi:10.1016/j.jtbi.2011.11.014)
-
Kocieniewski P, Faeder JR, Lipniacki T. 2012 The interplay of double phosphorylation and scaffolding in MAPK pathways. J. Theor. Biol. 295, 116-124. (doi:10.1016/j.jtbi.2011.11.014)
-
(2012)
J. Theor. Biol.
, vol.295
, pp. 116-124
-
-
Kocieniewski, P.1
Faeder, J.R.2
Lipniacki, T.3
-
85
-
-
0034705227
-
Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties
-
(doi:10.1073/pnas. 97.11.5818)
-
Levchenko A, Bruck J, Sternberg PW. 2000 Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl Acad. Sci. USA 97, 5818-5823. (doi:10.1073/pnas. 97.11.5818)
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 5818-5823
-
-
Levchenko, A.1
Bruck, J.2
Sternberg, P.W.3
-
86
-
-
0028845251
-
2+/calmodulin activates the calmodulin-dependent protein kinase I cascade, via three independent mechanisms
-
(doi:10.1074/jbc.270.45.27186)
-
2+/calmodulin activates the calmodulin-dependent protein kinase I cascade, via three independent mechanisms. J. Biol. Chem. 270, 27 186-27 191. (doi:10.1074/jbc.270.45.27186)
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 27186-27191
-
-
Hawley, S.A.1
Selbert, M.A.2
Goldstein, E.G.3
Edelman, A.M.4
Carling, D.5
Hardie, D.G.6
-
87
-
-
0025915269
-
Evidence that AMP triggers phosphorylation as well as direct allosteric activation of rat liver AMP-activated protein kinase: A sensitive mechanism to protect the cell against ATP depletion
-
(doi:10.1111/j.1432-1033.1991.tb16172.x)
-
Moore F, Weekes J, Hardie DG. 1991 Evidence that AMP triggers phosphorylation as well as direct allosteric activation of rat liver AMP-activated protein kinase: a sensitive mechanism to protect the cell against ATP depletion. Eur. J. Biochem. 199, 691-697. (doi:10.1111/j.1432-1033.1991. tb16172.x)
-
(1991)
Eur. J. Biochem.
, vol.199
, pp. 691-697
-
-
Moore, F.1
Weekes, J.2
Hardie, D.G.3
-
88
-
-
0029561919
-
0-AMP inhibits dephosphorylation, as well as promoting phosphorylation, of the AMP-activated protein kinase: Studies using bacterially expressed human protein phosphatase-2Ca and native bovine protein phosphatase-2AC
-
(doi:10.1016/0014-5793(95)01368-7)
-
0-AMP inhibits dephosphorylation, as well as promoting phosphorylation, of the AMP-activated protein kinase: studies using bacterially expressed human protein phosphatase-2Ca and native bovine protein phosphatase-2AC. FEBS Lett. 377, 421-425. (doi:10.1016/0014-5793(95)01368-7)
-
(1995)
FEBS Lett.
, vol.377
, pp. 421-425
-
-
Davies, S.P.1
Helps, N.R.2
Cohen, P.T.3
Hardie, D.G.4
-
89
-
-
0024786438
-
Purification and characterization of the AMP-activated protein kinase: Copurification of acetyl-coa carboxylase kinase and 3-hydroxy-3-methylglutaryl- coa reductase kinase activities
-
(doi:10.1111/j.1432-1033.1989. tb15186.x)
-
Carling D, Clarke PR, Zammit VA, Hardie DG. 1989 Purification and characterization of the AMP-activated protein kinase: copurification of acetyl-CoA carboxylase kinase and 3-hydroxy-3-methylglutaryl-CoA reductase kinase activities. Eur. J. Biochem. 186, 129-136. (doi:10.1111/j.1432-1033.1989. tb15186.x)
-
(1989)
Eur. J. Biochem.
, vol.186
, pp. 129-136
-
-
Carling, D.1
Clarke, P.R.2
Zammit, V.A.3
Hardie, D.G.4
-
90
-
-
0033560109
-
AMP-activated protein kinase: An ultrasensitive system for monitoring cellular energy charge
-
(doi:10.1042/0264-6021:3380717)
-
Hardie DG, Salt IP, Hawley SA, Davies SP. 1999 AMP-activated protein kinase: an ultrasensitive system for monitoring cellular energy charge. Biochem. J. 338, 717-722. (doi:10.1042/0264-6021:3380717)
-
(1999)
Biochem. J.
, vol.338
, pp. 717-722
-
-
Hardie, D.G.1
Salt, I.P.2
Hawley, S.A.3
Davies, S.P.4
-
91
-
-
0033525830
-
Regulation of the hypoxia-inducible transcription factor 1a by the ubiquitin-proteasome pathway
-
(doi:10.1074/jbc.274.10.6519)
-
Kallio PJ, Wilson WJ, O'Brien S, Makino Y, Poellinger L. 1999 Regulation of the hypoxia-inducible transcription factor 1a by the ubiquitin-proteasome pathway. J. Biol. Chem. 274, 6519-6525. (doi:10. 1074/jbc.274.10.6519)
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 6519-6525
-
-
Kallio, P.J.1
Wilson, W.J.2
O'Brien, S.3
Makino, Y.4
Poellinger, L.5
-
92
-
-
0032493368
-
2-dependent degradation domain via the ubiquitin-proteasome pathway
-
(doi:10.1073/pnas. 95.14.7987)
-
2-dependent degradation domain via the ubiquitin-proteasome pathway. Proc. Natl Acad. Sci. USA 95, 7987-7992. (doi:10.1073/pnas. 95.14.7987)
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 7987-7992
-
-
Huang, L.E.1
Gu, J.2
Schau, M.3
Bunn, H.F.4
-
93
-
-
0037097861
-
FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor
-
(doi:10.1101/gad.991402)
-
Lando D, Peet DJ, Gorman JJ, Whelan DA, Whitelaw ML, Bruick RK. 2002 FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor. Genes Dev. 16, 1466-1471. (doi:10.1101/gad.991402)
-
(2002)
Genes Dev.
, vol.16
, pp. 1466-1471
-
-
Lando, D.1
Peet, D.J.2
Gorman, J.J.3
Whelan, D.A.4
Whitelaw, M.L.5
Bruick, R.K.6
-
94
-
-
0036469038
-
Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch
-
(doi:10.1126/science.1068592)
-
Lando D, Peet DJ, Whelan DA, Gorman JJ, Whitelaw ML. 2002 Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch. Science 295, 858-861. (doi:10.1126/science.1068592)
-
(2002)
Science
, vol.295
, pp. 858-861
-
-
Lando, D.1
Peet, D.J.2
Whelan, D.A.3
Gorman, J.J.4
Whitelaw, M.L.5
-
95
-
-
77957912885
-
Hypoxia-dependent sequestration of an oxygen sensor by a widespread structural motif can shape the hypoxic response - A predictive kinetic model
-
(doi:10.1186/1752-0509-4-139)
-
Schmierer B, Novak B, Schofield CJ. 2010 Hypoxia-dependent sequestration of an oxygen sensor by a widespread structural motif can shape the hypoxic response-a predictive kinetic model. BMC Syst. Biol. 4, 139. (doi:10.1186/1752-0509-4-139)
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 139
-
-
Schmierer, B.1
Novak, B.2
Schofield, C.J.3
-
97
-
-
0024322837
-
Quantitation of erythropoietin-producing cells in kidneys of mice by in situ hybridization: Correlation with hematocrit, renal erythropoietin mRNA, and serum erythropoietin concentration
-
Koury ST, Koury MJ, Bondurant MC, Caro J, Graber SE. 1989 Quantitation of erythropoietin-producing cells in kidneys of mice by in situ hybridization: correlation with hematocrit, renal erythropoietin mRNA, and serum erythropoietin concentration. Blood 74, 645-651.
-
(1989)
Blood
, vol.74
, pp. 645-651
-
-
Koury, S.T.1
Koury, M.J.2
Bondurant, M.C.3
Caro, J.4
Graber, S.E.5
-
98
-
-
0027458517
-
In vivo and in vitro regulation of erythropoietin mRNA: Measurement by competitive polymerase chain reaction
-
Fandrey J, Bunn HF. 1993 In vivo and in vitro regulation of erythropoietin mRNA: measurement by competitive polymerase chain reaction. Blood 81, 617-623.
-
(1993)
Blood
, vol.81
, pp. 617-623
-
-
Fandrey, J.1
Bunn, H.F.2
-
99
-
-
24744453945
-
Specific patterns of electrophile adduction trigger keap1 ubiquitination and nrf2 activation
-
(doi:10.1074/jbc. M503346200)
-
Hong F, Sekhar KR, Freeman ML, Liebler DC. 2005 Specific patterns of electrophile adduction trigger Keap1 ubiquitination and Nrf2 activation. J. Biol. Chem. 280, 31 768-31 775. (doi:10.1074/jbc. M503346200)
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 31768-31775
-
-
Hong, F.1
Sekhar, K.R.2
Freeman, M.L.3
Liebler, D.C.4
-
100
-
-
33344469643
-
Oxidative and electrophilic stresses activate nrf2 through inhibition of ubiquitination activity of keap1
-
(doi:10.1128/MCB.26.1. 221-229.2006)
-
Kobayashi A, Kang MI, Watai Y, Tong KI, Shibata T, Uchida K, Yamamoto M. 2006 Oxidative and electrophilic stresses activate Nrf2 through Inhibition of ubiquitination activity of Keap1. Mol. Cell. Biol. 26, 221-229. (doi:10.1128/MCB.26.1. 221-229.2006)
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 221-229
-
-
Kobayashi, A.1
Kang, M.I.2
Watai, Y.3
Tong, K.I.4
Shibata, T.5
Uchida, K.6
Yamamoto, M.7
-
101
-
-
77950352188
-
An internal ribosomal entry site mediates redox-sensitive translation of nrf2
-
(doi:10.1093/nar/gkp1048)
-
Li W, Thakor N, Xu EY, Huang Y, Chen C, Yu R, Holcik M, Kong AN. 2010 An internal ribosomal entry site mediates redox-sensitive translation of Nrf2. Nucleic Acids Res. 38, 778-788. (doi:10.1093/nar/gkp1048)
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 778-788
-
-
Li, W.1
Thakor, N.2
Xu, E.Y.3
Huang, Y.4
Chen, C.5
Yu, R.6
Holcik, M.7
Kong, A.N.8
-
102
-
-
33748752586
-
Nrf2 possesses a redox-sensitive nuclear exporting signal in the neh5 transactivation domain
-
(doi:10.1074/jbc.M602746200)
-
Li W, Yu SW, Kong AN. 2006 Nrf2 possesses a redox-sensitive nuclear exporting signal in the Neh5 transactivation domain. J. Biol. Chem. 281, 27 251-27 263. (doi:10.1074/jbc.M602746200)
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 27251-27263
-
-
Li, W.1
Yu, S.W.2
Kong, A.N.3
-
103
-
-
0030792712
-
Control of TRAIL-induced apoptosis by a family of signaling and decoy receptors
-
(doi:10.1126/science.277.5327.818)
-
Sheridan JP et al. 1997 Control of TRAIL-induced apoptosis by a family of signaling and decoy receptors. Science 277, 818-821. (doi:10.1126/science.277. 5327.818)
-
(1997)
Science
, vol.277
, pp. 818-821
-
-
Sheridan, J.P.1
-
104
-
-
0027181936
-
Interleukin-1 type II receptor: A decoy target for IL-1 that is regulated by IL-4
-
(doi:10.1126/science. 8332913)
-
Colotta F et al. 1993 Interleukin-1 type II receptor: a decoy target for IL-1 that is regulated by IL-4. Science 261, 472-475. (doi:10.1126/science. 8332913)
-
(1993)
Science
, vol.261
, pp. 472-475
-
-
Colotta, F.1
-
105
-
-
46249127495
-
Structural basis for EGFR ligand sequestration by argos
-
(doi:10.1038/nature06978)
-
Klein DE, Stayrook SE, Shi F, Narayan K, Lemmon MA. 2008 Structural basis for EGFR ligand sequestration by Argos. Nature 453, 1271-1275. (doi:10.1038/nature06978)
-
(2008)
Nature
, vol.453
, pp. 1271-1275
-
-
Klein, D.E.1
Stayrook, S.E.2
Shi, F.3
Narayan, K.4
Lemmon, M.A.5
-
106
-
-
4344611655
-
Argos inhibits epidermal growth factor receptor signalling by ligand sequestration
-
(doi:10.1038/nature02840)
-
Klein DE, Nappi VM, Reeves GT, Shvartsman SY, Lemmon MA. 2004 Argos inhibits epidermal growth factor receptor signalling by ligand sequestration. Nature 430, 1040-1044. (doi:10.1038/nature02840)
-
(2004)
Nature
, vol.430
, pp. 1040-1044
-
-
Klein, D.E.1
Nappi, V.M.2
Reeves, G.T.3
Shvartsman, S.Y.4
Lemmon, M.A.5
-
107
-
-
0028335141
-
The expression pattern of id4, a novel dominant negative helix-loop-helix protein, is distinct from id1, id2 and id3
-
(doi:10.1093/nar/22.5.749)
-
Riechmann V, van Cruchten I, Sablitzky F. 1994 The expression pattern of Id4, a novel dominant negative helix-loop-helix protein, is distinct from Id1, Id2 and Id3. Nucleic Acids Res. 22, 749-755. (doi:10.1093/nar/22.5.749)
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 749-755
-
-
Riechmann, V.1
Van Cruchten, I.2
Sablitzky, F.3
-
108
-
-
0025238437
-
The protein id: A negative regulator of helix-loop-helix DNA binding proteins
-
(doi:10.1016/0092-8674(90)90214-Y)
-
Benezra R, Davis RL, Lockshon D, Turner DL, Weintraub H. 1990 The protein Id: a negative regulator of helix-loop-helix DNA binding proteins. Cell 61, 49-59. (doi:10.1016/0092-8674(90)90214-Y)
-
(1990)
Cell
, vol.61
, pp. 49-59
-
-
Benezra, R.1
Davis, R.L.2
Lockshon, D.3
Turner, D.L.4
Weintraub, H.5
-
109
-
-
0035924698
-
Emc, a negative HLH regulator with multiple functions in drosophila development
-
(doi:10.1038/sj.onc.1205162)
-
Campuzano S. 2001 Emc, a negative HLH regulator with multiple functions in Drosophila development. Oncogene 20, 8299-8307. (doi:10.1038/sj. onc.1205162)
-
(2001)
Oncogene
, vol.20
, pp. 8299-8307
-
-
Campuzano, S.1
-
110
-
-
0031754882
-
The anti-sigma factors
-
(doi:10.1146/annurev.micro.52.1.231)
-
Hughes KT, Mathee K. 1998 The anti-sigma factors. Annu. Rev. Microbiol. 52, 231-286. (doi:10.1146/annurev.micro.52.1.231)
-
(1998)
Annu. Rev. Microbiol.
, vol.52
, pp. 231-286
-
-
Hughes, K.T.1
Mathee, K.2
-
111
-
-
67149138163
-
Protein sequestration generates a flexible ultrasensitive response in a genetic network
-
(doi:10.1038/msb.2009.30)
-
Buchler NE, Cross FR. 2009 Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol. Syst. Biol. 5, 272. (doi:10. 1038/msb.2009.30)
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 272
-
-
Buchler, N.E.1
Cross, F.R.2
-
112
-
-
56949098506
-
Molecular titration and ultrasensitivity in regulatory networks
-
(doi:10.1016/j.jmb.2008.09.079)
-
Buchler NE, Louis M. 2008 Molecular titration and ultrasensitivity in regulatory networks. J. Mol. Biol. 384, 1106-1119. (doi:10.1016/j.jmb.2008.09. 079)
-
(2008)
J. Mol. Biol.
, vol.384
, pp. 1106-1119
-
-
Buchler, N.E.1
Louis, M.2
-
113
-
-
34547130813
-
Functional sequestration of transcription factor activity by repetitive DNA
-
(doi:10.1074/jbc.M702547200)
-
Liu X, Wu B, Szary J, Kofoed EM, Schaufele F. 2007 Functional sequestration of transcription factor activity by repetitive DNA. J. Biol. Chem. 282, 20 868-20 876. (doi:10.1074/jbc.M702547200)
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 20868-20876
-
-
Liu, X.1
Wu, B.2
Szary, J.3
Kofoed, E.M.4
Schaufele, F.5
-
114
-
-
84859206826
-
A regulatory role for repeated decoy transcription factor binding sites in target gene expression
-
(doi:10.1038/msb.2012.7)
-
Lee TH, Maheshri N. 2012 A regulatory role for repeated decoy transcription factor binding sites in target gene expression. Mol. Syst. Biol. 8, 576. (doi:10.1038/msb.2012.7)
-
(2012)
Mol. Syst. Biol.
, vol.8
, pp. 576
-
-
Lee, T.H.1
Maheshri, N.2
-
115
-
-
80055106927
-
High-precision, in vitro validation of the sequestration mechanism for generating ultrasensitive dose-response curves in regulatory networks
-
(doi:10.1371/journal.pcbi.1002171)
-
Ricci F, Vallee-Belisle A, Plaxco KW. 2011 High-precision, in vitro validation of the sequestration mechanism for generating ultrasensitive dose-response curves in regulatory networks. PLoS Comput. Biol. 7, e1002171. (doi:10.1371/journal.pcbi.1002171)
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Ricci, F.1
Vallee-Belisle, A.2
Plaxco, K.W.3
-
116
-
-
33947304756
-
Substrate competition as a source of ultrasensitivity in the inactivation of wee1
-
(doi:10.1016/j.cell. 2007.01.039)
-
Kim SY, Ferrell Jr JE. 2007 Substrate competition as a source of ultrasensitivity in the inactivation of Wee1. Cell 128, 1133-1145. (doi:10.1016/j.cell. 2007.01.039)
-
(2007)
Cell
, vol.128
, pp. 1133-1145
-
-
Kim, S.Y.1
Ferrell Jr., J.E.2
-
117
-
-
80051748138
-
Robust spindle alignment in drosophila neuroblasts by ultrasensitive activation of pins
-
(doi:10.1016/j.molcel.2011.06.030)
-
Smith NR, Prehoda KE. 2011 Robust spindle alignment in Drosophila neuroblasts by ultrasensitive activation of pins. Mol. Cell. 43, 540-549. (doi:10.1016/j.molcel.2011.06.030)
-
(2011)
Mol. Cell.
, vol.43
, pp. 540-549
-
-
Smith, N.R.1
Prehoda, K.E.2
-
118
-
-
63049120802
-
Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins
-
(doi:10.1074/mcp.M800340-MCP200)
-
Cockman ME, Webb JD, Kramer HB, Kessler BM, Ratcliffe PJ. 2009 Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins. Mol. Cell. Proteomics 8, 535-546. (doi:10. 1074/mcp.M800340-MCP200)
-
(2009)
Mol. Cell. Proteomics
, vol.8
, pp. 535-546
-
-
Cockman, M.E.1
Webb, J.D.2
Kramer, H.B.3
Kessler, B.M.4
Ratcliffe, P.J.5
-
119
-
-
0021741048
-
The branch point effect: Ultrasensitivity and subsensitivity to metabolic control
-
LaPorte DC, Walsh K, Koshland Jr DE. 1984 The branch point effect: ultrasensitivity and subsensitivity to metabolic control. J. Biol. Chem. 259, 14 068-14 075.
-
(1984)
J. Biol. Chem.
, vol.259
, pp. 14068-14075
-
-
LaPorte, D.C.1
Walsh, K.2
Koshland Jr., D.E.3
-
120
-
-
82655179954
-
How molecular competition influences fluxes in gene expression networks
-
(doi:10.1371/journal.pone.0028494)
-
De Vos D, Bruggeman FJ, Westerhoff HV, Bakker BM. 2011 How molecular competition influences fluxes in gene expression networks. PLoS ONE 6, e28494. (doi:10.1371/journal.pone.0028494)
-
(2011)
PLoS ONE
, vol.6
-
-
De Vos, D.1
Bruggeman, F.J.2
Westerhoff, H.V.3
Bakker, B.M.4
-
121
-
-
0017041893
-
Theoretical considerations of the sensitivity conferred by substrate cycles in vivo
-
Crabtree B. 1976 Theoretical considerations of the sensitivity conferred by substrate cycles in vivo. Biochem. Soc. Trans. 4, 999-1002.
-
(1976)
Biochem. Soc. Trans.
, vol.4
, pp. 999-1002
-
-
Crabtree, B.1
-
122
-
-
0021847426
-
Metabolic control and its analysis. Additional relationships between elasticities and control coefficients
-
(doi:10.1111/j.1432-1033.1985. tb08876.x)
-
Fell DA, Sauro HM. 1985 Metabolic control and its analysis. Additional relationships between elasticities and control coefficients. Eur. J. Biochem. 148, 555-561. (doi:10.1111/j.1432-1033.1985. tb08876.x)
-
(1985)
Eur. J. Biochem.
, vol.148
, pp. 555-561
-
-
Fell, D.A.1
Sauro, H.M.2
-
123
-
-
3142564584
-
The small RNA chaperone hfq and multiple small RNAs control quorum sensing in vibrio harveyi and vibrio cholerae
-
(doi:10.1016/j.cell.2004.06.009)
-
Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL. 2004 The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69-82. (doi:10.1016/j.cell.2004. 06.009)
-
(2004)
Cell
, vol.118
, pp. 69-82
-
-
Lenz, D.H.1
Mok, K.C.2
Lilley, B.N.3
Kulkarni, R.V.4
Wingreen, N.S.5
Bassler, B.L.6
-
124
-
-
55949097145
-
Small RNAs establish delays and temporal thresholds in gene expression
-
(doi:10.1529/biophysj.108.133819)
-
Legewie S, Dienst D, Wilde A, Herzel H, Axmann IM. 2008 Small RNAs establish delays and temporal thresholds in gene expression. Biophys. J. 95, 3232-3238. (doi:10.1529/biophysj.108.133819)
-
(2008)
Biophys. J.
, vol.95
, pp. 3232-3238
-
-
Legewie, S.1
Dienst, D.2
Wilde, A.3
Herzel, H.4
Axmann, I.M.5
-
125
-
-
54049118804
-
A quantitative comparison of sRNA-based and protein-based gene regulation
-
(doi:10.1038/msb. 2008.58)
-
Mehta P, Goyal S, Wingreen NS. 2008 A quantitative comparison of sRNA-based and protein-based gene regulation. Mol. Syst. Biol. 4, 221. (doi:10.1038/msb. 2008.58)
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 221
-
-
Mehta, P.1
Goyal, S.2
Wingreen, N.S.3
-
126
-
-
34548668642
-
Quantitative characteristics of gene regulation by small RNA
-
(doi:10.1371/journal. pbio.0050229)
-
Levine E, Zhang Z, Kuhlman T, Hwa T. 2007 Quantitative characteristics of gene regulation by small RNA. PLoS Biol. 5, e229. (doi:10.1371/journal. pbio.0050229)
-
(2007)
PLoS Biol.
, vol.5
-
-
Levine, E.1
Zhang, Z.2
Kuhlman, T.3
Hwa, T.4
-
127
-
-
80052266532
-
MicroRNAs can generate thresholds in target gene expression
-
(doi:10.1038/ng.905)
-
Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, van Oudenaarden A. 2011 MicroRNAs can generate thresholds in target gene expression. Nat. Genet. 43, 854-859. (doi:10.1038/ng.905)
-
(2011)
Nat. Genet.
, vol.43
, pp. 854-859
-
-
Mukherji, S.1
Ebert, M.S.2
Zheng, G.X.3
Tsang, J.S.4
Sharp, P.A.5
Van Oudenaarden, A.6
-
128
-
-
0022449017
-
Determinator - Inhibitor pairs as a mechanism for threshold setting in development: A possible function for pseudogenes
-
(doi:10.1073/pnas.83.3.679)
-
McCarrey JR, Riggs AD. 1986 Determinator - inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. Proc. Natl Acad. Sci. USA 83, 679-683. (doi:10.1073/pnas.83.3.679)
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 679-683
-
-
McCarrey, J.R.1
Riggs, A.D.2
-
129
-
-
0017705507
-
Posttranslational covalent modification of proteins
-
(doi:10.1126/science.337487)
-
Uy R, Wold F. 1977 Posttranslational covalent modification of proteins. Science 198, 890-896. (doi:10.1126/science.337487)
-
(1977)
Science
, vol.198
, pp. 890-896
-
-
Uy, R.1
Wold, F.2
-
130
-
-
0021715523
-
Ultrasensitivity in biochemical systems controlled by covalent modification: Interplay between zero-order and multistep effects
-
Goldbeter A, Koshland Jr DE. 1984 Ultrasensitivity in biochemical systems controlled by covalent modification: interplay between zero-order and multistep effects. J. Biol. Chem. 259, 14 441-14 447.
-
(1984)
J. Biol. Chem.
, vol.259
, pp. 14441-14447
-
-
Goldbeter, A.1
Koshland Jr., D.E.2
-
131
-
-
0020592357
-
Phosphorylation of isocitrate dehydrogenase as a demonstration of enhanced sensitivity in covalent regulation
-
(doi:10.1038/305286a0)
-
LaPorte DC, Koshland Jr DE. 1983 Phosphorylation of isocitrate dehydrogenase as a demonstration of enhanced sensitivity in covalent regulation. Nature 305, 286-290. (doi:10.1038/305286a0)
-
(1983)
Nature
, vol.305
, pp. 286-290
-
-
LaPorte, D.C.1
Koshland Jr., D.E.2
-
132
-
-
0022517716
-
Zero-order ultrasensitivity in the regulation of glycogen phosphorylase
-
(doi:10.1073/pnas.83.9.2865)
-
Meinke MH, Bishop JS, Edstrom RD. 1986 Zero-order ultrasensitivity in the regulation of glycogen phosphorylase. Proc. Natl Acad. Sci. USA 83, 2865-2868. (doi:10.1073/pnas.83.9.2865)
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 2865-2868
-
-
Meinke, M.H.1
Bishop, J.S.2
Edstrom, R.D.3
-
133
-
-
0025850506
-
Muscle glycogenolysis: Regulation of the cyclic interconversion of phosphorylase a and phosphorylase b
-
Meinke MH, Edstrom RD. 1991 Muscle glycogenolysis: regulation of the cyclic interconversion of phosphorylase a and phosphorylase b. J. Biol. Chem. 266, 2259-2266.
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 2259-2266
-
-
Meinke, M.H.1
Edstrom, R.D.2
-
134
-
-
33746931732
-
Threshold responses to morphogen gradients by zero-order ultrasensitivity
-
(doi:10.1038/msb4100036)
-
Melen GJ, Levy S, Barkai N, Shilo BZ. 2005 Threshold responses to morphogen gradients by zero-order ultrasensitivity. Mol. Syst. Biol. 1, 0028. (doi:10.1038/msb4100036)
-
(2005)
Mol. Syst. Biol.
, vol.1
, pp. 0028
-
-
Melen, G.J.1
Levy, S.2
Barkai, N.3
Shilo, B.Z.4
-
135
-
-
0023573908
-
Experimental evidence for a zero-order ultrasensitivity in a simple substrate cycle
-
(doi:10.1016/0006-291X(87)90412-8)
-
Cimino A, Hervagault JF. 1987 Experimental evidence for a zero-order ultrasensitivity in a simple substrate cycle. Biochem. Biophys. Res. Commun. 149, 615-620. (doi:10.1016/0006-291X(87)90412-8)
-
(1987)
Biochem. Biophys. Res. Commun.
, vol.149
, pp. 615-620
-
-
Cimino, A.1
Hervagault, J.F.2
-
136
-
-
33749350211
-
Transcriptional dynamics of the embryonic stem cell switch
-
(doi:10.1371/journal.pcbi.0020123)
-
Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C. 2006 Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol. 2, e123. (doi:10.1371/journal.pcbi.0020123)
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Chickarmane, V.1
Troein, C.2
Nuber, U.A.3
Sauro, H.M.4
Peterson, C.5
-
137
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
(doi:10.1016/j.cell.2005.08.020)
-
Boyer LA et al. 2005 Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956. (doi:10.1016/j.cell.2005.08.020)
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
-
138
-
-
33745456986
-
Core transcriptional regulatory circuitry in human hepatocytes
-
(doi:10.1038/msb4100059)
-
Odom DT et al. 2006 Core transcriptional regulatory circuitry in human hepatocytes. Mol. Syst. Biol. 2, 0017. (doi:10.1038/msb4100059)
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 0017
-
-
Odom, D.T.1
-
139
-
-
0028364906
-
MyoD1 promoter autoregulation is mediated by two proximal E-boxes
-
(doi:10.1093/nar/22.12.2234)
-
Zingg JM, Pedraza-Alva G, Jost JP. 1994 MyoD1 promoter autoregulation is mediated by two proximal E-boxes. Nucleic Acids Res. 22, 2234-2241. (doi:10.1093/nar/22.12.2234)
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2234-2241
-
-
Zingg, J.M.1
Pedraza-Alva, G.2
Jost, J.P.3
-
140
-
-
20144368117
-
Potential autoregulation of transcription factor PU.1 by an upstream regulatory element
-
(doi:10.1128/MCB.25.7.2832-2845.2005)
-
Okuno Y et al. 2005 Potential autoregulation of transcription factor PU.1 by an upstream regulatory element. Mol. Cell. Biol. 25, 2832-2845. (doi:10. 1128/MCB.25.7.2832-2845.2005)
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 2832-2845
-
-
Okuno, Y.1
-
141
-
-
0033983960
-
A GATA box in the GATA-1 gene hematopoietic enhancer is a critical element in the network of GATA factors and sites that regulate this gene
-
(doi:10.1128/MCB.20.2.713-723.2000)
-
Nishimura S, Takahashi S, Kuroha T, Suwabe N, Nagasawa T, Trainor C, Yamamoto M. 2000 A GATA box in the GATA-1 gene hematopoietic enhancer is a critical element in the network of GATA factors and sites that regulate this gene. Mol. Cell. Biol. 20, 713-723. (doi:10.1128/MCB.20.2.713-723.2000)
-
(2000)
Mol. Cell. Biol.
, vol.20
, pp. 713-723
-
-
Nishimura, S.1
Takahashi, S.2
Kuroha, T.3
Suwabe, N.4
Nagasawa, T.5
Trainor, C.6
Yamamoto, M.7
-
142
-
-
78349256632
-
The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response
-
(doi:10.1088/1478-3975/7/3/036005)
-
Tiwari A, Balazsi G, Gennaro ML, Igoshin OA. 2010 The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Phys. Biol. 7, 036005. (doi:10.1088/1478-3975/ 7/3/036005)
-
(2010)
Phys. Biol.
, vol.7
, pp. 036005
-
-
Tiwari, A.1
Balazsi, G.2
Gennaro, M.L.3
Igoshin, O.A.4
-
143
-
-
50349087322
-
Positive receptor feedback during lineage commitment can generate ultrasensitivity to ligand and confer robustness to a bistable switch
-
(doi:10.1529/biophysj.107.120600)
-
Palani S, Sarkar CA. 2008 Positive receptor feedback during lineage commitment can generate ultrasensitivity to ligand and confer robustness to a bistable switch. Biophys. J. 95, 1575-1589. (doi:10. 1529/biophysj.107.120600)
-
(2008)
Biophys. J.
, vol.95
, pp. 1575-1589
-
-
Palani, S.1
Sarkar, C.A.2
-
144
-
-
79551684408
-
A bistable switch underlying B-cell differentiation and its disruption by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin
-
(doi:10.1093/toxsci/kfq035)
-
Bhattacharya S, Conolly RB, Kaminski NE, Thomas RS, Andersen ME, Zhang Q. 2010 A bistable switch underlying B-cell differentiation and its disruption by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol. Sci. 115, 51-65. (doi:10.1093/toxsci/kfq035)
-
(2010)
Toxicol. Sci.
, vol.115
, pp. 51-65
-
-
Bhattacharya, S.1
Conolly, R.B.2
Kaminski, N.E.3
Thomas, R.S.4
Andersen, M.E.5
Zhang, Q.6
-
145
-
-
79958097395
-
Emergence of switch-like behavior in a large family of simple biochemical networks
-
(doi:10.1371/journal.pcbi.1002039)
-
Siegal-Gaskins D, Mejia-Guerra MK, Smith GD, Grotewold E. 2011 Emergence of switch-like behavior in a large family of simple biochemical networks. PLoS Comput. Biol. 7, e1002039. (doi:10. 1371/journal.pcbi.1002039)
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Siegal-Gaskins, D.1
Mejia-Guerra, M.K.2
Smith, G.D.3
Grotewold, E.4
-
146
-
-
42149184620
-
Ultrasensitive gene regulation by positive feedback loops in nucleosome modification
-
(doi:10.1038/msb.2008.21)
-
Sneppen K, Micheelsen MA, Dodd IB. 2008 Ultrasensitive gene regulation by positive feedback loops in nucleosome modification. Mol. Syst. Biol. 4, 182. (doi:10.1038/msb.2008.21)
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 182
-
-
Sneppen, K.1
Micheelsen, M.A.2
Dodd, I.B.3
-
147
-
-
34249080596
-
Theoretical analysis of epigenetic cell memory by nucleosome modification
-
(doi:10.1016/j.cell.2007.02.053)
-
Dodd IB, Micheelsen MA, Sneppen K, Thon G. 2007 Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129, 813-822. (doi:10.1016/j.cell.2007.02.053)
-
(2007)
Cell
, vol.129
, pp. 813-822
-
-
Dodd, I.B.1
Micheelsen, M.A.2
Sneppen, K.3
Thon, G.4
-
148
-
-
77952093377
-
The scaffold protein ste5 directly controls a switch-like mating decision in yeast
-
(doi:10.1038/nature08946)
-
Malleshaiah MK, Shahrezaei V, Swain PS, Michnick SW. 2010 The scaffold protein Ste5 directly controls a switch-like mating decision in yeast. Nature 465, 101-105. (doi:10.1038/nature08946)
-
(2010)
Nature
, vol.465
, pp. 101-105
-
-
Malleshaiah, M.K.1
Shahrezaei, V.2
Swain, P.S.3
Michnick, S.W.4
-
149
-
-
0041836230
-
2+/calmodulin-dependent protein kinase II-protein phosphatase 1 switch facilitates specificity in postsynaptic calcium signaling
-
(doi:10.1073/pnas. 1932759100)
-
2+/calmodulin-dependent protein kinase II-protein phosphatase 1 switch facilitates specificity in postsynaptic calcium signaling. Proc. Natl Acad. Sci. USA 100, 10 512-10 517. (doi:10.1073/pnas. 1932759100)
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 10512-10517
-
-
Bradshaw, J.M.1
Kubota, Y.2
Meyer, T.3
Schulman, H.4
-
150
-
-
8344237449
-
Hydroxylation of HIF-1: Oxygen sensing at the molecular level
-
(doi:10.1152/physiol.00001.2004)
-
Semenza GL. 2004 Hydroxylation of HIF-1: oxygen sensing at the molecular level. Physiology (Bethesda) 19, 176-182. (doi:10.1152/physiol. 00001.2004)
-
(2004)
Physiology (Bethesda)
, vol.19
, pp. 176-182
-
-
Semenza, G.L.1
-
151
-
-
22144443131
-
Nonlinear protein degradation and the function of genetic circuits
-
(doi:10.1073/pnas.0409553102)
-
Buchler NE, Gerland U, Hwa T. 2005 Nonlinear protein degradation and the function of genetic circuits. Proc. Natl Acad. Sci. USA 102, 9559-9564. (doi:10.1073/pnas.0409553102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 9559-9564
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
152
-
-
0033855774
-
Fluctuations and quality of control in biological cells: Zero-order ultrasensitivity reinvestigated
-
(doi:10.1016/S0006-3495(00)76377-6)
-
Berg OG, Paulsson J, Ehrenberg M. 2000 Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J. 79, 1228-1236. (doi:10.1016/S0006-3495(00)76377-6)
-
(2000)
Biophys. J.
, vol.79
, pp. 1228-1236
-
-
Berg, O.G.1
Paulsson, J.2
Ehrenberg, M.3
-
153
-
-
33644966561
-
Effects of sequestration on signal transduction cascades
-
(doi:10.1111/j.1742-4658. 2006.05105.x)
-
Bluthgen N, Bruggeman FJ, Legewie S, Herzel H, Westerhoff HV, Kholodenko BN. 2006 Effects of sequestration on signal transduction cascades. FEBS J. 273, 895-906. (doi:10.1111/j.1742-4658. 2006.05105.x)
-
(2006)
FEBS J.
, vol.273
, pp. 895-906
-
-
Bluthgen, N.1
Bruggeman, F.J.2
Legewie, S.3
Herzel, H.4
Westerhoff, H.V.5
Kholodenko, B.N.6
-
154
-
-
74049084055
-
Introducing total substrates simplifies theoretical analysis at non-negligible enzyme concentrations: Pseudo first-order kinetics and the loss of zero-order ultrasensitivity
-
(doi:10.1007/s00285-009-0267-6)
-
Pedersen MG, Bersani AM. 2010 Introducing total substrates simplifies theoretical analysis at non-negligible enzyme concentrations: pseudo first-order kinetics and the loss of zero-order ultrasensitivity. J. Math. Biol. 60, 267-283. (doi:10.1007/s00285-009-0267-6)
-
(2010)
J. Math. Biol.
, vol.60
, pp. 267-283
-
-
Pedersen, M.G.1
Bersani, A.M.2
-
155
-
-
77953387357
-
Signaling properties of a covalent modification cycle are altered by a downstream target
-
(doi:10.1073/pnas.0913815107)
-
Ventura AC, Jiang P, Van Wassenhove L, Del Vecchio D, Merajver SD, Ninfa AJ. 2010 Signaling properties of a covalent modification cycle are altered by a downstream target. Proc. Natl Acad. Sci. USA 107, 10 032-10 037. (doi:10.1073/pnas.0913815107)
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 10032-10037
-
-
Ventura, A.C.1
Jiang, P.2
Van Wassenhove, L.3
Del Vecchio, D.4
Merajver, S.D.5
Ninfa, A.J.6
-
156
-
-
35748929940
-
Enzyme localization can drastically affect signal amplification in signal transduction pathways
-
(doi:10.1371/journal.pcbi.0030195)
-
van Albada SB, ten Wolde PR. 2007 Enzyme localization can drastically affect signal amplification in signal transduction pathways. PLoS Comput. Biol. 3, 1925-1934. (doi:10.1371/journal.pcbi.0030195)
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 1925-1934
-
-
Van Albada, S.B.1
Ten Wolde, P.R.2
-
157
-
-
84865575045
-
Realistic enzymology for post-translational modification: Zero-order ultrasensitivity revisited
-
(doi:10.1016/j.jtbi.2012.07.012)
-
Xu Y, Gunawardena J. 2012 Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited. J. Theor. Biol. 311, 139-152. (doi:10.1016/j.jtbi.2012.07.012)
-
(2012)
J. Theor. Biol.
, vol.311
, pp. 139-152
-
-
Xu, Y.1
Gunawardena, J.2
-
158
-
-
7644238181
-
Biological robustness
-
(doi:10.1038/nrg1471)
-
Kitano H. 2004 Biological robustness. Nat. Rev. Genet. 5, 826-837. (doi:10.1038/nrg1471)
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 826-837
-
-
Kitano, H.1
-
159
-
-
79959859399
-
Robust network topologies for generating switch-like cellular responses
-
(doi:10.1371/journal.pcbi.1002085)
-
Shah NA, Sarkar CA. 2011 Robust network topologies for generating switch-like cellular responses. PLoS Comput. Biol. 7, e1002085. (doi:10.1371/journal.pcbi.1002085)
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Shah, N.A.1
Sarkar, C.A.2
-
160
-
-
0242515913
-
The JNK cascade as a biochemical switch in Mammalian cells: Ultrasensitive and all-or-none responses
-
(doi:10.1016/S0960-9822(03)00083-6)
-
Bagowski CP, Besser J, Frey CR, Ferrell Jr JE. 2003 The JNK cascade as a biochemical switch in mammalian cells: ultrasensitive and all-or-none responses. Curr. Biol. 13, 315-320. (doi:10.1016/S0960-9822(03)00083-6)
-
(2003)
Curr. Biol.
, vol.13
, pp. 315-320
-
-
Bagowski, C.P.1
Besser, J.2
Frey, C.R.3
Ferrell Jr., J.E.4
-
161
-
-
78650929625
-
Tunable signal processing in synthetic MAP kinase cascades
-
(doi:10.1016/j. cell.2010.12.014)
-
O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA. 2011 Tunable signal processing in synthetic MAP kinase cascades. Cell 144, 119-131. (doi:10.1016/j. cell.2010.12.014)
-
(2011)
Cell
, vol.144
, pp. 119-131
-
-
O'Shaughnessy, E.C.1
Palani, S.2
Collins, J.J.3
Sarkar, C.A.4
-
162
-
-
0037605637
-
Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible
-
(doi:10.1063/1.1349894)
-
Ferrell JE, Xiong W. 2001 Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible. Chaos 11, 227-236. (doi:10.1063/1.1349894)
-
(2001)
Chaos
, vol.11
, pp. 227-236
-
-
Ferrell, J.E.1
Xiong, W.2
-
163
-
-
1242274449
-
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
-
(doi:10.1073/pnas.0308265100)
-
Angeli D, Ferrell Jr JE, Sontag ED. 2004 Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl Acad. Sci. USA 101, 1822-1827. (doi:10.1073/pnas.0308265100)
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 1822-1827
-
-
Angeli, D.1
Ferrell Jr., J.E.2
Sontag, E.D.3
-
164
-
-
67149084325
-
Network dynamics
-
(doi:10.1007/978-1-59745-243-4-13)
-
Sauro HM. 2009 Network dynamics. Methods Mol. Biol. 541, 269. (doi:10.1007/978-1-59745-243-4-13)
-
(2009)
Methods Mol. Biol.
, vol.541
, pp. 269
-
-
Sauro, H.M.1
-
166
-
-
70349288028
-
Cellular stress response pathway system as a sentinel ensemble in toxicological screening
-
(doi:10.1093/toxsci/kfp140)
-
Simmons SO, Fan CY, Ramabhadran R. 2009 Cellular stress response pathway system as a sentinel ensemble in toxicological screening. Toxicol. Sci. 111, 202-225. (doi:10.1093/toxsci/kfp140)
-
(2009)
Toxicol. Sci.
, vol.111
, pp. 202-225
-
-
Simmons, S.O.1
Fan, C.Y.2
Ramabhadran, R.3
-
168
-
-
0016201107
-
Optimal design of feedback control by inhibition: Steady state considerations
-
(doi:10.1007/BF01732019)
-
Savageau MA. 1974 Optimal design of feedback control by inhibition:
-
(1974)
J. Mol. EVol.
, vol.4
, pp. 139-156
-
-
Savageau, M.A.1
-
169
-
-
78449248996
-
Systematic quantification of negative feedback mechanisms in the extracellular signal-regulated kinase (ERK) signaling network
-
(doi:10.1074/jbc.M110.148759)
-
Cirit M, Wang CC, Haugh JM. 2010 Systematic quantification of negative feedback mechanisms in the extracellular signal-regulated kinase (ERK) signaling network. J. Biol. Chem. 285, 36 736-36 744. (doi:10.1074/jbc.M110.148759)
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 36736-36744
-
-
Cirit, M.1
Wang, C.C.2
Haugh, J.M.3
-
170
-
-
78650635354
-
The Mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier
-
ra90 (doi:10.1126/scisignal.2001212)
-
Sturm OE et al. 2010 The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Sci. Signal. 3, ra90. (doi:10.1126/scisignal. 2001212)
-
(2010)
Sci. Signal.
, vol.3
-
-
Sturm, O.E.1
-
171
-
-
62549083590
-
Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression
-
(doi:10.1073/pnas. 0809901106)
-
Nevozhay D, Adams RM, Murphy KF, Josic K, Balazsi G. 2009 Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc. Natl Acad. Sci. USA 106, 5123-5128. (doi:10.1073/pnas. 0809901106)
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 5123-5128
-
-
Nevozhay, D.1
Adams, R.M.2
Murphy, K.F.3
Josic, K.4
Balazsi, G.5
-
172
-
-
0022575044
-
Repetitive transient rises in cytoplasmic free calcium in hormone-stimulated hepatocytes
-
(doi:10.1038/319600a0)
-
Woods NM, Cuthbertson KS, Cobbold PH. 1986 Repetitive transient rises in cytoplasmic free calcium in hormone-stimulated hepatocytes. Nature 319, 600-602. (doi:10.1038/319600a0)
-
(1986)
Nature
, vol.319
, pp. 600-602
-
-
Woods, N.M.1
Cuthbertson, K.S.2
Cobbold, P.H.3
-
173
-
-
77954541844
-
Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing
-
(doi:10.1038/nature09145)
-
Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. 2010 Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466, 267-271. (doi:10.1038/nature09145)
-
(2010)
Nature
, vol.466
, pp. 267-271
-
-
Tay, S.1
Hughey, J.J.2
Lee, T.K.3
Lipniacki, T.4
Quake, S.R.5
Covert, M.W.6
-
174
-
-
33745451921
-
Oscillations and variability in the p53 system
-
(doi:10.1038/msb4100068)
-
Geva-Zatorsky N et al. 2006 Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 0033. (doi:10.1038/msb4100068)
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 0033
-
-
Geva-Zatorsky, N.1
-
175
-
-
77951173628
-
Damped oscillations in the adaptive response of the iron homeostasis network of E
-
(doi:10.1111/j.1365-2958.2010. 07111.x)
-
Amir A, Meshner S, Beatus T, Stavans J. 2010 Damped oscillations in the adaptive response of the iron homeostasis network of E. coli. Mol. Microbiol. 76, 428-436. (doi:10.1111/j.1365-2958.2010. 07111.x)
-
(2010)
Coli. Mol. Microbiol.
, vol.76
, pp. 428-436
-
-
Amir, A.1
Meshner, S.2
Beatus, T.3
Stavans, J.4
-
176
-
-
61349115583
-
Glycolytic oscillations in isolated rabbit ventricular myocytes
-
(doi:10.1074/jbc.M804794200)
-
Yang JH, Yang L, Qu Z, Weiss JN. 2008 Glycolytic oscillations in isolated rabbit ventricular myocytes. J. Biol. Chem. 283, 36 321-36 327. (doi:10.1074/jbc.M804794200)
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 36321-36327
-
-
Yang, J.H.1
Yang, L.2
Qu, Z.3
Weiss, J.N.4
-
177
-
-
79952637804
-
Modeling the cell cycle: Why do certain circuits oscillate?
-
(doi:10.1016/j.cell.2011.03.006)
-
Ferrell Jr JE, Tsai TY, Yang Q. 2011 Modeling the cell cycle: why do certain circuits oscillate? Cell 144, 874-885. (doi:10.1016/j.cell.2011.03.006)
-
(2011)
Cell
, vol.144
, pp. 874-885
-
-
Ferrell Jr., J.E.1
Tsai, T.Y.2
Yang, Q.3
-
178
-
-
56749160113
-
Design principles of biochemical oscillators
-
(doi:10.1038/nrm2530)
-
Novak B, Tyson JJ. 2008 Design principles of biochemical oscillators. Nat. Rev. Mol. Cell Biol. 9, 981-991. (doi:10.1038/nrm2530)
-
(2008)
Nat. Rev. Mol. Cell Biol.
, vol.9
, pp. 981-991
-
-
Novak, B.1
Tyson, J.J.2
-
179
-
-
67650373897
-
On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems
-
(doi:10.1186/1752-0509-3-51)
-
Nguyen LK, Kulasiri D. 2009 On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems. BMC Syst. Biol. 3, 51. (doi:10.1186/1752-0509-3-51)
-
(2009)
BMC Syst. Biol.
, vol.3
, pp. 51
-
-
Nguyen, L.K.1
Kulasiri, D.2
-
180
-
-
0016788494
-
Optimal design of feedback control by inhibition: Dynamic considerations
-
(doi:10.1007/BF01741242)
-
Savageau MA. 1975 Optimal design of feedback control by inhibition: dynamic considerations. J. Mol. Evol. 5, 199-222. (doi:10.1007/BF01741242)
-
(1975)
J. Mol. EVol.
, vol.5
, pp. 199-222
-
-
Savageau, M.A.1
-
181
-
-
0034019315
-
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
-
(doi:10.1046/j. 1432-1327.2000.01197.x)
-
Kholodenko BN. 2000 Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267, 1583-1588. (doi:10.1046/j. 1432-1327.2000.01197.x)
-
(2000)
Eur. J. Biochem.
, vol.267
, pp. 1583-1588
-
-
Kholodenko, B.N.1
-
182
-
-
71449121678
-
Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor
-
(doi:10.1038/msb.2009.90)
-
Shankaran H, Ippolito DL, Chrisler WB, Resat H, Bollinger N, Opresko LK, Wiley HS. 2009 Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol. Syst. Biol. 5, 332. (doi:10.1038/msb.2009.90)
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 332
-
-
Shankaran, H.1
Ippolito, D.L.2
Chrisler, W.B.3
Resat, H.4
Bollinger, N.5
Opresko, L.K.6
Wiley, H.S.7
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