-
1
-
-
24944489952
-
Stimulus specificity of gene expression programs determined by temporal control of IKK activity
-
Werner SL, Barken D, 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
-
2
-
-
84858728161
-
Lessons from mathematically modeling the NF-κB pathway
-
Basak S, Behar M, Hoffmann A (2012) Lessons from mathematically modeling the NF-κB pathway. Immunol Rev 246:221–238
-
(2012)
Immunol Rev
, vol.246
, pp. 221-238
-
-
Basak, S.1
Behar, M.2
Hoffmann, A.3
-
3
-
-
0037044575
-
The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation
-
Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective 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
-
4
-
-
48749085156
-
Encoding NF-kappaB temporal control in response to TNF: Distinct roles for the negative regulators IkappaBalpha and A 20
-
Werner SL, Kearns JD, Zadorozhnaya V, Lynch C, O’Dea E, Boldin MP, Ma A, Baltimore D, Hoffmann A (2008) Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A 20. Genes Dev 22:2093–2101
-
(2008)
Genes Dev
, vol.22
, pp. 2093-2101
-
-
Werner, S.L.1
Kearns, J.D.2
Zadorozhnaya, V.3
Lynch, C.4
O’Dea, E.5
Boldin, M.P.6
Ma, A.7
Baltimore, D.8
Hoffmann, A.9
-
5
-
-
33747388013
-
IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression
-
Kearns JD, Basak S, Werner SL, Huang CS, Hoffmann A (2006) IkappaBepsilon provides negative feedback to control NF-kappaB oscillations, signaling dynamics, and inflammatory gene expression. J Cell Biol 173:659–664
-
(2006)
J Cell Biol
, vol.173
, pp. 659-664
-
-
Kearns, J.D.1
Basak, S.2
Werner, S.L.3
Huang, C.S.4
Hoffmann, A.5
-
6
-
-
66449092314
-
Kinetic control of negative feedback regulators of NF-kappaB/ RelA determines their pathogen- and cytokine-receptor signaling specificity
-
Shih VF-SF, Kearns JD, Basak S, Savinova OV, Ghosh G, Hoffmann A (2009) Kinetic control of negative feedback regulators of NF-kappaB/ RelA determines their pathogen- and cytokine-receptor signaling specificity. Proc Natl Acad Sci U S A 106:9619–9624
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 9619-9624
-
-
Shih, V.-S.1
Kearns, J.D.2
Basak, S.3
Savinova, O.V.4
Ghosh, G.5
Hoffmann, A.6
-
7
-
-
33846323310
-
A fourth IkappaB protein within the NF-kappaB signaling module
-
Basak S, Kim H, Kearns JD, Tergaonkar V, O’Dea E, Werner SL, Benedict CA, Ware CF, Ghosh G, Verma IM, Hoffmann A (2007) A fourth IkappaB protein within the NF-kappaB signaling module. Cell 128:369–381
-
(2007)
Cell
, vol.128
, pp. 369-381
-
-
Basak, S.1
Kim, H.2
Kearns, J.D.3
Tergaonkar, V.4
O’Dea, E.5
Werner, S.L.6
Benedict, C.A.7
Ware, C.F.8
Ghosh, G.9
Verma, I.M.10
Hoffmann, A.11
-
8
-
-
84869411578
-
Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways
-
Shih VF-SF, Davis-Turak J, Macal M, Huang JQ, Ponomarenko J, Kearns JD, Yu T, Fagerlund R, Asagiri M, Zuniga EI, Hoffmann A (2012) Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways. Nat Immunol 13: 1162–1170
-
(2012)
Nat Immunol
, vol.13
, pp. 1162-1170
-
-
Shih, V.-S.1
Davis-Turak, J.2
Macal, M.3
Huang, J.Q.4
Ponomarenko, J.5
Kearns, J.D.6
Yu, T.7
Fagerlund, R.8
Asagiri, M.9
Zuniga, E.I.10
Hoffmann, A.11
-
9
-
-
43249090157
-
UV as an amplifier rather than inducer of NF-kappaB activity
-
O’Dea EL, Kearns JD, Hoffmann A (2008) UV as an amplifier rather than inducer of NF-kappaB activity. Mol Cell 30:632–641
-
(2008)
Mol Cell
, vol.30
, pp. 632-641
-
-
O’Dea, E.L.1
Kearns, J.D.2
Hoffmann, A.3
-
10
-
-
84879812351
-
Tunable signal processing through a kinase control cycle: The IKK signaling node
-
Behar M, Hoffmann A (2013) Tunable signal processing through a kinase control cycle: the IKK signaling node. Biophys J 105:231–241
-
(2013)
Biophys J
, vol.105
, pp. 231-241
-
-
Behar, M.1
Hoffmann, A.2
-
11
-
-
0030610362
-
A cytokine-responsive IkappaB kinase that activates the transcription factor NF-kappaB
-
DiDonato JA, Hayakawa M, Rothwarf DM, Zandi E, Karin M (1997) A cytokine-responsive IkappaB kinase that activates the transcription factor NF-kappaB. Nature 388: 548–554
-
(1997)
Nature
, vol.388
, pp. 548-554
-
-
Didonato, J.A.1
Hayakawa, M.2
Rothwarf, D.M.3
Zandi, E.4
Karin, M.5
-
12
-
-
84902658640
-
Tuneable resolution as a systems biology approach for multi-scale, multicompartment computational models
-
Kirschner DE, Hunt CA, Marino S, Fallahi- Sichani M, Linderman JJ (2014) Tuneable resolution as a systems biology approach for multi-scale, multicompartment computational models. Wiley Interdiscip Rev Syst Biol Med 6:289–309
-
(2014)
Wiley Interdiscip Rev Syst Biol Med
, vol.6
, pp. 289-309
-
-
Kirschner, D.E.1
Hunt, C.A.2
Marino, S.3
Fallahi- Sichani, M.4
Linderman, J.J.5
-
13
-
-
66249136447
-
Non-genetic origins of cellto- cell variability in TRAIL-induced apoptosis
-
Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK (2009) Non-genetic origins of cellto- cell variability in TRAIL-induced apoptosis. Nature 459:428–432
-
(2009)
Nature
, vol.459
, pp. 428-432
-
-
Spencer, S.L.1
Gaudet, S.2
Albeck, J.G.3
Burke, J.M.4
Sorger, P.K.5
-
14
-
-
77953934646
-
BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92
-
(2010)
BMC Syst Biol
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.I.10
Snoep, J.L.11
Hucka, M.12
Le Novère, N.13
Laibe, C.14
-
15
-
-
84862214722
-
SABIO-RK–database for biochemical reaction kinetics
-
Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Müller W (2012) SABIO-RK–database for biochemical reaction kinetics. Nucleic Acids Res 40:D790
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D790
-
-
Wittig, U.1
Kania, R.2
Golebiewski, M.3
Rey, M.4
Shi, L.5
Jong, L.6
Algaa, E.7
Weidemann, A.8
Sauer-Danzwith, H.9
Mir, S.10
Krebs, O.11
Bittkowski, M.12
Wetsch, E.13
Rojas, I.14
Müller, W.15
-
16
-
-
68449103579
-
The systems biology graphical notation
-
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H (2009) The systems biology graphical notation. Nat Biotechnol 27:735–741
-
(2009)
Nat Biotechnol
, vol.27
, pp. 735-741
-
-
Le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Schreiber, F.5
Sorokin, A.6
Demir, E.7
Wegner, K.8
Aladjem, M.I.9
Wimalaratne, S.M.10
Bergman, F.T.11
Gauges, R.12
Ghazal, P.13
Kawaji, H.14
Li, L.15
Matsuoka, Y.16
Villéger, A.17
Boyd, S.E.18
Calzone, L.19
Courtot, M.20
Dogrusoz, U.21
Freeman, T.C.22
Funahashi, A.23
Ghosh, S.24
Jouraku, A.25
Kim, S.26
Kolpakov, F.27
Luna, A.28
Sahle, S.29
Schmidt, E.30
Watterson, S.31
Wu, G.32
Goryanin, I.33
Kell, D.B.34
Sander, C.35
Sauro, H.36
Snoep, J.L.37
Kohn, K.38
Kitano, H.39
more..
-
17
-
-
33845368513
-
COPASI—a COmplex PAthway SImulator
-
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U (2006) COPASI—a COmplex PAthway SImulator. Bioinformatics 22:3067–3074
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
19
-
-
0032406131
-
Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
-
Mendes P, Kell D (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14:869–883
-
(1998)
Bioinformatics
, vol.14
, pp. 869-883
-
-
Mendes, P.1
Kell, D.2
|