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Tue Feb 1 09:30:45 2005
The I kappa B-NF-kappa B signaling module:
Temporal control and selective gene activation

Hoffmann A, Levchenko A, Scott ML, Baltimore D
SCIENCE 298 (5596): 1241-1245 2002
and the citing papers

Nodes: 104, Authors: 431, Journals: 63, Outer References: 5144, Words: 500
Collection span: 2002 - 2005
View: Overview. Sorted by LCR.
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
1536561 2004 GENES & DEVELOPMENT 18(18):2195-2224
Hayden MS; Ghosh S
Signaling to NF-kappa B
00
2527100 2004 SCIENCE 306(5296):704-708
Nelson DE; Ihekwaba AEC; Elliott M; Johnson JR; Gibney CA; et al.
Oscillations in NF-kappa B signaling control the dynamics of gene expression
00
3438102 2004 TRENDS IN BIOCHEMICAL SCIENCES 29(12):641-647
Papin JA; Reed JL; Palsson BO
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
01
433539 2003 SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL 79(12):726-739
Cho KH; Shin SY; Kolch W; Wolkenhauer O
Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF alpha-mediated NF-kappa B signal transduction pathway
00
531542 2004 BIOCHEMICAL SOCIETY TRANSACTIONS 32:1090-1092
Nelson DE; See V; Nelson G; White MRH
Oscillations in transcription factor dynamics: a new way to control gene expression
00
634456 2004 CURRENT OPINION IN GENETICS & DEVELOPMENT 14(4):440-445
Kerszberg M
Noise, delays, robustness, canalization and all that
00
734077 2004 JOURNAL OF THEORETICAL BIOLOGY 228(2):195-215
Lipniacki T; Paszek P; Brasier AR; Luxon B; Kimmel M
Mathematical model of NF-kappa B regulatory module
00
831487 2004 NATURE GENETICS 36(2):113-114
Tyson JJ
Monitoring p53's pulse
00
927410 2003 BIOTECHNOLOGY AND BIOENGINEERING 84(7):773-782
Levchenko A
Dynamical and integrative cell signaling: Challenges for the new biology
02
1028212 2003 CANCER RESEARCH 63(24):8837-8847
Dadke D; Fryer BH; Golemis EA; Field J
Activation of p21-activated kinase 1-nuclear factor kappa B signaling by Kaposi's sarcoma-associated herpes virus G protein-coupled receptor during cellular transformation
03
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
1122316 2003 CURRENT BIOLOGY 13(16):1409-1413
Monk NAM
Oscillatory expression of Hes1, p53, and NF-kappa B driven by transcriptional time delays
410
12278220 2003 ENDOCRINE REVIEWS 24(4):488-522
De Bosscher K; Vanden Berghe W; Haegeman G
The interplay between the glucocorticoid receptor and nuclear factor-kappa B or activator protein-1: Molecular mechanisms for gene repression
118
1325526 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(25):23094-23100
Malek S; Huang DB; Huxford T; Ghosh S; Ghosh G
X-ray crystal structure of an I kappa B beta center dot NF-kappa B p65 homodimer complex
39
1424327 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(25):23101-23106
Chen Y; Wu J; Ghosh G
kappa B-Ras binds to the unique insert within the ankyrin repeat domain of I kappa B beta and regulates cytoplasmic retention of I kappa B beta center dot NF-kappa B complexes
16
1524435 2003 MOLECULAR CELL 12(5):1287-1300
Schmidt C; Peng BL; Li ZK; Sclabas GM; Fujioka S; et al.
Mechanisms of proinflammatory cytokine-induced biphasic NF-kappa B activation
213
1623850 2004 CELL 117(6):713-720
Kalir S; Alon U
Using a quantitative blueprint to reprogram the dynamics of the flagella gene network
04
1726951 2004 CHEMBIOCHEM 5(10):1334-1347
Murrell MF; Yarema KJ; Levchenko A
The systems biology of glycosylation
00
18214654 2004 CLINICAL SCIENCE 107(1):13-25
Schoemaker MH; Moshage H
Defying death: the hepatocyte's survival kit
00
19211257 2004 CURRENT PHARMACEUTICAL DESIGN 10(23):2827-2837
Bacher S; Schmitz ML
The NF-kappa B pathway as a potential target for autoimmune disease therapy
01
2025468 2004 JOURNAL OF BIOLOGICAL CHEMISTRY 279(31):32869-32881
Marchetti L; Klein M; Schlett K; Pfizenmaier K; Eisel ULM
Tumor necrosis factor (TNF)-mediated neuroprotection against glutamate-induced excitotoxicity is enhanced by N-methyl-D-aspartate receptor activation - Essential role of a TNF receptor 2-mediated phosphatidylinositol 3-kinase-dependent NF-kappa B pathway
00
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
2122972 2004 JOURNAL OF EXPERIMENTAL MEDICINE 200(1):107-113
Saccani S; Marazzi I; Beg AA; Natoli G
Degradation of promoter-bound p65/RelA is essential for the prompt termination of the nuclear factor kappa B response
00
22225875 2004 JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 5(2):113-137
Kumbhakar M; Nath S; Mukherjee T; Mittal JP; Pal H
Single-molecule detection in exploring nanoenvironments: an overview
00
2323986 2004 NATURE BIOTECHNOLOGY 22(10):1253-1259
Butcher EC; Berg EL; Kunkel EJ
Systems biology in drug discovery
00
2423088 2004 NATURE GENETICS 36(2):147-150
Lahav G; Rosenfeld N; Sigal A; Geva-Zatorsky N; Levine AJ; et al.
Dynamics of the p53-Mdm2 feedback loop in individual cells
310
2523390 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(2):580-585
Francois P; Hakim V
Design of genetic networks with specified functions by evolution in silico
06
2624692 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(16):5934-5939
Yeger-Lotem E; Sattath S; Kashtan N; Itzkovitz S; Milo R; et al.
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction
17
2723794 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(47):16537-16542
Aguilera C; Hoya-Arias R; Haegeman G; Espinosa L; Bigas A
Recruitment of I kappa B alpha to the hes1 promoter is associated with transcriptional repression
00
2829695 2004 PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 85(2-3):163-178
Puglisi JL; Wang F; Bers DM
Modeling the isolated cardiac myocyte
00
2925196 2004 PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 85(2-3):261-278
Saucerman JJ; McCulloch AD
Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation
01
3026597 2004 PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 86(1):45-76
Mariani L; Lohning M; Radbruch A; Hofer T
Transcriptional control networks of cell differentiation: insights from helper T lymphocytes
00
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
31280103 2004 TRENDS IN CELL BIOLOGY 14(12):661-669
Eungdamrong NJ; Iyengar R
Computational approaches for modeling regulatory cellular networks
00
32171 2002 SCIENCE 298(5596):1189-1190
Ting AY; Endy D
Decoding NF-kappa B signaling
58
331233 2003 ANTIMICROBIAL AGENTS AND CHEMOTHERAPY 47(12):3704-3707
Choi JH; Song MJ; Kim SH; Choi SM; Lee DG; et al.
Effect of moxiloxacin on production of proinflammatory cytokines from human peripheral blood mononuclear cells
01
341384 2003 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 305(2):211-214
Lee ZH; Kim HH
Signal transduction by receptor activator of nuclear factor kappa B in osteoclasts
012
351925 2003 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 311(4):1117-1132
Feske S; Okamura H; Hogan PG; Rao A
Ca2+/calcineurin signalling in cells of the immune system
05
361256 2003 BIOCHEMICAL SOCIETY TRANSACTIONS 31:925-929
Lewis RS
Calcium oscillations in T-cells: mechanisms and consequences for gene expression
12
371237 2003 BIOCHEMICAL SOCIETY TRANSACTIONS 31:1503-1509
Cho KH; Wolkenhauer O
Analysis and modelling of signal transduction pathways in systems biology
01
3811138 2003 BIOESSAYS 25(8):767-780
Liou HC; Hsia CY
Distinctions between c-Rel and other NF-kappa B proteins in immunity and disease
03
391819 2003 BIOTECHNOLOGY AND BIOENGINEERING 84(7):763-772
Covert MW; Famili I; Palsson BO
Identifying constraints that govern cell behavior: A key to converting conceptual to computational models in biology?
25
4014111 2003 BLOOD 102(6):2259-2267
Choi M; Rolle S; Wellner M; Cardoso MC; Scheidereit C; et al.
Inhibition of NF-kappa B by a TAT-NEMO-binding domain peptide accelerates constitutive apoptosis and abrogates LPS-delayed neutrophil apoptosis
09
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
4117613 2003 CHRONOBIOLOGY INTERNATIONAL 20(4):559-575
Merrow M; Dragovic Z; Tan Y; Meyer G; Sveric K; et al.
Combining theoretical and experimental approaches to understand the circadian clock
00
42110614 2003 CURRENT BIOLOGY 13(5):R198-R207
Roenneberg T; Merrow M
The network of time: Understanding the molecular circadian system
017
4311815 2003 CURRENT BIOLOGY 13(16):R632-R634
Pourquie O; Goldbeter A
Segmentation clock: Insights from computational models
01
4416317 2003 CURRENT OPINION IN CELL BIOLOGY 15(2):221-231
Tyson JJ; Chen KC; Novak B
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
937
4519918 2003 EMBO JOURNAL 22(11):2552-2560
Santoro MG; Rossi A; Amici C
New embo member's review - NF-kappa B and virus infection: who controls whom
118
4615219 2003 EMBO JOURNAL 22(20):5530-5539
Hoffmann A; Leung TH; Baltimore D
Genetic analysis of NF-kappa B/Rel transcription factors defines functional specificities
212
4715721 2003 ENDOCRINOLOGY 144(9):3828-3835
Etgen AM; Acosta-Martinez M
Participation of growth factor signal transduction pathways in estradiol facilitation of female reproductive behavior
02
481722 2003 FEBS LETTERS 541(1-3):176-177
Jensen MH; Sneppen K; Tiana G
Sustained oscillations and time delays in gene expression of protein Hes1
00
4911323 2003 GENOME RESEARCH 13(11):2413-2422
Cho KH; Shin SY; Lee HW; Wolkenhauer O
Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway
23
5013724 2003 HEPATOLOGY 38(6):1540-1551
Cavin LG; Romieu-Mourez R; Panta GR; Sun JY; Factor VM; et al.
Inhibition of CK2 activity by TGF-beta 1 promotes I kappa B-alpha protein stabilization and apoptosis of immortalized hepatocytes
02
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
5114525 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(10):8286-8293
Komarova SV; Pilkington MF; Weidema AF; Dixon SJ; Sims SM
RANK ligand-induced elevation of cytosolic Ca2+ accelerates nuclear translocation of nuclear factor kappa B in osteoclasts
011
5214928 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(33):30881-30888
Yang L; Ross K; Qwarnstrom EE
RelA control of I kappa B alpha phosphorylation - A positive feedback loop for high affinity NF-kappa B complexes
12
5312429 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(47):46541-46548
Viatour P; Legrand-Poels S; van Lint C; Warnier M; Merville MP; et al.
Cytoplasmic I kappa B alpha increases NF-kappa B-independent transcription through binding to histone deacetylase (HDAC) 1 and HDAC3
111
5414130 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(48):47997-48003
Saucerman JJ; Brunton LL; Michailova AP; McCulloch AD
Modeling beta-adrenergic control of cardiac myocyte contractility in silico
310
5513131 2003 JOURNAL OF BIOMEDICAL SCIENCE 10(5):468-474
Wong PMC; Chung SW
A functional connection between RanGTP,NF-kappa B and septic shock
02
5613832 2003 JOURNAL OF CELL BIOLOGY 161(3):497-505
Jacquet M; Renault G; Lallet S; De Mey J; Goldbeter A
Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae
05
5715733 2003 JOURNAL OF CELLULAR PHYSIOLOGY 197(3):357-369
Seguin CA; Bernier SM
TNF alpha suppresses link protein and type II collagen expression in chondrocytes: Role of MEK1/2 and NF-kappa B signaling pathways
00
5816534 2003 JOURNAL OF IMMUNOLOGY 170(11):5615-5624
Dolganiuc A; Kodys K; Kopasz A; Marshall C; Do T; et al.
Hepatitis C virus core and nonstructural protein 3 proteins induce pro-and anti-inflammatory cytokines and inhibit dendritic cell differentiation
017
5912336 2003 NATURE IMMUNOLOGY 4(10):933-936
Chakraborty AK; Dustin ML; Shaw AS
In silico models for cellular and molecular immunology: successes, promises and challenges
03
6019037 2003 NEURAL NETWORKS 16(9):1389-1398
Kikuchi S; Fujimoto K; Kitagawa N; Fuchikawa T; Abe M; et al.
Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A
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6112538 2003 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100(24):14235-14240
Idel S; Dansky HM; Breslow JL
A20, a regulator of NF kappa B, maps to an atherosclerosis locus and differs between parental sensitive C57BL/6J and resistant FVB/N strains
03
6214440 2003 THROMBOSIS AND HAEMOSTASIS 90(3):528-537
Kolev K; Skopal J; Simon L; Csonka E; Machovich R; et al.
Matrix metalloproteinase-9 expression in post-hypoxic human brain capillary endothelial cells: H2O2 as a trigger and NF-kappa B as a signal transducer
05
6312741 2004 ARTHRITIS AND RHEUMATISM 50(11):3541-3548
Agarwal S; Deschner J; Long P; Verma A; Hofman C; et al.
Role of NF-kappa B transcription factors in antiinflammatory and proinflammatory actions of mechanical signals
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6414543 2004 BIOPHYSICAL JOURNAL 86(3):1270-1281
Feng XJ; Rabitz H
Optimal identification of biochemical reaction networks
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6514544 2004 BIOPHYSICAL JOURNAL 87(1):37-46
Papin JA; Palsson BO
The JAK-STAT signaling network in the human B-cell: An extreme signaling pathway analysis
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6613445 2004 BIOTECHNOLOGY AND BIOENGINEERING 86(3):317-331
Wiback SJ; Mahadevan R; Palsson BO
Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: The Escherichia coli spectrum
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6715146 2004 BIOTECHNOLOGY AND BIOENGINEERING 88(1):121-132
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Dynamics of gene silencing by RNA interference
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68110447 2004 BIOTECHNOLOGY PROGRESS 20(2):426-442
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A dynamic mathematical model to clarify signaling circuitry underlying programmed cell death control in Arabidopsis disease resistance
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6915048 2004 BLOOD 104(2):409-414
Sahni A; Guo M; Sahni SK; Francis CW
Interleukin-1 beta but not IL-1 alpha at binds to fibrinogen and fibrin and has enhanced activity in the bound form
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7014449 2004 CANCER RESEARCH 64(18):6511-6523
Loercher A; Lee TL; Ricker JL; Howard A; Geoghegen J; et al.
Nuclear factor-kappa B is an important modulator of the altered gene expression profile and malignant phenotype in squamous cell carcinoma
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7116252 2004 CHEMBIOCHEM 5(10):1365-1374
Vayttaden SJ; Ajay SM; Bhalla US
A spectrum of models of signaling pathways
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Circulating mononuclear cells in the obese are in a proinflammatory state
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7318155 2004 CURRENT GENOMICS 5(7):545-557
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Exploring toll-like receptor regulation of innate immunity with the tools of systems biology
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A dual role for lkk alpha in tooth development
04
7515259 2004 DRUGS OF THE FUTURE 29(7):733-739
Matsumori A
The role of NF-kappa B in the pathogenesis of heart failure and endotoxemia
00
7615060 2004 EXPERIMENTAL CELL RESEARCH 296(2):173-182
Ross DA; Kadesch T
Consequences of notch-mediated induction of Jagged1
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7713362 2004 GENES AND IMMUNITY 5(5):354-362
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cis-element clustering correlates with dose-dependent pro-and antisignaling effects of IL18
00
7813863 2004 HEPATOLOGY 40(5):1180-1189
Kimura K; Nagaki M; Takai S; Satake S; Moriwaki H
Pivotal role of nuclear factor kappa B signaling in anti-CD40-induced liver injury in mice
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7915864 2004 IMMUNITY 21(6):877-889
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TRAIL-R as a negative regulator of innate immune cell responses
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Protein-protein interaction networks: from interactions to networks
04
#LCRNCRNodes / Date / Journal / AuthorsLCSGCS
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Temporal control of NF-kappa B activation by ERK differentially regulates interleukin-1 beta-induced gene expression
03
8215467 2004 JOURNAL OF BIOLOGICAL CHEMISTRY 279(6):4285-4291
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Down-regulation of the tumor suppressor PTEN by the tumor necrosis factor-alpha/nuclear factor-kappa B (NF-kappa B)-inducing kinase/NF-kappa B pathway is linked to a default I kappa B-alpha autoregulatory loop
03
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Human tribbles, a protein family controlling mitogen-activated protein kinase cascades
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Vascular endothelial growth factor-and thrombin-induced termination factor, down syndrome critical region-1, attenuates endothelial cell proliferation and angiogenesis
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8514771 2004 JOURNAL OF BIOLOGICAL CHEMISTRY 279(52):54708-54715
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Suppressor of cytokine signaling (SOCS) proteins indirectly regulate toll-like receptor signaling in innate immune cells
00
8615573 2004 JOURNAL OF IMMUNOLOGY 173(9):5583-5590
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NF-kB regulates expression of the MHC class I-related chain A gene-in activated T lymphocytes
00
8714274 2004 JOURNAL OF NEUROSCIENCE 24(33):7324-7334
Rojo AI; Salinas M; Martin D; Perona R; Cuadrado A
Regulation of Cu/Zn-superoxide dismutase expression via the phosphatidylinositol 3 kinase/Akt pathway and nuclear factor-kappa B
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8815676 2004 JOURNAL OF THEORETICAL BIOLOGY 227(2):283-297
Papin JA; Palsson BO
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03
8914578 2004 JOURNAL OF THEORETICAL BIOLOGY 230(3):301-312
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9116080 2004 MOLECULAR AND CELLULAR BIOLOGY 24(3):1007-1021
Vasudevan KM; Gurumurthy S; Rangnekar VM
Suppression of PTEN expression by NF-kappa B prevents apoptosis
08
9214481 2004 MOLECULAR PHARMACOLOGY 65(2):342-349
Nemeth ZH; Wong HR; Odoms K; Deitch EA; Szabo C; et al.
Proteasome inhibitors induce inhibitory kappa B (I kappa B) kinase activation, I kappa B alpha degradation, and nuclear factor kappa B activation in HT-29 cells
03
9311182 2004 MOLECULAR PHARMACOLOGY 66(1):70-75
Sung MH; Simon R
In silico simulation of inhibitor drug effects on nuclear factor-kappa B pathway dynamics
01
9413783 2004 MOLECULES AND CELLS 18(2):200-206
Kwon WJ; Kim SH; Park YO; Cho M; Kang CD; et al.
IKK gamma inhibits activation of NF-kappa B by NIK
00
9517284 2004 MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS 551(1-2):199-211
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01
9612885 2004 NATURE 427(6970):167-171
Zhou HL; Wertz I; O'Rourke K; Ultsch M; Seshagiri S; et al.
Bcl10 activates the NF-kappa B pathway through ubiquitination of NEMO
128
97111189 2004 NATURE REVIEWS IMMUNOLOGY 4(4):269-277
Reth M; Brummer T
Feedback regulation of lymphocyte signalling
02
9815191 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(3):745-750
Mukhopadhyay P; Zheng M; Bedzyk LA; LaRossa RA; Storz G
Prominent roles of the NorR and Fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species
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9913793 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(19):7404-7408
Claud EC; Lu L; Anton PM; Savidge T; Walker WA; et al.
Developmentally regulated I kappa B expression in intestinal epithelium and susceptibility to flagellin-induced inflammation
01
10014998 2004 PROTEIN SCIENCE 13(7):1767-1777
Croy CH; Bergqvist S; Huxford T; Ghosh G; Komives EA
Biophysical characterization of the free I kappa B alpha ankyrin repeat domain in solution
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10114099 2004 RADIATION RESEARCH 162(5):536-546
Murley JS; Kataoka Y; Cao DC; Li JJ; Oberley LW; et al.
Delayed radioprotection by NF kappa B-mediated induction of Sod2 (MnSOD) in SA-NH tumor cells after exposure to clinically used thiol-containing drugs
00
102139101 2004 THROMBOSIS AND HAEMOSTASIS 92(4):858-866
Guo M; Sahni SK; Sahni A; Francis CW
Fibrinogen regulates the expression of inflammatory chemokines through NF-kappa B activation of endothelial cells
00
103132104 2005 FEBS LETTERS 579(1):141-144
Iwai K; Lee BR; Hashiguchi M; Fukushima A; Iwashima M
IkB-alpha-specific transcript regulation by the C-terminal end of c-Rel
00
1040192 2002 SCIENCE 298(5596):1241-1245
Hoffmann A; Levchenko A; Scott ML; Baltimore D
The I kappa B-NF-kappa B signaling module: Temporal control and selective gene activation
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