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For: Udalova IA, Mott R, Field D, Kwiatkowski D. Quantitative prediction of NF-kappa B DNA-protein interactions. Proc Natl Acad Sci U S A 2002;99:8167-72. [PMID: 12048232 PMCID: PMC123039 DOI: 10.1073/pnas.102674699] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Parra RG, Komives EA, Wolynes PG, Ferreiro DU. Frustration in physiology and molecular medicine. Mol Aspects Med 2025;103:101362. [PMID: 40273505 DOI: 10.1016/j.mam.2025.101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 03/25/2025] [Accepted: 03/27/2025] [Indexed: 04/26/2025]
2
Parra RG, Komives EA, Wolynes PG, Ferreiro DU. Frustration In Physiology And Molecular Medicine. ARXIV 2025:arXiv:2502.03851v1. [PMID: 39975445 PMCID: PMC11838788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
3
Tamburini B, Di Liberto D, Pratelli G, Rizzo C, Barbera LL, Lauricella M, Carlisi D, Maggio A, Palumbo Piccionello A, D’Anneo A, Caccamo N, Guggino G. Extra Virgin Olive Oil Polyphenol-Enriched Extracts Exert Antioxidant and Anti-Inflammatory Effects on Peripheral Blood Mononuclear Cells from Rheumatoid Arthritis Patients. Antioxidants (Basel) 2025;14:171. [PMID: 40002358 PMCID: PMC11851824 DOI: 10.3390/antiox14020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 01/28/2025] [Accepted: 01/28/2025] [Indexed: 02/27/2025]  Open
4
Enhanced Transcriptional Strength of HIV-1 Subtype C Minimizes Gene Expression Noise and Confers Stability to the Viral Latent State. J Virol 2023;97:e0137622. [PMID: 36533949 PMCID: PMC9888270 DOI: 10.1128/jvi.01376-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
5
Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem 2022;298:102349. [PMID: 35934050 PMCID: PMC9440430 DOI: 10.1016/j.jbc.2022.102349] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022]  Open
6
Singh A, Martinez-Yamout MA, Wright PE, Dyson H. Structural and dynamic studies of DNA recognition by NF-κB p50 RHR homodimer using methyl NMR spectroscopy. Nucleic Acids Res 2022;50:7147-7160. [PMID: 35748866 PMCID: PMC9262625 DOI: 10.1093/nar/gkac535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022]  Open
7
Ghosh G, Wang VYF. Origin of the Functional Distinctiveness of NF-κB/p52. Front Cell Dev Biol 2021;9:764164. [PMID: 34888310 PMCID: PMC8650618 DOI: 10.3389/fcell.2021.764164] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022]  Open
8
Long X, Yang Z, Li Y, Sun Q, Li X, Kuang E. BRLF1-dependent viral and cellular transcriptomes and transcriptional regulation during EBV primary infection in B lymphoma cells. Genomics 2021;113:2591-2604. [PMID: 34087421 DOI: 10.1016/j.ygeno.2021.05.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/17/2021] [Accepted: 05/30/2021] [Indexed: 12/11/2022]
9
Fazal N, Khawaja H, Naseer N, Khan AJ, Latief N. Daphne mucronata enhances cell proliferation and protects human adipose stem cells against monosodium iodoacetate induced oxidative stress in vitro. Adipocyte 2020;9:495-508. [PMID: 32867575 PMCID: PMC7714443 DOI: 10.1080/21623945.2020.1812242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 01/01/2023]  Open
10
Nejatbakhsh Samimi L, Farhadi E, Tahmasebi MN, Jamshidi A, Sharafat Vaziri A, Mahmoudi M. NF-κB signaling in rheumatoid arthritis with focus on fibroblast-like synoviocytes. AUTOIMMUNITY HIGHLIGHTS 2020. [PMCID: PMC7414649 DOI: 10.1186/s13317-020-00135-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
11
Yang JH, Chen WT, Lee MC, Fang WH, Hsu YJ, Chin-Lin, Chen HC, Chang HL, Chen CF, Tu MY, Kuo CW, Lin YH, Hsiao PJ, Su SL. Investigation of the variants at the binding site of inflammatory transcription factor NF-κB in patients with end-stage renal disease. BMC Nephrol 2019;20:300. [PMID: 31382928 PMCID: PMC6683452 DOI: 10.1186/s12882-019-1471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/19/2019] [Indexed: 12/12/2022]  Open
12
Wu J, Wang Q, Dai W, Wang W, Yue M, Wang J. Massive GGAAs in genomic repetitive sequences serve as a nuclear reservoir of NF-κB. J Genet Genomics 2018;45:193-203. [PMID: 29748061 DOI: 10.1016/j.jgg.2018.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/01/2022]
13
Autophagy acts through TRAF3 and RELB to regulate gene expression via antagonism of SMAD proteins. Nat Commun 2017;8:1537. [PMID: 29146913 PMCID: PMC5691083 DOI: 10.1038/s41467-017-00859-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/01/2017] [Indexed: 01/17/2023]  Open
14
Primate lentiviruses use at least three alternative strategies to suppress NF-κB-mediated immune activation. PLoS Pathog 2017;13:e1006598. [PMID: 28859166 PMCID: PMC5597281 DOI: 10.1371/journal.ppat.1006598] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/13/2017] [Accepted: 08/22/2017] [Indexed: 01/02/2023]  Open
15
Zhao J, Li D, Seo J, Allen AS, Gordân R. Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2017;10229:336-352. [PMID: 28691125 DOI: 10.1007/978-3-319-56970-3_21] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
16
Sharma V, Monti P, Fronza G, Inga A. Human transcription factors in yeast: the fruitful examples of P53 and NF-кB. FEMS Yeast Res 2016;16:fow083. [PMID: 27683095 DOI: 10.1093/femsyr/fow083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2016] [Indexed: 12/31/2022]  Open
17
Sharma V, Jordan JJ, Ciribilli Y, Resnick MA, Bisio A, Inga A. Quantitative Analysis of NF-κB Transactivation Specificity Using a Yeast-Based Functional Assay. PLoS One 2015;10:e0130170. [PMID: 26147604 PMCID: PMC4493129 DOI: 10.1371/journal.pone.0130170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/18/2015] [Indexed: 11/18/2022]  Open
18
Andrilenas KK, Penvose A, Siggers T. Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics 2014;14:17-29. [PMID: 25431149 DOI: 10.1093/bfgp/elu046] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
19
Du W, Gao J, Wang T, Wang J. Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites. PLoS One 2014;9:e101490. [PMID: 24992458 PMCID: PMC4081663 DOI: 10.1371/journal.pone.0101490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 06/09/2014] [Indexed: 11/18/2022]  Open
20
Ramachandran S, Karp PH, Osterhaus SR, Jiang P, Wohlford-Lenane C, Lennox KA, Jacobi AM, Praekh K, Rose SD, Behlke MA, Xing Y, Welsh MJ, McCray PB. Post-transcriptional regulation of cystic fibrosis transmembrane conductance regulator expression and function by microRNAs. Am J Respir Cell Mol Biol 2014;49:544-51. [PMID: 23646886 DOI: 10.1165/rcmb.2012-0430oc] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
21
Liu H, Yang J, Yuan Y, Xia Z, Chen M, Xie L, Ma X, Wang J, Ouyang S, Wu Q, Yu F, Zhou X, Yang Y, Cao Y, Hu J, Yin B. Regulation of Mcl-1 by constitutive activation of NF-κB contributes to cell viability in human esophageal squamous cell carcinoma cells. BMC Cancer 2014;14:98. [PMID: 24529193 PMCID: PMC3930545 DOI: 10.1186/1471-2407-14-98] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 02/11/2014] [Indexed: 11/10/2022]  Open
22
Eggeling R, Gohr A, Keilwagen J, Mohr M, Posch S, Smith AD, Grosse I. On the value of intra-motif dependencies of human insulator protein CTCF. PLoS One 2014;9:e85629. [PMID: 24465627 PMCID: PMC3899044 DOI: 10.1371/journal.pone.0085629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/05/2013] [Indexed: 01/08/2023]  Open
23
Abbas AK, Le K, Pimmett VL, Bell DA, Cairns E, DeKoter RP. Negative regulation of the peptidylarginine deiminase type IV promoter by NF-κB in human myeloid cells. Gene 2014;533:123-31. [DOI: 10.1016/j.gene.2013.09.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/26/2013] [Indexed: 01/01/2023]
24
An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example. PLoS One 2013;8:e76109. [PMID: 24130762 PMCID: PMC3794954 DOI: 10.1371/journal.pone.0076109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/20/2013] [Indexed: 12/29/2022]  Open
25
Xing Y, Yang Y, Zhou F, Wang J. Characterization of genome-wide binding of NF-κB in TNFα-stimulated HeLa cells. Gene 2013;526:142-9. [PMID: 23688556 DOI: 10.1016/j.gene.2013.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 04/28/2013] [Accepted: 05/01/2013] [Indexed: 01/06/2023]
26
Ryzhakov G, Teixeira A, Saliba D, Blazek K, Muta T, Ragoussis J, Udalova IA. Cross-species analysis reveals evolving and conserved features of the nuclear factor κB (NF-κB) proteins. J Biol Chem 2013;288:11546-54. [PMID: 23508954 PMCID: PMC3630861 DOI: 10.1074/jbc.m113.451153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
27
Cyrne L, Oliveira-Marques V, Marinho HS, Antunes F. H2O2 in the Induction of NF-κB-Dependent Selective Gene Expression. Methods Enzymol 2013;528:173-88. [DOI: 10.1016/b978-0-12-405881-1.00010-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
28
Gu GM, Wang JK. [DNA-binding profiles of mammalian transcription factors]. YI CHUAN = HEREDITAS 2012;34:950-68. [PMID: 22917900 DOI: 10.3724/sp.j.1005.2012.00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
29
Tan M, Yu D, Jin Y, Dou L, Li B, Wang Y, Yue J, Liang L. An information transmission model for transcription factor binding at regulatory DNA sites. Theor Biol Med Model 2012;9:19. [PMID: 22672438 PMCID: PMC3442977 DOI: 10.1186/1742-4682-9-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 05/17/2012] [Indexed: 11/10/2022]  Open
30
Wee KB, Yio WK, Surana U, Chiam KH. Transcription factor oscillations induce differential gene expressions. Biophys J 2012;102:2413-23. [PMID: 22713556 DOI: 10.1016/j.bpj.2012.04.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 01/04/2023]  Open
31
Chromatin immunoprecipitation analysis of NFκB transcriptional regulation by nuclear IκBα in human macrophages. Methods Mol Biol 2012;809:121-34. [PMID: 22113272 DOI: 10.1007/978-1-61779-376-9_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
32
Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding. Nat Immunol 2011;13:95-102. [PMID: 22101729 PMCID: PMC3242931 DOI: 10.1038/ni.2151] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/26/2011] [Indexed: 12/14/2022]
33
Antonaki A, Demetriades C, Polyzos A, Banos A, Vatsellas G, Lavigne MD, Apostolou E, Mantouvalou E, Papadopoulou D, Mosialos G, Thanos D. Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements. J Biol Chem 2011;286:38768-38782. [PMID: 21896491 DOI: 10.1074/jbc.m111.234161] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
34
Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk M, Angelov D, Dimitrov S, Udalova IA, Ragoussis J. Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biol 2011;12:R70. [PMID: 21801342 PMCID: PMC3218832 DOI: 10.1186/gb-2011-12-7-r70] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 07/11/2011] [Accepted: 07/29/2011] [Indexed: 12/21/2022]  Open
35
Venkatesha SH, Berman BM, Moudgil KD. Herbal medicinal products target defined biochemical and molecular mediators of inflammatory autoimmune arthritis. Bioorg Med Chem 2011;19:21-9. [PMID: 21115252 PMCID: PMC3020797 DOI: 10.1016/j.bmc.2010.10.053] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/18/2010] [Accepted: 10/25/2010] [Indexed: 11/18/2022]
36
Shlomai J. Redox control of protein-DNA interactions: from molecular mechanisms to significance in signal transduction, gene expression, and DNA replication. Antioxid Redox Signal 2010;13:1429-76. [PMID: 20446770 DOI: 10.1089/ars.2009.3029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
37
Oeckinghaus A, Ghosh S. The NF-kappaB family of transcription factors and its regulation. Cold Spring Harb Perspect Biol 2010;1:a000034. [PMID: 20066092 DOI: 10.1101/cshperspect.a000034] [Citation(s) in RCA: 2120] [Impact Index Per Article: 141.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
38
Natoli G. Control of NF-kappaB-dependent transcriptional responses by chromatin organization. Cold Spring Harb Perspect Biol 2010;1:a000224. [PMID: 20066094 DOI: 10.1101/cshperspect.a000224] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
39
Oliveira-Marques V, Marinho HS, Cyrne L, Antunes F. Role of hydrogen peroxide in NF-kappaB activation: from inducer to modulator. Antioxid Redox Signal 2009;11:2223-43. [PMID: 19496701 DOI: 10.1089/ars.2009.2601] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
40
Oliveira-Marques V, Marinho HS, Cyrne L, Antunes F. Modulation of NF-kappaB-dependent gene expression by H2O2: a major role for a simple chemical process in a complex biological response. Antioxid Redox Signal 2009;11:2043-53. [PMID: 19014314 DOI: 10.1089/ars.2008.2279] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
41
Gowrisankar S, Jegga AG. Regression based predictor for p53 transactivation. BMC Bioinformatics 2009;10:215. [PMID: 19602281 PMCID: PMC2719629 DOI: 10.1186/1471-2105-10-215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 07/14/2009] [Indexed: 11/10/2022]  Open
42
Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM. OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. BMC Bioinformatics 2009;10:208. [PMID: 19583839 PMCID: PMC2718928 DOI: 10.1186/1471-2105-10-208] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/07/2009] [Indexed: 12/29/2022]  Open
43
Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Handling Counterintuitive Results. J Mol Evol 2009;68:654-64. [DOI: 10.1007/s00239-009-9238-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 03/30/2009] [Accepted: 04/15/2009] [Indexed: 01/26/2023]
44
Mittler G, Butter F, Mann M. A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genes Dev 2009;19:284-93. [PMID: 19015324 PMCID: PMC2652210 DOI: 10.1101/gr.081711.108] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 11/04/2008] [Indexed: 12/15/2022]
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Roman-Blas JA, Jimenez SA. Targeting NF-kappaB: a promising molecular therapy in inflammatory arthritis. Int Rev Immunol 2009;27:351-74. [PMID: 18853343 DOI: 10.1080/08830180802295740] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Okamoto H, Cujec TP, Yamanaka H, Kamatani N. Molecular aspects of rheumatoid arthritis: role of transcription factors. FEBS J 2008;275:4463-70. [PMID: 18662303 DOI: 10.1111/j.1742-4658.2008.06582.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Veprintsev DB, Fersht AR. Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA. Nucleic Acids Res 2008;36:1589-98. [PMID: 18234719 PMCID: PMC2275157 DOI: 10.1093/nar/gkm1040] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 10/30/2007] [Accepted: 10/31/2007] [Indexed: 12/23/2022]  Open
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Gunewardena S, Zhang Z. A hybrid model for robust detection of transcription factor binding sites. ACTA ACUST UNITED AC 2008;24:484-91. [PMID: 18184687 DOI: 10.1093/bioinformatics/btm629] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Natoli G, Chiocca S. Nuclear Ubiquitin Ligases, NF- B Degradation, and the Control of Inflammation. Sci Signal 2008;1:pe1. [DOI: 10.1126/stke.11pe1] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Levitsky VG, Ignatieva EV, Ananko EA, Turnaev II, Merkulova TI, Kolchanov NA, Hodgman TC. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinformatics 2007;8:481. [PMID: 18093302 PMCID: PMC2265442 DOI: 10.1186/1471-2105-8-481] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2007] [Accepted: 12/19/2007] [Indexed: 12/22/2022]  Open
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