1Doll R (1998) Uncovering the effects of smoking: historical perspective. Stat Methods Med Res 7: 87-117.
2 Sopori ML, Kozak W (1998) Immunomodulatory effects of cigarette smoke. J Neuroimmunol 83: 148-156.
3 Winkler AR, Nocka KN, Williams CM (2012) Smoke exposure of human macrophages reduces HDAC3 activity, resulting in enhanced inflammatory cytokine production. Pulm Pharmacol Ther 25: 286-292.
4 Arcavi L, Benowitz NL (2004) Cigarette smoking and infection. Arch Intern Med 164: 2206-2216.
5Masdottir B, Jonsson T, Manfredsdottir V, Vikingsson A, Brekkan A, et al. (2000) Smoking, rheumatoid factor isotypes and severity of rheumatoid arthritis. Rheumatology (Oxford) 39: 1202-1205.
6Wogan GN, Hecht SS, Felton JS, Conney AH, Loeb LA (2004) Environmental and chemical carcinogenesis. Semin Cancer Biol 14: 473-486..
7Hecht SS (2003) Tobacco carcinogens, their biomarkers and tobacco-induced cancer. Nat Rev Cancer 3: 733-744.
8Stampfli MR, Anderson GP (2009) How cigarette smoke skews immune responses to promote infection, lung disease and cancer. Nat Rev Immunol 9: 377-384.
9Boyle JO, Giimiis ZH, Kacker A, Choksi VL, Bocker JM, et al. (2010) Effects of Cigarette Smoke on the Human Oral Mucosal Transcriptome. Cancer Prev Res (Phila) 3: 266-278.
10 van der Vaart H, Postma DS, Timens W, ten Hacken NH (2004) Acute effects of cigarette smoke on inflammation and oxidative stress: a review. Thorax 59: 713-721.
11 Maunders H, Patwardhan §, Phillips J, Clack A, Richter A (2006) Human bronchial epithelial cell transcriptome: gene expression changes following acute exposure to whole cigarette smoke in vitro. Am J Physiol Lung Cell Mol Physiol 292: 1248-1256.
12Abbud RA, Finegan CK, Guay LA, Rich EA (1995) E Enhanced production of human immunodeficiency virus type 1 by in vitro-infected alveolar macrophages from otherwise healthy cigarette smokers. J Infect Dis 172: 859-863.
13Rock RB GG, Aravalli RN, Hu S, Sheng WS, Peterson PK. (2007) Potentiation of HIV-1 expression in microglial cells by nicotine: involvement of transforming growth factor-beta 1. J Neuroimmune Pharmacol 3: 143-149.
14Chao A, Bulterys M, Musanganire F, Habimana P, Nawrocki P, et al. (1994) Risk factors associated with prevalent HIV-1 infection among pregnant women in Rwanda. Int J Epidemiol 23: 371-380.
15Boulos R, Halsey NA, Holt E, Ruff A, Brutus JR, et al. (1990) HIV-1 in Haitian women 1982-1988. The Cite Soleil/JHU AIDS Project Team. J Acquir Immune Defic Syndr 3: 721-728.
16Burns DN, Kramer A, Yellin F, Fuchs D, Wachter H, et al. (1991) Cigarette smoking: a modifier of human immunodeficiency virus type 1 infection? J Acquir Immune Defic Syndr 4: 76-83.
17Wright WR, Parzych K, Crawford D, Mein C, Mitchell JA, et al. (2012) Inflammatory transcriptome profiling of human monocytes exposed acutely to cigarette smoke. PLoS One 7: e30120.
18Hackett NR, Butler MW, Shaykhiev R, Salit J, Omberg L, et al. (2012) RNASeq quantification of the human small airway epithelium transcriptome. BMC Genomics 13: 82.
19 Beane J, Vick J, Schembri F, Anderlind C, Gower A, et al. (2011) Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila) 4: 803-817.
20 Fu W, Sanders-Beer BE, Katz KS, Maglott DR, Pruitt KD, et al. (2009) Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 37: D417-D422.
21Ptak RG, Fu W, Sanders-Beer BE, Dickerson JE, Pinney JW, et al. (2008) Cataloguing the HIV type 1 human protein interaction network. AIDS Res Hum Retroviruses 24: 1497-1502.
22Konig R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, et al. (2010) Human host factors required for influenza virus replication. Nature 463: 813-817.
23Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, et al. (2008) RNA interference screen for human genes associated with West Nile virus infection. Nature 455: 242-245.
24Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
25Gusev Y (2008) Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods 44: 61-72.
26Muller T;, Schrotter A, Loosse C, Helling S, Stephan C, et al. (2011) Sense and nonsense of pathway analysis software in proteomics. J Proteome Res 10: 5398-5408.
27Morou AK, Porichis F, Krambovitis E, Sourvinos G, Spandidos DA, et al. (2011) The HIV-1 gp120/V3 modifies the response of uninfected CD4 T cells to antigen presentation: mapping of the specific transcriptional signature. J Transl Med 9: 160.
28Francis AC, Di Primio C, Allouch A, Cereseto A (2011) Role of phosphorylation in the nuclear biology of HIV-1. Curr Med Chem 18: 2904-2912.
29Li PL, Wang T, Buckley KA, Chenine AL, Popov S, et al. (2005) Phosphorylation of HIV Nef by cAMP-dependent protein kinase. Virology 331: 367- 374,
30 Barnitz RA, Wan F, Tripuraneni V, Bolton DL, Lenardo MJ (2010) Protein kinase A phosphorylation activates Vpr-induced cell cycle arrest during human immunodeficiency virus type 1 infection. J Virol 84: 6410-6424.
31Debaisieux S, Rayne F, Yezid H, Beaumelle B (2012) The ins and outs of HIV-1 Tat. Traffic 13: 355-363.
32Kogan M, Rappaport J (2011) HIV-1 accessory protein Vpr: relevance in the pathogenesis of HIV and potential for therapeutic intervention. Retrovirology 8: 25.
33Felzien LK, Woffendin C, Hottiger MO, Subbramanian RA, Cohen EA, et al. (1998) HIV transcriptional activation by the accessory protein, VPR, is mediated by the p300 co-activator. Proc Natl Acad Sci U S A 95: 5281-5286.
34Zhang HS, Sang WW, Ruan Z, Wang YO (2011) Akt/Nox2/NF-«B signaling pathway is involved in Tat-induced HIV-1 long terminal repeat (LTR) transactivation. Arch Biochem Biophys 505: 266-272.
35Rohr O, Aunis D, Schaeffer E (1997) COUP-TF and Sp] interact and cooperate in the transcriptional activation of the human immunodeficiency virus type 1 long terminal repeat in human microglial cells. J Biol Chem 272: 31149- 31155.
36Majello B, De Luca P, Hagen G, Suske G, Lania L (1994) Different members of the Sp1 multigene family exert opposite transcriptional regulation of the long terminal repeat of HIV-1. Nucleic Acids Res 22: 4914-4921.
37Nogues G, Kadener S, Cramer P, Bentley D, Kornblihtt AR (2002) Transcriptional activators differ in their abilities to control alternative splicing. J Biol Chem 277: 43110-43114
38Amini S, Saunders M, Kelley K, Khalili K, Sawaya BE (2004) Interplay between HIV-1 Vpr and Sp1 modulates p21(WAF1) gene expression in human astrocytes. J Biol Chem 279: 46046-46056.
39Jakobovits A, Rosenthal A, Capon DJ (1990) Trans-activation of HIV-1 LTR-directed gene expression by tat requires protein kinase C. EMBO J 9: 1165-1170.
40Zhao H, Li J, Jiang L (2004) Inhibition of HIV-1 TAR RNA-Tat peptide complexation using poly(acrylic acid). Biochem Biophys Res Commun 320: 95-99.
41Kino T, Slobodskaya O, Pavlakis GN, Chrousos GP (2002) Nuclear receptor coactivator p160 proteins enhance the HIV-1 long terminal repeat promoter by bridging promoter-bound factors and the Tat-P-TEFb complex. J Biol Chem 277: 2396-2405.
42Munier S, Delcroix-Genete D, Carthagena L, Gumez A, Hazan U (2005) Characterization of two candidate genes, NCoA3 and IRF8, potentially involved in the control of HIV-1 latency. Retrovirology 2: 73.
43Sune C, Hayashi T, Liu Y, Lane WS, Young RA, et al. (1997) CA150, a nuclear protein associated with the RNA polymerase II holoenzyme, is involved in Tat-activated human immunodeficiency virus type 1 transcription. Mol Cell Biol 17: 6029-6039.
44Tyagi M, Rusnati M, Presta M, Giacca M (2001) Internalization of HIV-1 tat requires cell surface heparan sulfate proteoglycans. J Biol Chem 276: 3254- 3261.
45 Hakansson S, Caffrey M (2003) Structural and dynamic properties of the HIV-1 tat transduction domain in the free and heparin-bound states. Biochemistry 42: 8999-9006.
46Sawaya BE, Khalili K, Gordon J, Taube R, Amini S (2000) Cooperative interaction between HIV-1 regulatory proteins Tat and Vpr modulates transcription of the viral genome. J Biol Chem 275: 35209-35214.
47Kino T, Pavlakis GN (2004) Partner molecules of accessory protein Vpr of the human immunodeficiency virus type 1. DNA Cell Biol 23: 193-205.
48Ariumi Y, Trono D (2006) Ataxia-telangiectasia-mutated (ATM) protein can enhance human immunodeficiency virus type 1 replication by stimulating Rev function. J Virol 80: 2445-2452.
49 Kinoshita SM, Taguchi S (2008) NF-IL6 (C/EBPbeta) induces HIV-1 replication by inhibiting cytidine deaminase APOBEC3G. Proc Natl Acad Sci U S A 105: 15022-15027.
50Amendola A, Rodolfo C, Di Caro A, Ciccosanti F, Falasca L, et al. (2001) "Tissue" transglutaminase expression in HIV-infected cells: an enzyme with an antiviral effect? Ann N Y Acad Sci 946: 108-120.
51Cordelier P, Zern MA, Strayer DS (2003) HIV-1 proprotein processing as a target for gene therapy. Gene Ther 10: 467-477.
52 Anderson ED, Thomas L, Hayflick JS, Thomas G (1993) Inhibition of HIV1 gp160-dependent membrane fusion by a furin-directed alpha 1-antitrypsin variant. J Biol Chem 268: 24887-24891.
53Daily A, Nath A, Hersh LB (2006) Tat peptides inhibit neprilysin. J Neurovirol 12: 153-160.
54Battaglia PA, Longo E, Ciotta C, Del Grosso ME, Ambrosini E, et al. (1994) Genetic tests to reveal TAT homodimer formation and select TAT homodimer inhibitor. Biochem Biophys Res Commun 201: 701-708.