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1.
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Zhou R, Rana TM. RNA-based mechanisms regulating host-virus interactions. Immunol Rev. 2013 May; 253(1):97-111.
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2.
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Yang CS, Rana TM. Learning the molecular mechanisms of the reprogramming factors: let's start from microRNAs. Mol Biosyst. 2013 Jan 27; 9(1):10-7.
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3.
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Li Z, Rana TM. A kinase inhibitor screen identifies small-molecule enhancers of reprogramming and iPS cell generation. Nat Commun. 2012 Sep 25; 3:1085.
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4.
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Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM. Design, Synthesis, and Biological and Structural Evaluations of Novel HIV-1 Protease Inhibitors To Combat Drug Resistance. J Med Chem. 2012 Jul 26; 55(14):6328-41.
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5.
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Baigude H, Ahsanullah , Li Z, Zhou Y, Rana TM. miR-TRAP: A Benchtop Chemical Biology Strategy to Identify microRNA Targets. Angew Chem Int Ed Engl. 2012 Jun 11; 51(24):5880-3.
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6.
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Ali A, Wang J, Nathans RS, Cao H, Sharova N, Stevenson M, Rana TM. Synthesis and Structure-Activity Relationship Studies of HIV-1 Virion Infectivity Factor (Vif) Inhibitors that Block Viral Replication. ChemMedChem. 2012 Jul; 7(7):1217-29.
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7.
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Zhou H, Arcila ML, Li Z, Lee EJ, Henzler C, Liu J, Rana TM, Kosik KS. Deep annotation of mouse iso-miR and iso-moR variation. Nucleic Acids Res. 2012 Jul 1; 40(13):5864-75.
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8.
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Li Z, Rana TM. Using MicroRNAs to Enhance the Generation of Induced Pluripotent Stem Cells. Curr Protoc Stem Cell Biol. 2012 Mar; Chapter 4:Unit4A.4.
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9.
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Li Z, Rana TM. Molecular Mechanisms of RNA-Triggered Gene Silencing Machineries. Acc Chem Res. 2012 Jul 17; 45(7):1122-31.
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10.
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O'Brien SK, Knight KL, Rana TM. Phosphorylation of histone H1 by P-TEFb is a necessary step in skeletal muscle differentiation. J Cell Physiol. 2012 Jan; 227(1):383-9.
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11.
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Baigude H, Rana TM. Interfering Nanoparticles for Silencing MicroRNAs. Methods Enzymol. 2012; 509:339-53.
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12.
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Yang CS, Lopez CG, Rana TM. Discovery of nonsteroidal anti-inflammatory drug and anticancer drug enhancing reprogramming and induced pluripotent stem cell generation. Stem Cells. 2011 Oct; 29(10):1528-36.
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13.
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Yang CS, Li Z, Rana TM. microRNAs modulate iPS cell generation. RNA. 2011 Aug; 17(8):1451-60.
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14.
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Li Z, Yang CS, Nakashima K, Rana TM. Small RNA-mediated regulation of iPS cell generation. EMBO J. 2011 Mar 2; 30(5):823-34.
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15.
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Su J, Baigude H, McCarroll J, Rana TM. Silencing microRNA by interfering nanoparticles in mice. Nucleic Acids Res. 2011 Mar 1; 39(6):e38.
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16.
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Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Schiffer CA, Rana TM. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones. J Med Chem. 2010 Nov 11; 53(21):7699-708.
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17.
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Lu CC, Li Z, Chu CY, Feng J, Feng J, Sun R, Rana TM. MicroRNAs encoded by Kaposi's sarcoma-associated herpesvirus regulate viral life cycle. EMBO Rep. 2010 Oct; 11(10):784-90.
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18.
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Ghosh A, Mukherjee K, Jiang X, Zhou Y, McCarroll J, Qu J, Swain PM, Baigude H, Rana TM. Design and assembly of new nonviral RNAi delivery agents by microwave-assisted quaternization (MAQ) of tertiary amines. Bioconjug Chem. 2010 Sep 15; 21(9):1581-7.
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19.
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James V, Zhang Y, Foxler DE, de Moor CH, Kong YW, Webb TM, Self TJ, Feng Y, Lagos D, Chu CY, Rana TM, Morley SJ, Longmore GD, Bushell M, Sharp TV. LIM-domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA-mediated gene silencing. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12499-504.
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20.
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O'Brien SK, Cao H, Nathans R, Ali A, Rana TM. P-TEFb kinase complex phosphorylates histone H1 to regulate expression of cellular and HIV-1 genes. J Biol Chem. 2010 Sep 24; 285(39):29713-20.
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21.
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Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 2010 May; 84(10):5368-78.
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22.
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McCarroll J, Baigude H, Yang CS, Rana TM. Nanotubes functionalized with lipids and natural amino acid dendrimers: a new strategy to create nanomaterials for delivering systemic RNAi. Bioconjug Chem. 2010 Jan; 21(1):56-63.
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23.
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Das S, Pan D, Bera AK, Rana T, Bandyopadhyay S, De S, Das SK, Bhattacharya D, Bandyopadhyay SK. Stress inducible heat shock protein 70: a potent molecular and toxicological signature in arsenic exposed broiler chickens. Mol Biol Rep. 2010 Oct; 37(7):3151-5.
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24.
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Baigude H, Rana TM. Delivery of therapeutic RNAi by nanovehicles. Chembiochem. 2009 Oct 12; 10(15):2449-54.
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25.
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Pan D, Bera AK, Das S, Bandyopadhyay S, Rana T, Bandyopadhyay S, Das SK, Bhattacharya D. Use of zinc chloride as alternative stimulant for in vitro study of nitric oxide production pathway in avian splenocyte culture. Mol Biol Rep. 2010 Jun; 37(5):2223-6.
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26.
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Ali A, Ghosh A, Nathans RS, Sharova N, O'Brien S, Cao H, Stevenson M, Rana TM. Identification of flavopiridol analogues that selectively inhibit positive transcription elongation factor (P-TEFb) and block HIV-1 replication. Chembiochem. 2009 Aug 17; 10(12):2072-80.
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27.
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Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM. Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell. 2009 Jun 26; 34(6):696-709.
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28.
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Bélanger F, Baigude H, Rana TM. U30 of 7SK RNA forms a specific photo-cross-link with Hexim1 in the context of both a minimal RNA-binding site and a fully reconstituted 7SK/Hexim1/P-TEFb ribonucleoprotein complex. J Mol Biol. 2009 Mar 6; 386(4):1094-107.
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29.
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Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. Additivity in the analysis and design of HIV protease inhibitors. J Med Chem. 2009 Feb 12; 52(3):737-54.
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30.
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Nathans R, Cao H, Sharova N, Ali A, Sharkey M, Stranska R, Stevenson M, Rana TM. Small-molecule inhibition of HIV-1 Vif. Nat Biotechnol. 2008 Oct; 26(10):1187-92.
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31.
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Cao H, Yang CS, Rana TM. Evolutionary emergence of microRNAs in human embryonic stem cells. PLoS One. 2008; 3(7):e2820.
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32.
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Chu CY, Rana TM. Potent RNAi by short RNA triggers. RNA. 2008 Sep; 14(9):1714-9.
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33.
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Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc. 2008 May 14; 130(19):6099-113.
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34.
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Wang H, Ghosh A, Baigude H, Yang CS, Qiu L, Xia X, Zhou H, Rana TM, Xu Z. Therapeutic gene silencing delivered by a chemically modified small interfering RNA against mutant SOD1 slows amyotrophic lateral sclerosis progression. J Biol Chem. 2008 Jun 6; 283(23):15845-52.
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35.
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Chu CY, Rana TM. Small RNAs: regulators and guardians of the genome. J Cell Physiol. 2007 Nov; 213(2):412-9.
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36.
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Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres. J Med Chem. 2007 Sep 6; 50(18):4316-28.
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37.
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Robb GB, Rana TM. RNA helicase A interacts with RISC in human cells and functions in RISC loading. Mol Cell. 2007 May 25; 26(4):523-37.
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38.
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Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des. 2007 May; 69(5):298-313.
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39.
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Baigude H, McCarroll J, Yang CS, Swain PM, Rana TM. Design and creation of new nanomaterials for therapeutic RNAi. ACS Chem Biol. 2007 Apr 24; 2(4):237-41.
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40.
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Chiu YL, Cao H, Rana TM. Quantitative analysis of RNA-mediated protein-protein interactions in living cells by FRET. Chem Biol Drug Des. 2007 Apr; 69(4):233-9.
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41.
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Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol. 2007 Jan; 8(1):23-36.
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42.
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Ali A, Reddy GS, Cao H, Anjum SG, Nalam MN, Schiffer CA, Rana TM. Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. J Med Chem. 2006 Dec 14; 49(25):7342-56.
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43.
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Richter SN, Bélanger F, Zheng P, Rana TM. Dynamics of nascent mRNA folding and RNA-protein interactions: an alternative TAR RNA structure is involved in the control of HIV-1 mRNA transcription. Nucleic Acids Res. 2006; 34(15):4278-92.
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44.
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Chu CY, Rana TM. Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol. 2006 Jul; 4(7):e210.
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45.
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Wichroski MJ, Robb GB, Rana TM. Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. PLoS Pathog. 2006 May; 2(5):e41.
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46.
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Cao H, Tamilarasu N, Rana TM. Orientation and affinity of HIV-1 Tat fragments in Tat-TAR complex determined by fluorescence resonance energy transfer. Bioconjug Chem. 2006 Mar-Apr; 17(2):352-8.
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47.
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Lee CW, Cao H, Ichiyama K, Rana TM. Design and synthesis of a novel peptidomimetic inhibitor of HIV-1 Tat-TAR interactions: squaryldiamide as a new potential bioisostere of unsubstituted guanidine. Bioorg Med Chem Lett. 2005 Oct 1; 15(19):4243-6.
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48.
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Chiu YL, Dinesh CU, Chu CY, Ali A, Brown KM, Cao H, Rana TM. Dissecting RNA-interference pathway with small molecules. Chem Biol. 2005 Jun; 12(6):643-8.
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49.
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Brown KM, Chu CY, Rana TM. Target accessibility dictates the potency of human RISC. Nat Struct Mol Biol. 2005 May; 12(5):469-70.
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50.
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Lee HK, Cao H, Rana TM. Design, microwave-assisted synthesis, and photophysical properties of small molecule organic antennas for luminescence resonance energy transfer. J Comb Chem. 2005 Mar-Apr; 7(2):279-84.
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51.
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Ping YH, Rana TM. Mechanism of site-specific psoralen photoadducts formation in triplex DNA directed by psoralen-conjugated oligonucleotides. Biochemistry. 2005 Feb 22; 44(7):2501-9.
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52.
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Robb GB, Brown KM, Khurana J, Rana TM. Specific and potent RNAi in the nucleus of human cells. Nat Struct Mol Biol. 2005 Feb; 12(2):133-7.
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53.
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Ping YH, Chu CY, Cao H, Jacque JM, Stevenson M, Rana TM. Modulating HIV-1 replication by RNA interference directed against human transcription elongation factor SPT5. Retrovirology. 2004; 1:46.
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54.
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Wichroski MJ, Ichiyama K, Rana TM. Analysis of HIV-1 viral infectivity factor-mediated proteasome-dependent depletion of APOBEC3G: correlating function and subcellular localization. J Biol Chem. 2005 Mar 4; 280(9):8387-96.
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55.
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Chiu YL, Ali A, Chu CY, Cao H, Rana TM. Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells. Chem Biol. 2004 Aug; 11(8):1165-75.
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56.
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Zhang L, Rana TM. Solid-phase synthesis of alpha-(2-(benzylthio)-1,4-dihydro-6-methyl-4-p-tolylpyrimidine-5-carboxamido) acids: a new strategy to create diversity in heterocyclic scaffolds. J Comb Chem. 2004 Jul-Aug; 6(4):457-9.
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57.
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Lee HK, Rana TM. Microwave-assisted parallel synthesis of a 4,6-diamino-2,2-dimethyl-1,2-dihydro-1-phenyl-s-triazine library. J Comb Chem. 2004 Jul-Aug; 6(4):504-8.
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58.
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Chiu YL, Cao H, Jacque JM, Stevenson M, Rana TM. Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1). J Virol. 2004 Mar; 78(5):2517-29.
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59.
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Gelman MA, Richter S, Cao H, Umezawa N, Gellman SH, Rana TM. Selective binding of TAR RNA by a Tat-derived beta-peptide. Org Lett. 2003 Oct 2; 5(20):3563-5.
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60.
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Chiu YL, Rana TM. siRNA function in RNAi: a chemical modification analysis. RNA. 2003 Sep; 9(9):1034-48.
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61.
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Hwang S, Tamilarasu N, Kibler K, Cao H, Ali A, Ping YH, Jeang KT, Rana TM. Discovery of a small molecule Tat-trans-activation-responsive RNA antagonist that potently inhibits human immunodeficiency virus-1 replication. J Biol Chem. 2003 Oct 3; 278(40):39092-103.
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62.
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Hamma T, Saleh A, Huq I, Rana TM, Miller PS. Inhibition of HIV tat-TAR interactions by an antisense oligo-2'-O-methylribonucleoside methylphosphonate. Bioorg Med Chem Lett. 2003 Jun 2; 13(11):1845-8.
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63.
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Kesavan V, Tamilarasu N, Cao H, Rana TM. A new class of RNA-binding oligomers: peptoid amide and ester analogues. Bioconjug Chem. 2002 Nov-Dec; 13(6):1171-5.
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64.
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Chiu YL, Rana TM. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol Cell. 2002 Sep; 10(3):549-61.
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65.
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Chiu YL, Ho CK, Saha N, Schwer B, Shuman S, Rana TM. Tat stimulates cotranscriptional capping of HIV mRNA. Mol Cell. 2002 Sep; 10(3):585-97.
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66.
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Zhou C, Rana TM. A bimolecular mechanism of HIV-1 Tat protein interaction with RNA polymerase II transcription elongation complexes. J Mol Biol. 2002 Jul 26; 320(5):925-42.
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67.
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Richter S, Ping YH, Rana TM. TAR RNA loop: a scaffold for the assembly of a regulatory switch in HIV replication. Proc Natl Acad Sci U S A. 2002 Jun 11; 99(12):7928-33.
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68.
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Richter S, Cao H, Rana TM. Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-Tat-TAR ternary complex formation. Biochemistry. 2002 May 21; 41(20):6391-7.
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69.
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Dinman JD, Richter S, Plant EP, Taylor RC, Hammell AB, Rana TM. The frameshift signal of HIV-1 involves a potential intramolecular triplex RNA structure. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5331-6.
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70.
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Wang Z, Shah K, Rana TM. Probing Tat peptide-TAR RNA interactions by psoralen photo-cross-linking. Biochemistry. 2001 May 29; 40(21):6458-64.
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71.
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O'Brien TP, Li QJ, Sauerburger F, Reviglio VE, Rana T, Ashraf MF. The role of matrix metalloproteinases in ulcerative keratolysis associated with perioperative diclofenac use. Ophthalmology. 2001 Apr; 108(4):656-9.
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72.
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Tamilarasu N, Zhang J, Hwang S, Rana TM. A new strategy for site-specific protein modification: analysis of a Tat peptide-TAR RNA interaction. Bioconjug Chem. 2001 Mar-Apr; 12(2):135-8.
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73.
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Tamilarasu N, Huq I, Rana TM. Targeting RNA with peptidomimetic oligomers in human cells. Bioorg Med Chem Lett. 2001 Feb 26; 11(4):505-7.
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74.
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Chiu YL, Coronel E, Ho CK, Shuman S, Rana TM. HIV-1 Tat protein interacts with mammalian capping enzyme and stimulates capping of TAR RNA. J Biol Chem. 2001 Apr 20; 276(16):12959-66.
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75.
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Ping YH, Rana TM. DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 Tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation. J Biol Chem. 2001 Apr 20; 276(16):12951-8.
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76.
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Zhang J, Tamilarasu N, Hwang S, Garber ME, Huq I, Jones KA, Rana TM. HIV-1 TAR RNA enhances the interaction between Tat and cyclin T1. J Biol Chem. 2000 Nov 3; 275(44):34314-9.
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77.
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Tamilarasu N, Huq I, Rana TM. Design, synthesis, and biological activity of a cyclic peptide: an inhibitor of HIV-1 tat-TAR interactions in human cells. Bioorg Med Chem Lett. 2000 May 1; 10(9):971-4.
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78.
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Hwang S, Tamilarasu N, Rana TM. Selection of HIV replication inhibitors: chemistry and biology. Adv Pharmacol. 2000; 49:167-97.
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79.
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Hwang S, Tamilarasu N, Ryan K, Huq I, Richter S, Still WC, Rana TM. Inhibition of gene expression in human cells through small molecule-RNA interactions. Proc Natl Acad Sci U S A. 1999 Nov 9; 96(23):12997-3002.
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80.
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Rana TM, Jeang KT. Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA. Arch Biochem Biophys. 1999 May 15; 365(2):175-85.
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81.
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Wang Z, Huq I, Rana TM. Proximity of a Tat peptide to the HIV-1 TAR RNA loop region determined by site-specific photo-cross-linking. Bioconjug Chem. 1999 May-Jun; 10(3):512-9.
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82.
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Huq I, Ping YH, Tamilarasu N, Rana TM. Controlling human immunodeficiency virus type 1 gene expression by unnatural peptides. Biochemistry. 1999 Apr 20; 38(16):5172-7.
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83.
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Ping YH, Rana TM. Tat-associated kinase (P-TEFb): a component of transcription preinitiation and elongation complexes. J Biol Chem. 1999 Mar 12; 274(11):7399-404.
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84.
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Huq I, Tamilarasu N, Rana TM. Visualizing tertiary folding of RNA and RNA-protein interactions by a tethered iron chelate: analysis ofHIV-1 Tat-TAR complex. Nucleic Acids Res. 1999 Feb 15; 27(4):1084-93.
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85.
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Wang Z, Rana TM. Probing RNA-protein interactions by psoralen photocrosslinking. Methods Mol Biol. 1999; 118:49-62.
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86.
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Wang Z, Rana TM. RNA-protein interactions in the Tat-trans-activation response element complex determined by site-specific photo-cross-linking. Biochemistry. 1998 Mar 24; 37(12):4235-43.
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87.
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Huq I, Wang X, Rana TM. Specific recognition of HIV-1 TAR RNA by a D-Tat peptide. Nat Struct Biol. 1997 Nov; 4(11):881-2.
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88.
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Huq I, Rana TM. Probing the proximity of the core domain of an HIV-1 Tat fragment in a Tat-TAR complex by affinity cleaving. Biochemistry. 1997 Oct 14; 36(41):12592-9.
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89.
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Ping YH, Liu Y, Wang X, Neenhold HR, Rana TM. Dynamics of RNA-protein interactions in the HIV-1 Rev-RRE complex visualized by 6-thioguanosine-mediated photocrosslinking. RNA. 1997 Aug; 3(8):850-60.
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90.
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Wang Z, Rana TM. DNA damage-dependent transcriptional arrest and termination of RNA polymerase II elongation complexes in DNA template containing HIV-1 promoter. Proc Natl Acad Sci U S A. 1997 Jun 24; 94(13):6688-93.
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91.
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Song AI, Rana TM. Synthesis of an amino acid analogue to incorporate p-aminobenzyl-EDTA in peptides. Bioconjug Chem. 1997 Mar-Apr; 8(2):249-52.
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92.
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Wang Z, Wang X, Rana TM. Protein orientation in the Tat-TAR complex determined by psoralen photocross-linking. J Biol Chem. 1996 Jul 19; 271(29):16995-8.
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93.
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Wang Z, Rana TM. RNA conformation in the Tat-TAR complex determined by site-specific photo-cross-linking. Biochemistry. 1996 May 21; 35(20):6491-9.
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94.
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Shah K, Neenhold H, Wang Z, Rana TM. Incorporation of an artificial protease and nuclease at the HIV-1 Tat binding site of trans-activation responsive RNA. Bioconjug Chem. 1996 May-Jun; 7(3):283-9.
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95.
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Liu Y, Wang Z, Rana TM. Visualizing a specific contact in the HIV-1 Tat protein fragment and trans-activation responsive region RNA complex by photocross-linking. J Biol Chem. 1996 Apr 26; 271(17):10391-6.
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96.
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Neenhold HR, Rana TM. Major groove opening at the HIV-1 Tat binding site of TAR RNA evidenced by a rhodium probe. Biochemistry. 1995 May 16; 34(19):6303-9.
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97.
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Shah K, Wu H, Rana TM. Synthesis of uridine phosphoramidite analogs: reagents for site-specific incorporation of photoreactive sites into RNA sequences. Bioconjug Chem. 1994 Nov-Dec; 5(6):508-12.
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98.
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Rana TM, Meares CF. N-terminal modification of immunoglobulin polypeptide chains tagged with isothiocyanato chelates. Bioconjug Chem. 1990 Sep-Oct; 1(5):357-62.
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