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Selected peer-reviewed research papers and reviews

(SomaGenics contributers are highlighted in bold)

A.Dallas, H. Ilves, H. Ma, D. J. Chin, I. MacLachlan, K. Klumpp, and B.H. Johnston (2014) Inhibition of hepatitis C virus in chimeric mice by sshRNAs:  sequence analysis of surviving virus shows added selective pressure of combination therapy. J. Virology May;88(9):4647-56. PMID: 24478422  pdfDownload PDF

Ma H. , Dallas A, Ilves H,Shorenstein J, Maclachlan I, Klumpp K, and Johnston BH (2014) Formulated minimal-length synthetic shRNAs are potent inhibitors of Hepatitis C virus in chimeric human-liver mice.  Gastroenterology, 146(1):63-66.e5. PMID: 24076507   pdfDownload PDF

A. Dallas and B.H. Johnston (2013) Design and Chemical Modification of Synthetic Short shRNAs as Potent RNAi Triggers.  In: siRNA Design, D. J. Taxman, ed., Methods in Molecular Biology series, Humana Press (Springer), New York.  PMID: 23027057   pdfDownload PDF

Dallas A, Ilves H, Shorenstein J, Judge A, Spitler R, Contag C, Ping Wong S, Harbottle RP, MacLachlan I, and Johnston BH (2013) Minimal-length synthetic shRNAs (sshRNAs) formulated with lipid nanoparticles are potent inhibitors of hepatitis C virus IRES-linked gene expression in mice.  Mol. Therapy–Nucleic Acids 17;2:e123. PMID: 24045712   pdfDownload PDF

Kolli S, Wong SP, Harbottle R, Johnston B, Thanou M, Miller AD. (2013) pH-Triggered Nanoparticle Mediated Delivery of siRNA to Liver Cells in Vitro and in Vivo. Bioconjug Chem. 24(3):314-32. PMID: 23305315   pdfDownload PDF

B.H. Johnston and Q. Ge (2012) Design of synthetic shRNAs for targeting hepatitis C: A new approach to antiviral therapeutics.  In: RNA Technologies, From Nucleic Acids Sequences to Molecular Medicine, V. A. Erdmann and J. Barciszewski, Eds., Springer, Berlin. DOI 10.1007/978-3-642-27426-8_18.  pdfDownload PDF

Dallas, Anne; Ilves, Heini; Ge, Qing; Kumar, Pavan; Shorenstein, Joshua; Kazakov, Sergei A.; Cuellar, Trinna L.; McManus, Michael T.; Behlke, Mark A.;, Johnston, Brian H. (2012) Right- and Left-loop short shRNAs have distinct and unusual mechanisms of gene silencing. Nucleic Acids Res. 40: 9255–9271. (Epub July 18, 2012) PMID: 22810205   pdfDownload PDF

Feng Li, Daniela Pignatta, Claire Bendix, Jacob O. Brunkard, Megan M. Cohn, Jeffery Tung, Haoyu Sun, Pavan Kumar, and Barbara Baker (2012) MicroRNA regulation of plant innate immune receptors. Proc. Natl. Acad. Sci. USA 109(5):1790-5 (Epub Jan. 18, 2012) PMID: 22307647   pdfDownload PDF

Kumar, P., Johnston, B.H., and Kazakov, S.A. (2011) miR-ID: a novel, circularization-based platform for detection of microRNAs. RNA 17(2):365-80 (Epub Dec. 17, 2010) PMID 21169480  pdfDownload PDF

Ge Q., Ilves H., Dallas A., Kumar P., Shorenstein J., Kazakov S.A., and Johnston B.H. (2010) Minimal-length short hairpin RNAs: The relationship of structure and RNAi activity. RNA 16(1):106-17 (Epub Dec. 1, 2009) PMID 19952116  pdfDownload PDF

Ge Q., Dallas A., Ilves H., Shorenstein J., Behlke M.A., Johnston B.H. (2010) Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs. RNA 16(1):118-30 (Epub Nov. 30, 2009) PMID 19948766   pdfDownload PDF

Dallas, A., Balatskaya, S.V., Kuo, T-C., Vlassov, A.V., Kaspar, R.L., Kisich, K., Kazakov, S.A., Johnston, B.H. (2008) Hairpin ribozyme-antisense RNA derivatives act as molecular Lassos. Nucleic Acids Res. 36(21):6752-66; (Epub Oct. 25, 2008) PMID 18953032   pdfDownload PDF

R.P. Hickerson, A. V. Vlassov, Q. Wang, D. Leake, H. Ilves,  C. H. Contag, B.H. Johnston, and R. L. Kaspar (2008) Stability study of unmodified siRNA and relevance to clinical use.  Oligonucleotides 18(4):345-54; (Epub Oct. 10, 2008) PMID 18844576   pdfDownload PDF

A.A. Seyhan, B.N. Alizadeh and B.H. Johnston (2007) RNA interference-mediated inhibition of Semliki Forest virus replication in mammalian cells.  Oligonucleotides 17(4): 473-84. PMID 18095875   pdfDownload PDF

Qian Wang, Heini Ilves,  Pauline Chu,  Christopher H. Contag, Devin Leake, Brian H. Johnston, and Roger L. Kaspar (2007)  Delivery and inhibition of reporter genes by small interfering and hairpin RNAs in a mouse skin model. J. Invest. Dermatol. 127(11):2577-84; (Epub May 24, 2007) PMID 17522708   pdfDownload PDF

Vlassov, A.V., Korba, B., Farrar, K. , Mukerjee, S., Seyhan, A.A., Ilves, H. Kaspar, R.L., Kazakov, S.A. and Johnston, B.H. (2007) shRNAs targeting hepatitis C: effects of sequence and structural features, and comparison with siRNA. Oligonucleotides 17:223-236. PMID 17638526   pdfDownload PDF

Ilves, H., Kaspar, R.L., Wang, Q., Seyhan, A.A., Vlassov, A.V., Contag, C.H. , Leake, D. and Johnston, B.H. (2006) Inhibition of hepatitis C IRES-mediated gene expression by small hairpin RNAs in human hepatocytes and mice. Ann. N.Y. Acad. Sci., 1082: 52-55. PMID 17145925   pdfDownload PDF

Seyhan, A.A., Vlassov, A.V. and Johnston, B.H. (2006) RNA interference from multimeric shRNAs generated by rolling circle transcription.  Oligonucleotides 16: 353-363. PMID 17155910   pdfDownload PDF

Kazakov, S.A., Balatskaya, S.V. and Johnston, B.H. (2006)  Ligation of the hairpin ribozyme in cis induced by freezing and dehydration. RNA 12: 446-456. PMID 16495237   pdfDownload PDF

Vlassov, A.V., Johnston, B.H., and Kazakov, S.A. (2005) Hairpin ribozyme-catalyzed ligation in water-alcohol solutions.  Oligonucleotides 15, 303-309. PMID 16396624   pdfDownload PDF

Wang, C.H. Contag, Ilves, H., Johnston, B.H., and Kaspar, R.L. (2005) Small hairpin RNAs efficiently inhibit hepatitis C IRES-mediated gene expression in human tissue culture cells and a mouse model. Mol. Therapy, 12:562-8. PMID 15953767   pdfDownload PDF

Vlassov, A.V., Kazakov, S.A., Johnston, B.H. and Landweber, L.F. (2005) The RNA World on Ice: A New Scenario for the Emergence of RNA Information, J. Mol. Evol., 61:264-73. PMID 16044244   pdfDownload PDF

Seyhan, A.A., Vlassov, A.V., Ilves, H., Egry, L., Kazakov, S.A., and Johnston, B.H. (2005) Complete, gene-specific siRNA libraries: production and expression in mammalian cells. RNA 11, 837-846. PMID 15840823   pdfDownload PDF

Vlassov, A.V., Koval, O.A., Johnston, B.H. and Kazakov, S.A. (2004) ROLL: a method of preparation of gene-specific oligonucleotide libraries. Oligonucleotides 14, 210-220. PMID 15625916   pdfDownload PDF

Vlassov, A.V., Johnston, B.H. and Kazakov, S.A. (2004) Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world. Nucl. Acids Res. 32, 2966-2974. PMID 15161960   pdfDownload PDF