sirna references

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[Meister2004Mechanisms] G. Meister and T. Tuschl. Mechanisms of gene silencing by double-stranded RNA. Nature, 431(7006):343-9, Sep 2004. [ bib | DOI | http | .pdf | Abstract ]
[Jones-Rhoades2004Computational] Matthew W Jones-Rhoades and David P Bartel. Computational identification of plant micrornas and their targets, including a stress-induced mirna. Mol Cell, 14(6):787-799, Jun 2004. [ bib | DOI | http | .pdf | Abstract ]
[John2004Human] Bino John, Anton J Enright, Alexei Aravin, Thomas Tuschl, Chris Sander, and Debora S Marks. Human microrna targets. PLoS Biol, 2(11):e363, Nov 2004. [ bib | DOI | http | .pdf | Abstract ]
[Jackson2004Noise] A. L. Jackson and P. S. Linsley. Noise amidst the silence: off-target effects of siRNAs? Trends Genet., 20(11):521-4, Nov 2004. [ bib | DOI | http | Abstract ]
[Hsieh2004library] A. C. Hsieh, R. Bo, J. Manola, F. Vazquez, O. Bare, A. Khvorova, S. Scaringe, and W. R. Sellers. A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res., 32(3):893-901, 2004. [ bib | DOI | http | .pdf | Abstract ]
[Hannon2004Unlocking] G. J. Hannon and J. J. Rossi. Unlocking the potential of the human genome with RNA interference. Nature, 431(7006):371-8, Sep 2004. [ bib | DOI | http | .pdf | Abstract ]
[Hall2004Unravelling] J. Hall. Unravelling the general properties of siRNAs: strength in numbers and lessons from the past. Nat. Rev. Genet., 5(7):552-7, Jul 2004. [ bib | DOI | http | .pdf ]
[Haley2004Kinetic] B. Haley and P. D. Zamore. Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol., 11(7):599-606, Jul 2004. [ bib | DOI | http | .pdf | Abstract ]
[Gong2004Picking] D. Gong and J. E. Ferrell. Picking a winner: new mechanistic insights into the design of effective siRNAs. Trends Biotechnol., 22(9):451-4, Sep 2004. [ bib | DOI | http | Abstract ]
[Ding2004Sfold] Y. Ding, C. Chan Yu, and C. E. Lawrence. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32(Web Server issue):W135-W141, Jul 2004. [ bib | DOI | http | Abstract ]
[Chalk2004Improved] A. M. Chalk, C. Wahlestedt, and E. L. L. Sonnhammer. Improved and automated prediction of effective siRNA. Biochem. Biophys. Res. Commun., 319(1):264-74, Jun 2004. [ bib | DOI | http | .pdf | Abstract ]
[Bartel2004MicroRNAs] David P Bartel. Micrornas: genomics, biogenesis, mechanism, and function. Cell, 116(2):281-297, Jan 2004. [ bib | .pdf | Abstract ]
[Amarzguioui2004algorithm] M. Amarzguioui and H. Prydz. An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun., 316(4):1050-8, Apr 2004. [ bib | DOI | http | Abstract ]
[Mittal2004Improving] V. Mittal. Improving the efficiency of RNA interference in mammals. Nat. Rev. Genet., 5(5):355-65, May 2004. [ bib | DOI | http ]
[Ma2004Structural] J.B. Ma, K. Ye, and D.J. Patel. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature, 429(6989):318-322, May 2004. [ bib | DOI | http | Abstract ]
[Yamada2005Accelerated] T. Yamada and S. Morishita. Accelerated off-target search algorithm for siRNA. Bioinformatics, 21(8):1316-24, Apr 2005. [ bib | DOI | http | Abstract ]
[Truss2005HuSiDa] M. Truss, M. Swat, S. M. Kielbasa, R. Schäfer, H. Herzel, and C. Hagemeier. HuSiDa-the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. Nucleic Acids Res., 33(Database issue):D108-11, Jan 2005. [ bib | DOI | http | Abstract ]
[Tomari2005Perspective] Y. Tomari and P. D. Zamore. Perspective: machines for RNAi. Genes Dev., 19(5):517-29, Mar 2005. [ bib | DOI | http | Abstract ]
[Tang2005siRNA] G. Tang. siRNA and miRNA: an insight into RISCs. Trends Biochem. Sci., 30(2):106-14, Feb 2005. [ bib | DOI | http | Abstract ]
[Qiu2005computational] S. Qiu, C. M. Adema, and T. Lane. A computational study of off-target effects of RNA interference. Nucleic Acids Res., 33(6):1834-1847, 2005. [ bib | DOI | http | Abstract ]
[Ma2005Structural] J-B. Ma, Y.-R. Yuan, G.. Meister, Y. Pei, T. Tuschl, and Patel D.J. Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus PIWI protein. Nature, 434:666-670, 2005. [ bib ]
[Lim2005Microarray] Lee P Lim, Nelson C Lau, Philip Garrett-Engele, Andrew Grimson, Janell M Schelter, John Castle, David P Bartel, Peter S Linsley, and Jason M Johnson. Microarray analysis shows that some micrornas downregulate large numbers of target mrnas. Nature, 433(7027):769-773, Feb 2005. [ bib | DOI | http | Abstract ]
[Lewis2005Conserved] Benjamin P Lewis, Christopher B Burge, and David P Bartel. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microrna targets. Cell, 120(1):15-20, Jan 2005. [ bib | DOI | http | .pdf | Abstract ]
[Huppi2005Defining] K. Huppi, S. E. Martin, and N. J. Caplen. Defining and assaying RNAi in mammalian cells. Mol. Cell, 17(1):1-10, Jan 2005. [ bib | DOI | http | Abstract ]
[Huesken2005Design] D. Huesken, J. Lange, C. Mickanin, J. Weiler, F. Asselbergs, J. Warner, B. Meloon, S. Engel, A. Rosenberg, D. Cohen, M. Labow, M. Reinhardt, F. Natt, and J. Hall. Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol., 23(8):995-1001, Aug 2005. [ bib | DOI | http | .pdf | Abstract ]
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[Brennecke2005Principles] Julius Brennecke, Alexander Stark, Robert B Russell, and Stephen M Cohen. Principles of microrna-target recognition. PLoS Biol, 3(3):e85, Mar 2005. [ bib | DOI | http | Abstract ]
[Boese2005Mechanistic] Q. Boese, D. Leake, A. Reynolds, S. Read, S. A. Scaringe, W. S. Marshall, and A. Khvorova. Mechanistic insights aid computational short interfering RNA design. Methods Enzymol., 392:73-96, 2005. [ bib | DOI | http | Abstract ]
[Teramoto2005Prediction] Reiji Teramoto, Mikio Aoki, Toru Kimura, and Masaharu Kanaoka. Prediction of siRNA functionality using generalized string kernel and support vector machine. FEBS Lett., 579(13):2878-82, May 2005. [ bib | DOI | http | .pdf | Abstract ]
[Schubert2005Local] S. Schubert, A. Grünweller, V. A. Erdmann, and J. Kurreck. Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. J. Mol. Biol., 348(4):883-893, May 2005. [ bib | DOI | http | Abstract ]
[Overhoff2005Local] M. Overhoff, M. Alken, R. K. Far, M. Lemaitre, B. Lebleu, G. Sczakiel, and I. Robbins. Local RNA target structure influences siRNA efficacy: a systematic global analysis. J. Mol. Biol., 348(4):871-881, May 2005. [ bib | DOI | http | Abstract ]
[Shabalina2006Computational] S. Shabalina, A. Spiridonov, and A. Ogurtsov. Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics, 7(1):65, Feb 2006. [ bib | DOI | http | .pdf | Abstract ]
[Ren2006siRecords] Y. Ren, W. Gong, Q. Xu, X. Zheng, D. Lin, Y. Wang, and T. Li. siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics, Jan 2006. [ bib | DOI | http | Abstract ]
[Pai2006Prospects] S. I. Pai, Y.-Y. Lin, B. Macaes, A. Meneshian, HungC.-F., and T.-C. Wu. Prospects of RNA interference therapy for cancer. Gene Ther., 13(6):464-477, Mar 2006. [ bib | DOI | http | Abstract ]
[Miranda2006pattern-based] Kevin C Miranda, Tien Huynh, Yvonne Tay, Yen-Sin Ang, Wai-Leong Tam, Andrew M Thomson, Bing Lim, and Isidore Rigoutsos. A pattern-based method for the identification of microrna binding sites and their corresponding heteroduplexes. Cell, 126(6):1203-1217, Sep 2006. [ bib | DOI | http | .pdf | Abstract ]
[Jia2006Demonstration] P. Jia, T. Shi, Y. Cai, and Y. Li. Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinformatics, 7:271, 2006. [ bib | DOI | http | .pdf | Abstract ]
[Didiano2006Perfect] Dominic Didiano and Oliver Hobert. Perfect seed pairing is not a generally reliable predictor for mirna-target interactions. Nat Struct Mol Biol, 13(9):849-851, Sep 2006. [ bib | DOI | http | .pdf | Abstract ]
[Vasudevan2007Switching] Shobha Vasudevan, Yingchun Tong, and Joan A Steitz. Switching from repression to activation: micrornas can up-regulate translation. Science, 318(5858):1931-1934, Dec 2007. [ bib | DOI | http | Abstract ]
[Lytle2007Target] J. Robin Lytle, Therese A Yario, and Joan A Steitz. Target mrnas are repressed as efficiently by microrna-binding sites in the 5' utr as in the 3' utr. Proc Natl Acad Sci U S A, 104(23):9667-9672, Jun 2007. [ bib | DOI | http | Abstract ]
[Kertesz2007role] Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul, and Eran Segal. The role of site accessibility in microrna target recognition. Nat Genet, 39(10):1278-1284, Oct 2007. [ bib | DOI | http | .pdf | Abstract ]
[Grimson2007MicroRNA] Andrew Grimson, Kyle Kai-How Farh, Wendy K Johnston, Philip Garrett-Engele, Lee P Lim, and David P Bartel. Microrna targeting specificity in mammals: determinants beyond seed pairing. Mol Cell, 27(1):91-105, Jul 2007. [ bib | DOI | http | .pdf | Abstract ]
[Ameres2007Molecular] Stefan Ludwig Ameres, Javier Martinez, and Renée Schroeder. Molecular basis for target rna recognition and cleavage by human risc. Cell, 130(1):101-112, Jul 2007. [ bib | DOI | http | .pdf | Abstract ]
[Morin2008Application] Ryan D Morin, Michael D O'Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, Anna-Liisa Prabhu, Yongjun Zhao, Helen McDonald, Thomas Zeng, Martin Hirst, Connie J Eaves, and Marco A Marra. Application of massively parallel sequencing to microrna profiling and discovery in human embryonic stem cells. Genome Res, 18(4):610-621, Apr 2008. [ bib | DOI | http | .pdf | Abstract ]
[Eulalio2008Getting] Ana Eulalio, Eric Huntzinger, and Elisa Izaurralde. Getting to the root of mirna-mediated gene silencing. Cell, 132(1):9-14, Jan 2008. [ bib | DOI | http | Abstract ]
[Didiano2008Molecular] Dominic Didiano and Oliver Hobert. Molecular architecture of a mirna-regulated 3' utr. RNA, 14(7):1297-1317, Jul 2008. [ bib | DOI | http | .pdf | Abstract ]
[Baek2008impact] Daehyun Baek, Judit Villén, Chanseok Shin, Fernando D Camargo, Steven P Gygi, and David P Bartel. The impact of micrornas on protein output. Nature, 455(7209):64-71, Sep 2008. [ bib | DOI | http | .pdf | Abstract ]
[Brodersen2009Revisiting] Peter Brodersen and Olivier Voinnet. Revisiting the principles of microrna target recognition and mode of action. Nat Rev Mol Cell Biol, 10(2):141-148, Feb 2009. [ bib | DOI | http | .pdf | Abstract ]

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