Methods
Amplified fluorescence determination of microRNAs in homogeneous solution with cationic conjugated polymers.
Zhang Y, Li Z, Cheng Y.
Chem Commun (Camb). 2008 Dec 28;(48):6579-81.
Rapid microRNA (miRNA) detection and classification via surface-enhanced Raman spectroscopy (SERS).
Driskell JD, Seto AG, Jones LP, Jokela S, Dluhy RA, Zhao YP, Tripp RA.
Biosens Bioelectron. 2008 Dec 1;24(4):923-8.
MiRE: a graphical R package for microRNA-related analysis.
Yan XQ, Tu K, Xie L, Li YX, Yin B, Gong YH, Yuan JG, Qiang BQ, Peng XZ.
Chin Med Sci J. 2008 Dec;23(4):202-4.
Fluorescence acquisition during hybridization phase in quantitative real-time PCR improves specificity and signal-to-noise ratio.
Mehndiratta M, Palanichamy JK, Ramalingam P, Pal A, Das P, Sinha S, Chattopadhyay P.
Biotechniques. 2008 Dec;45(6):625-6, 628, 630 passim.
Strategies for targeting lentiviral vectors.
Frecha C, Szécsi J, Cosset FL, Verhoeyen E.
Curr Gene Ther. 2008 Dec;8(6):449-60.
High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA.
Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F, Vandesompele J.
Nucleic Acids Res. 2008 Dec;36(21):e143.
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs.
Landthaler M, Gaidatzis D, Rothballer A, Chen PY, Soll SJ, Dinic L, Ojo T, Hafner M, Zavolan M, Tuschl T.
RNA. 2008 Dec;14(12):2580-96.
Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ.
Nat Methods. 2008 Dec;5(12):1023-5.
Reliable microRNA profiling in routinely processed formalin-fixed paraffin-embedded breast cancer specimens using fluorescence labelled
bead technology.
Hasemeier B, Christgen M, Kreipe H, Lehmann U.
BMC Biotechnol. 2008 Nov 27;8:90.
Focus on RNA isolation: obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue.
Wang WX, Wilfred BR, Baldwin DA, Isett RB, Ren N, Stromberg A, Nelson PT.
Biochim Biophys Acta. 2008 Nov;1779(11):749-57.
Technical variables in high-throughput miRNA expression profiling: much work remains to be done.
Nelson PT, Wang WX, Wilfred BR, Tang G.
Biochim Biophys Acta. 2008 Nov;1779(11):758-65.
A tightly regulated Pol III promoter for synthesis of miRNA genes in tandem.
Zhou H, Huang C, Xia XG.
Biochim Biophys Acta. 2008 Nov;1779(11):773-9.
Monitoring miRNA-mediated silencing in Drosophila melanogaster S2-cells.
Shah C, Förstemann K.
Biochim Biophys Acta. 2008 Nov;1779(11):766-72.
An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samples.
Zhang X, Chen J, Radcliffe T, Lebrun DP, Tron VA, Feilotter H.
J Mol Diagn. 2008 Nov;10(6):513-9.
siRNA, miRNA, and shRNA: in vivo applications.
Pushparaj PN, Aarthi JJ, Manikandan J, Kumar SD.
J Dent Res. 2008 Nov;87(11):992-1003.
Concatameric cloning of porcine microRNA molecules after assembly PCR.
Sharbati-Tehrani S, Kutz-Lohroff B, Scholven J, Einspanier R.
Biochem Biophys Res Commun. 2008 Oct 24;375(3):484-9.
A construct with fluorescent indicators for conditional expression of miRNA.
Qiu L, Wang H, Xia X, Zhou H, Xu Z.
BMC Biotechnol. 2008 Oct 7;8:77.
Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs.
Elkon R, Agami R.
PLoS Comput Biol. 2008 Oct 3;4(10):e1000189.
A polymerase chain reaction-based cloning strategy applicable to functional microRNA studies.
Boissonneault V, St-Gelais N, Plante I, Provost P.
Anal Biochem. 2008 Oct 1;381(1):166-8.
Prnp knockdown in transgenic mice using RNA interference.
Gallozzi M, Chapuis J, Le Provost F, Le Dur A, Morgenthaler C, Peyre C, Daniel-Carlier N, Pailhoux E, Vilotte M, Passet B, Herzog L,
Beringue V, Costa J, Tixador P, Tilly G, Laude H, Vilotte JL.
Transgenic Res. 2008 Oct;17(5):783-91.
Site-specific crosslinking of human microRNPs to RNA targets.
Kirino Y, Mourelatos Z.
RNA. 2008 Oct;14(10):2254-9.
A quantitative PCR method to detect blood microRNAs associated with tumorigenesis in transgenic mice.
Fan AC, Goldrick MM, Ho J, Liang Y, Bachireddy P, Felsher DW.
Mol Cancer. 2008 Sep 30;7:74.
A system for Cre-regulated RNA interference in vivo.
Stern P, Astrof S, Erkeland SJ, Schustak J, Sharp PA, Hynes RO.
Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13895-900.
A simplified miRNA-based gene silencing method for Drosophila melanogaster.
Haley B, Hendrix D, Trang V, Levine M.
Dev Biol. 2008 Sep 15;321(2):482-90.
Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods.
Ach RA, Wang H, Curry B.
BMC Biotechnol. 2008 Sep 11;8:69.
A random shRNA-encoding library for phenotypic selection and hit-optimization.
Wang Y, Wang YE, Cotticelli MG, Wilson RB.
PLoS ONE. 2008 Sep 9;3(9):e3171.
Serum microRNAs are promising novel biomarkers.
Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, Yerushalmi N, Benjamin H, Kushnir M, Cholakh H, Melamed N, Bentwich Z, Hod M,
Goren Y, Chajut A.
PLoS ONE. 2008 Sep 5;3(9):e3148.
Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation.
Vigneault F, Sismour AM, Church GM.
Nat Methods. 2008 Sep;5(9):777-9.
Accurate molecular characterization of formalin-fixed, paraffin-embedded tissues by microRNA expression profiling.
Szafranska AE, Davison TS, Shingara J, Doleshal M, Riggenbach JA, Morrison CD, Jewell S, Labourier E.
J Mol Diagn. 2008 Sep;10(5):415-23.
Minimizing variables among hairpin-based RNAi vectors reveals the potency of shRNAs.
Boudreau RL, Monteys AM, Davidson BL.
RNA. 2008 Sep;14(9):1834-44.
Establishment of cells to monitor Microprocessor through fusion genes of microRNA and GFP.
Tsutsui M, Hasegawa H, Adachi K, Miyata M, Huang P, Ishiguro N, Hamaguchi M, Iwamoto T.
Biochem Biophys Res Commun. 2008 Aug 8;372(4):856-61.
[Plasmid-mediated miRNA-1-2 specifically inhibits Hand2 protein expression in H9C2 cells]
Shan ZX, Lin QX, Deng CY, Zhou ZL, Zhang XC, Fu YH, Yu XY.
Nan Fang Yi Ke Da Xue Xue Bao. 2008 Aug;28(9):1559-61, 1567.
Highly sensitive and specific microRNA expression profiling using BeadArray technology.
Chen J, Lozach J, Garcia EW, Barnes B, Luo S, Mikoulitch I, Zhou L, Schroth G, Fan JB.
Nucleic Acids Res. 2008 Aug;36(14):e87.
Comparison of normalization methods with microRNA microarray.
Hua YJ, Tu K, Tang ZY, Li YX, Xiao HS.
Genomics. 2008 Aug;92(2):122-8.
A lentiviral vector with novel multiple cloning sites: stable transgene expression in vitro and in vivo.
Santhosh CV, Tamhane MC, Kamat RH, Patel VV, Mukhopadhyaya R.
Biochem Biophys Res Commun. 2008 Jul 4;371(3):546-50.
Novel fugu U6 promoter driven shRNA expression vector for efficient vector based RNAi in fish cell lines.
Zenke K, Kim KH.
Biochem Biophys Res Commun. 2008 Jul 4;371(3):480-3.
MicroRNAs as targets for engineering of CHO cell factories.
Müller D, Katinger H, Grillari J.
Trends Biotechnol. 2008 Jul;26(7):359-65.
Quantification of microRNA by gold nanoparticle probes.
Yang WJ, Li XB, Li YY, Zhao LF, He WL, Gao YQ, Wan YJ, Xia W, Chen T, Zheng H, Li M, Xu SQ.
Anal Biochem. 2008 May 15;376(2):183-8.
From sequence to function: using RNAi to elucidate mechanisms of human disease.
Wolters NM, MacKeigan JP.
Cell Death Differ. 2008 May;15(5):809-19.
Controlling morpholino experiments: don't stop making antisense.
Eisen JS, Smith JC.
Development. 2008 May;135(10):1735-43.
Enhanced bioaffinity sensing using surface plasmons, surface enzyme reactions, nanoparticles and diffraction gratings.
Lee HJ, Wark AW, Corn RM.
Analyst. 2008 May;133(5):596-601.
Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissues.
Doleshal M, Magotra AA, Choudhury B, Cannon BD, Labourier E, Szafranska AE.
J Mol Diagn. 2008 May;10(3):203-11.
Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal
and cancerous human solid tissues.
Peltier HJ, Latham GJ.
RNA. 2008 May;14(5):844-52.
Inferring microRNA activities by combining gene expression with microRNA target prediction.
Cheng C, Li LM.
PLoS ONE. 2008 Apr 23;3(4):e1989.
LNA-mediated microRNA silencing in non-human primates.
Elmén J, Lindow M, Schütz S, Lawrence M, Petri A, Obad S, Lindholm M, Hedtjärn M, Hansen HF, Berger U, Gullans S, Kearney P,
Sarnow P, Straarup EM, Kauppinen S.
Nature. 2008 Apr 17;452(7189):896-9.
miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample.
Sharbati-Tehrani S, Kutz-Lohroff B, Bergbauer R, Scholven J, Einspanier R.
BMC Mol Biol. 2008 Apr 10;9:34.
Closer to the completed unity: messenger and microRNA profiling. An introduction.
Falus A, Molnár V.
Semin Cancer Biol. 2008 Apr;18(2):77-8.
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
Parisien M, Major F.
Nature. 2008 Mar 6;452(7183):51-5.
Anatase nanosurface regulates microRNAs.
Palmieri A, Pezzetti F, Brunelli G, Arlotti M, Lo Muzio L, Scarano A, Rubini C, Sollazzo V, Massari L, Carinci F.
J Craniofac Surg. 2008 Mar;19(2):328-33.
Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
Lee I, Ajay SS, Chen H, Maruyama A, Wang N, McInnis MG, Athey BD.
Nucleic Acids Res. 2008 Mar;36(5):e27.
Unintentional miRNA ablation is a risk factor in gene knockout studies: a short report.
Osokine I, Hsu R, Loeb GB, McManus MT.
PLoS Genet. 2008 Feb;4(2):e34.
Profiling microRNA expression with microarrays.
Yin JQ, Zhao RC, Morris KV.
Trends Biotechnol. 2008 Feb;26(2):70-6.
Development of a dual-luciferase reporter system for in vivo visualization of MicroRNA biogenesis and posttranscriptional regulation.
Lee JY, Kim S, Hwang do W, Jeong JM, Chung JK, Lee MC, Lee DS.
J Nucl Med. 2008 Feb;49(2):285-94.
miR-122 targeting with LNA/2'-O-methyl oligonucleotide mixmers, peptide nucleic acids (PNA), and PNA-peptide conjugates.
Fabani MM, Gait MJ.
RNA. 2008 Feb;14(2):336-46.
Characterization of a newly developed chicken 44K Agilent microarray.
Li X, Chiang HI, Zhu J, Dowd SE, Zhou H.
BMC Genomics. 2008 Jan 31;9:60.
A fluorescence probe for assaying micro RNA maturation.
Davies BP, Arenz C.
Bioorg Med Chem. 2008 Jan 1;16(1):49-55.
Unlocking pathology archives for microRNA-profiling.
Hoefig KP, Thorns C, Roehle A, Kaehler C, Wesche KO, Repsilber D, Branke B, Thiere M, Feller AC, Merz H.
Anticancer Res. 2008 Jan-Feb;28(1A):119-23.
Part B--microRNAs: microRNA methods.
Schmittgen TD.
Methods. 2008 Jan;44(1):1-2.
Computational analysis of small RNA cloning data.
Berninger P, Gaidatzis D, van Nimwegen E, Zavolan M.
Methods. 2008 Jan;44(1):13-21.
Expression profiling of microRNA using oligo DNA arrays.
Liu CG, Spizzo R, Calin GA, Croce CM.
Methods. 2008 Jan;44(1):22-30.
Real-time PCR quantification of precursor and mature microRNA.
Schmittgen TD, Lee EJ, Jiang J, Sarkar A, Yang L, Elton TS, Chen C.
Methods. 2008 Jan;44(1):31-8.
In situ detection of precursor and mature microRNAs in paraffin embedded, formalin fixed tissues and cell preparations.
Nuovo GJ.
Methods. 2008 Jan;44(1):39-46.
Inhibition of microRNA with antisense oligonucleotides.
Esau CC.
Methods. 2008 Jan;44(1):55-60.
Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA.
Gusev Y.
Methods. 2008 Jan;44(1):61-72.
Chemical Synthesis of LNA-mCTP and its application for MicroRNA detection.
Kore AR, Hodeib M, Hu Z.
Nucleosides Nucleotides Nucleic Acids. 2008 Jan;27(1):1-17.
Intracellular siRNA and precursor miRNA trafficking using bioresponsive copolypeptides.
Rahbek UL, Howard KA, Oupicky D, Manickam DS, Dong M, Nielsen AF, Hansen TB, Besenbacher F, Kjems J.
J Gene Med. 2008 Jan;10(1):81-93.
Analysis of small endogenous RNAs.
Lau NC.
Curr Protoc Mol Biol. 2008 Jan;Chapter 26:Unit26.7.
Microfluidic-based enzymatic on-chip labeling of miRNAs.
Vorwerk S, Ganter K, Cheng Y, Hoheisel J, Stähler PF, Beier M.
N Biotechnol. 2008;25(2-3):142-9.
Quantification of microRNAs, splicing isoforms, and homologous mRNAs with the invader assay.
Eis PS, Garcia-Blanco MA.
Methods Mol Biol. 2008;488:279-318.
Design and delivery of antisense oligonucleotides to block microRNA function in cultured Drosophila and human cells.
Horwich MD, Zamore PD.
Nat Protoc. 2008;3(10):1537-49.
MicroRNA detection by northern blotting using locked nucleic acid probes.
Várallyay E, Burgyán J, Havelda Z.
Nat Protoc. 2008;3(2):190-6.
Direct detection of small RNAs using splinted ligation.
Maroney PA, Chamnongpol S, Souret F, Nilsen TW.
Nat Protoc. 2008;3(2):279-87.
miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes.
Castoldi M, Schmidt S, Benes V, Hentze MW, Muckenthaler MU.
Nat Protoc. 2008;3(2):321-9.
Small-molecule inhibitors of microrna miR-21 function.
Gumireddy K, Young DD, Xiong X, Hogenesch JB, Huang Q, Deiters A.
Angew Chem Int Ed Engl. 2008;47(39):7482-4.
RNA structure and modeling: progress and techniques.
Chai D.
Prog Nucleic Acid Res Mol Biol. 2008;82:71-100.
MicroRNA expression profiling using microarrays.
Liu CG, Calin GA, Volinia S, Croce CM.
Nat Protoc. 2008;3(4):563-78.
A comparison of normalization techniques for microRNA microarray data.
Rao Y, Lee Y, Jarjoura D, Ruppert AS, Liu CG, Hsu JC, Hagan JP.
Stat Appl Genet Mol Biol. 2008;7:Article22.
High-throughput real-time PCR.
Schmittgen TD, Lee EJ, Jiang J.
Methods Mol Biol. 2008;429:89-98.
Modular reporter hairpin ribozymes for analyzing molecular interactions.
Najafi-Shoushtari SH, Famulok M.
Methods Mol Biol. 2008;429:237-50.
Improved northern blot method for enhanced detection of small RNA.
Pall GS, Hamilton AJ.
Nat Protoc. 2008;3(6):1077-84.
Analyzing real-time PCR data by the comparative C(T) method.
Schmittgen TD, Livak KJ.
Nat Protoc. 2008;3(6):1101-8.
An overview of the identification, detection, and functional analysis of Drosophila microRNAs.
Sokol NS.
Methods Mol Biol. 2008;420:319-34.
Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines.
Ruike Y, Ichimura A, Tsuchiya S, Shimizu K, Kunimoto R, Okuno Y, Tsujimoto G.
J Hum Genet. 2008;53(6):515-23.
Individual mRNA expression profiles reveal the effects of specific microRNAs.
Arora A, Simpson DA.
Genome Biol. 2008;9(5):R82.
In vitro RNA cleavage assay for Argonaute-family proteins.
Miyoshi K, Uejima H, Nagami-Okada T, Siomi H, Siomi MC.
Methods Mol Biol. 2008;442:29-43.
Identifying siRNA-induced off-targets by microarray analysis.
Anderson E, Boese Q, Khvorova A, Karpilow J.
Methods Mol Biol. 2008;442:45-63.
Detection of siRNAs and miRNAs.
Kauppinen S, Havelda Z.
Methods Mol Biol. 2008;451:217-27.
Using synthetic precursor and inhibitor miRNAs to understand miRNA function.
Ford LP, Cheng A.
Methods Mol Biol. 2008;419:289-301.
Multiplexed detection methods for profiling microRNA expression in biological samples.
Wark AW, Lee HJ, Corn RM.
Angew Chem Int Ed Engl. 2008;47(4):644-52.
A simple method for profiling miRNA expression.
Wang JW, Cheng JQ.
Methods Mol Biol. 2008;414:183-90.