Methods
Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies.
Liu YP, Vink MA, Westerink JT, Ramirez de Arellano E, Konstantinova P, Ter Brake O, Berkhout B.
RNA. 2010 Jul;16(7):1328-39.
High-performance quantification of mature microRNAs by real-time RT-PCR using deoxyuridine-incorporated oligonucleotides and
hemi-nested primers.
Wan G, Lim QE, Too HP.
RNA. 2010 Jul;16(7):1436-45.
Robust microRNA stability in degraded RNA preparations from human tissue and cell samples.
Jung M, Schaefer A, Steiner I, Kempkensteffen C, Stephan C, Erbersdobler A, Jung K.
Clin Chem. 2010 Jun;56(6):998-1006.
Reduced seed region-based off-target activity with lentivirus-mediated RNAi.
Klinghoffer RA, Magnus J, Schelter J, Mehaffey M, Coleman C, Cleary MA.
RNA. 2010 May;16(5):879-84.
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential
microRNA expression.
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C.
RNA. 2010 May;16(5):991-1006.
A mammalian reporter system for fast and quantitative detection of intracellular A-to-I RNA editing levels.
Gommans WM, McCane J, Nacarelli GS, Maas S.
Anal Biochem. 2010 Apr 15;399(2):230-6.
Simple and sensitive detection of microRNAs with ligase chain reaction.
Yan J, Li Z, Liu C, Cheng Y.
Chem Commun (Camb). 2010 Apr 14;46(14):2432-4.
A miR-21 hairpin structure-based gene knockdown vector.
Yue J, Sheng Y, Ren A, Penmatsa S.
Biochem Biophys Res Commun. 2010 Apr 9;394(3):667-72.
Membrane-based hybridization capture of intracellular peptide nucleic acid.
Shin D, Nam M, Yoon Y, Kim M.
Anal Biochem. 2010 Apr 1;399(1):135-7.
Lost in the space of bioinformatic tools: a constantly updated survival guide for genetic epidemiology. The GenEpi Toolbox.
Coassin S, Brandstätter A, Kronenberg F.
Atherosclerosis. 2010 Apr;209(2):321-35.
Comparison of approaches for efficient gene silencing induced by microRNA-based short hairpin RNA and indicator gene expression.
Shan ZX, Lin QX, Deng CY, Zhou ZL, Tan HH, Fu YH, Li XH, Zhu JN, Mai LP, Kuang SJ, Lin SG, Yu XY.
Mol Biol Rep. 2010 Apr;37(4):1831-9.
Toward a system-level understanding of microRNA pathway via mathematical modeling.
Wang X, Li Y, Xu X, Wang YH.
Biosystems. 2010 Apr;100(1):31-8.
mRNA and microRNA quality control for RT-qPCR analysis.
Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW.
Methods. 2010 Apr;50(4):237-43.
Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available.
Benes V, Castoldi M.
Methods. 2010 Apr;50(4):244-9.
Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR).
Kroh EM, Parkin RK, Mitchell PS, Tewari M.
Methods. 2010 Apr;50(4):298-301.
Expanding applications of protein analysis using proximity ligation and qPCR.
Swartzman E, Shannon M, Lieu P, Chen SM, Mooney C, Wei E, Kuykendall J, Tan R, Settineri T, Egry L, Ruff D.
Methods. 2010 Apr;50(4):S23-6.
Improved microRNA quantification in total RNA from clinical samples.
Andreasen D, Fog JU, Biggs W, Salomon J, Dahslveen IK, Baker A, Mouritzen P.
Methods. 2010 Apr;50(4):S6-9.
The ongoing evolution of qPCR.
Pfaffl MW.
Methods. 2010 Apr;50(4):215-6.
A sensitive non-radioactive northern blot method to detect small RNAs.
Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, Nichols M, John B.
Nucleic Acids Res. 2010 Apr;38(7):e98.
Improvement of tissue preparation for laser capture microdissection: application for cell type-specific miRNA expression profiling in
colorectal tumors.
Wang S, Wang L, Zhu T, Gao X, Li J, Wu Y, Zhu H.
BMC Genomics. 2010 Mar 10;11:163.
Chimeric tRNAs as tools to induce proteome damage and identify components of stress responses.
Geslain R, Cubells L, Bori-Sanz T, Alvarez-Medina R, Rossell D, Martí E, de Pouplana LR.
Nucleic Acids Res. 2010 Mar 1;38(5):e30.
Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs.
Pradervand S, Weber J, Lemoine F, Consales F, Paillusson A, Dupasquier M, Thomas J, Richter H, Kaessmann H, Beaudoing E,
Hagenbüchle O, Harshman K.
Biotechniques. 2010 Mar;48(3):219-22.
Identifying co-regulating microRNA groups.
An J, Choi KP, Wells CA, Chen YP.
J Bioinform Comput Biol. 2010 Feb;8(1):99-115.
Computational approaches for microRNA studies: a review.
Li L, Xu J, Yang D, Tan X, Wang H.
Mamm Genome. 2010 Feb;21(1-2):1-12.
mRNA and micro-RNA expression analysis in laser-capture microdissected prostate biopsies: valuable tool for risk assessment and
prevention trials.
Nonn L, Vaishnav A, Gallagher L, Gann PH.
Exp Mol Pathol. 2010 Feb;88(1):45-51.
Ultrahighly sensitive homogeneous detection of DNA and microRNA by using single-silver-nanoparticle counting.
Xu F, Dong C, Xie C, Ren J.
Chemistry. 2010 Jan 18;16(3):1010-6.
A personalized microRNA microarray normalization method using a logistic regression model.
Wang B, Wang XF, Howell P, Qian X, Huang K, Riker AI, Ju J, Xi Y.
Bioinformatics. 2010 Jan 15;26(2):228-34.
Metal cation mediated-capillary electrophoresis of nucleic acids.
Li T, Zhang D, Luo W, Lu M, Wang Z, Song Y, Wang H.
Anal Chem. 2010 Jan 15;82(2):487-90.
miRMaid: a unified programming interface for microRNA data resources.
Jacobsen A, Krogh A, Kauppinen S, Lindow M.
BMC Bioinformatics. 2010 Jan 14;11:29.
Antisense gets a grip on miR-122 in chimpanzees.
Branch AD, Rice CM.
Sci Transl Med. 2010 Jan 6;2(13):13ps1.
Polymerase-endonuclease amplification reaction (PEAR) for large-scale enzymatic production of antisense oligonucleotides.
Wang X, Gou D, Xu SY.
PLoS One. 2010 Jan 1;5(1):e8430.
MicroRazerS: rapid alignment of small RNA reads.
Emde AK, Grunert M, Weese D, Reinert K, Sperling SR.
Bioinformatics. 2010 Jan 1;26(1):123-4.
Gene expression profiling of MicroRNAs in small-bowel transplantation paraffin-embedded mucosal biopsy tissue.
Sotolongo B, Asaoka T, Island E, Carreno M, Delacruz V, Cova D, Russo C, Tryphonopoulos P, Moon J, Weppler D, Tzakis A, Ruiz P.
Transplant Proc. 2010 Jan-Feb;42(1):62-5.
Exosomes from human saliva as a source of microRNA biomarkers.
Michael A, Bajracharya SD, Yuen PS, Zhou H, Star RA, Illei GG, Alevizos I.
Oral Dis. 2010 Jan;16(1):34-8.
A combined immunoprecipitation, mass spectrometric and nucleic acid sequencing approach to determine microRNA-mediated
post-transcriptional gene regulatory networks.
Savas JN, Tanese N.
Brief Funct Genomic Proteomic. 2010 Jan;9(1):24-31.
[Advances in approaches for the quantitative detection of microRNAs]
Jing H, Song QX, Zhou GH.
Yi Chuan. 2010 Jan;32(1):31-40.
Validation of extraction methods for total RNA and miRNA from bovine blood prior to quantitative gene expression analyses.
Hammerle-Fickinger A, Riedmaier I, Becker C, Meyer HH, Pfaffl MW, Ulbrich SE.
Biotechnol Lett. 2010 Jan;32(1):35-44.
Consensus miRNA expression profiles derived from interplatform normalization of microarray data.
Bargaje R, Hariharan M, Scaria V, Pillai B.
RNA. 2010 Jan;16(1):16-25.
Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application.
Jackson AL, Linsley PS.
Nat Rev Drug Discov. 2010 Jan;9(1):57-67.
Intron-mediated RNA interference, intronic microRNAs, and applications.
Ying SY, Chang CP, Lin SL.
Methods Mol Biol. 2010;629:205-37.
Inhibition of the microRNA pathway in zebrafish by siRNA.
Fjose A, Zhao XF.
Methods Mol Biol. 2010;629:239-55.
In situ hybridization detection of microRNAs.
Song R, Ro S, Yan W.
Methods Mol Biol. 2010;629:287-94.
qRT-PCR of Small RNAs.
Varkonyi-Gasic E, Hellens RP.
Methods Mol Biol. 2010;631:109-22.
Cloning new small RNA sequences.
Tagami Y, Inaba N, Watanabe Y.
Methods Mol Biol. 2010;631:123-38.
Lentiviral vector-mediated expression of pre-miRNAs and antagomiRs.
Scherr M, Venturini L, Eder M.
Methods Mol Biol. 2010;614:175-85.
Profiling microRNA expression with the Illumina BeadChip platform.
Tsao J, Yau P, Winegarden N.
Methods Mol Biol. 2010;632:73-86.
Quantitative RT-PCR methods for mature microRNA expression analysis.
Fiedler SD, Carletti MZ, Christenson LK.
Methods Mol Biol. 2010;630:49-64.
Strategies in designing multigene expression units to downregulate HIV-1.
Zhang J, Rossi JJ.
Methods Mol Biol. 2010;623:123-36.
Methods for isolation of total RNA to recover miRNAs and other small RNAs from diverse species.
Accerbi M, Schmidt SA, De Paoli E, Park S, Jeong DH, Green PJ.
Methods Mol Biol. 2010;592:31-50.
Directed gene silencing with artificial microRNAs.
Schwab R, Ossowski S, Warthmann N, Weigel D.
Methods Mol Biol. 2010;592:71-88.
High-throughput approaches for miRNA expression analysis.
Lu C, Souret F.
Methods Mol Biol. 2010;592:107-25.
In situ detection of miRNAs using LNA probes.
Havelda Z.
Methods Mol Biol. 2010;592:127-36.
Transient assays for the analysis of miRNA processing and function.
de Felippes FF, Weigel D.
Methods Mol Biol. 2010;592:255-64.