Targets
A strategy to rapidly identify the functional targets of microRNAs by combining bioinformatics and mRNA cytoplasmic/nucleic ratios in
culture cells.
Li J, Xia W, Huang B, Chen L, Su X, Li S, Wang F, Ding H, Shao N.
FEBS Lett. 2010 Jul 16;584(14):3198-202.
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures.
Tsang JS, Ebert MS, van Oudenaarden A.
Mol Cell. 2010 Apr 9;38(1):140-53.
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich
A, Wardle GS, Dewell S, Zavolan M, Tuschl T.
Cell. 2010 Apr 2;141(1):129-41.
Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.
Sales G, Coppe A, Bicciato S, Bortoluzzi S, Romualdi C.
Nucleic Acids Res. 2010 Apr;38(7):e97.
Comparison and integration of target prediction algorithms for microRNA studies.
Zhang Y, Verbeek FJ.
J Integr Bioinform. 2010 Mar 25;7(3).
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature.
Naeem H, Küffner R, Csaba G, Zimmer R.
BMC Bioinformatics. 2010 Mar 16;11:135.
Tandem affinity purification of miRNA target mRNAs (TAP-Tar).
Nonne N, Ameyar-Zazoua M, Souidi M, Harel-Bellan A.
Nucleic Acids Res. 2010 Mar 1;38(4):e20.
Analyzing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level.
Pais H, Nicolas FE, Soond SM, Swingler TE, Clark IM, Chantry A, Moulton V, Dalmay T.
RNA. 2010 Mar;16(3):489-94.
MicroRNAs align with accessible sites in target mRNAs.
Pan W, Xin P, Clawson GA.
J Cell Biochem. 2010 Feb 15;109(3):509-18.
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals.
Takane K, Fujishima K, Watanabe Y, Sato A, Saito N, Tomita M, Kanai A.
BMC Genomics. 2010 Feb 9;11:101.
Experimental identification of microRNA targets.
Ørom UA, Lund AH.
Gene. 2010 Feb 1;451(1-2):1-5.
Prediction of novel miRNAs and associated target genes in Glycine max.
Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G.
BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S14.
MTar: a computational microRNA target prediction architecture for human transcriptome.
Chandra V, Girijadevi R, Nair AS, Pillai SS, Pillai RM.
BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S2.
Target prediction and a statistical sampling algorithm for RNA-RNA interaction.
Huang FW, Qin J, Reidys CM, Stadler PF.
Bioinformatics. 2010 Jan 15;26(2):175-81.
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and
their targets.
Ritchie W, Flamant S, Rasko JE.
Bioinformatics. 2010 Jan 15;26(2):223-7.
Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3'UTR.
Sun G, Li H, Rossi JJ.
Nucleic Acids Res. 2010 Jan;38(1):239-52.
Profiling of miRNA expression and prediction of target genes.
Sioud M, Cekaite L.
Methods Mol Biol. 2010;629:257-71.
Expander: from expression microarrays to networks and functions.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R.
Nat Protoc. 2010;5(2):303-22.
In silico method for systematic analysis of feature importance in microRNA-mRNA interactions.
Xiao J, Li Y, Wang K, Wen Z, Li M, Zhang L, Guang X.
BMC Bioinformatics. 2009 Dec 16;10:427.
Adenosine deamination in human transcripts generates novel microRNA binding sites.
Borchert GM, Gilmore BL, Spengler RM, Xing Y, Lanier W, Bhattacharya D, Davidson BL.
Hum Mol Genet. 2009 Dec 15;18(24):4801-7.
Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy.
Liu B, Li J, Tsykin A, Liu L, Gaur AB, Goodall GJ.
BMC Bioinformatics. 2009 Dec 10;10:408.
Insight into microRNA regulation by analyzing the characteristics of their targets in humans.
Hu Z.
BMC Genomics. 2009 Dec 10;10:594.
Lost in translation: an assessment and perspective for computational microRNA target identification.
Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG.
Bioinformatics. 2009 Dec 1;25(23):3049-55.
Progress in miRNA target prediction and identification.
Xia W, Cao G, Shao N.
Sci China C Life Sci. 2009 Dec;52(12):1123-30.
A probabilistic framework to improve microrna target prediction by incorporating proteomics data.
Li J, Min R, Bonner A, Zhang Z.
J Bioinform Comput Biol. 2009 Dec;7(6):955-72.
Abundant conserved microRNA target sites in the 5'-untranslated region and coding sequence.
Zhou X, Duan X, Qian J, Li F.
Genetica. 2009 Nov;137(2):159-64.
A high throughput experimental approach to identify miRNA targets in human cells.
Tan LP, Seinen E, Duns G, de Jong D, Sibon OC, Poppema S, Kroesen BJ, Kok K, van den Berg A.
Nucleic Acids Res. 2009 Nov;37(20):e137.
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.
Bandyopadhyay S, Mitra R.
Bioinformatics. 2009 Oct 15;25(20):2625-31.
Accurate microRNA target prediction correlates with protein repression levels.
Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA,
Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG.
BMC Bioinformatics. 2009 Sep 18;10:295.
The relationship between the evolution of microRNA targets and the length of their UTRs.
Cheng C, Bhardwaj N, Gerstein M.
BMC Genomics. 2009 Sep 14;10:431.
Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets.
Hong X, Hammell M, Ambros V, Cohen SM.
Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):15085-90.
Conserved expression patterns predict microRNA targets.
Ritchie W, Rajasekhar M, Flamant S, Rasko JE.
PLoS Comput Biol. 2009 Sep;5(9):e1000513.
Statistical use of argonaute expression and RISC assembly in microRNA target identification.
Stanhope SA, Sengupta S, den Boon J, Ahlquist P, Newton MA.
PLoS Comput Biol. 2009 Sep;5(9):e1000516.
Discovery of functional miRNA-mRNA regulatory modules with computational methods.
Liu B, Li J, Tsykin A.
J Biomed Inform. 2009 Aug;42(4):685-91.
Regulatory element identification in subsets of transcripts: comparison and integration of current computational methods.
Fan D, Bitterman PB, Larsson O.
RNA. 2009 Aug;15(8):1469-82.
A novel putative miRNA target enhancer signal.
Schmidt T, Mewes HW, Stümpflen V.
PLoS One. 2009 Jul 31;4(7):e6473.
Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.
Chi SW, Zang JB, Mele A, Darnell RB.
Nature. 2009 Jul 23;460(7254):479-86.
Assessing potential miRNA targets based on a Markov model.
Fu HY, Xue DY, Zhang XD, Yang PY.
Genet Mol Res. 2009 Jul 21;8(3):848-60.
DIANA-microT web server: elucidating microRNA functions through target prediction.
Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K,
Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W273-6.
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists.
Antonov AV, Dietmann S, Wong P, Lutter D, Mewes HW.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W323-8.
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression.
Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W356-62.
MirZ: an integrated microRNA expression atlas and target prediction resource.
Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W266-72.
Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.
Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S.
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S20.
Conditions of appreciable influence of microRNA on a large number of target mRNAs.
Zhdanov VP.
Mol Biosyst. 2009 Jun;5(6):638-43.
Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNA-target mRNAs.
Hsu RJ, Yang HJ, Tsai HJ.
Nucleic Acids Res. 2009 Jun;37(10):e77.
Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH.
Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA.
PLoS One. 2009 May 29;4(5):e5745.
Redefining microRNA targets.
Seitz H.
Curr Biol. 2009 May 26;19(10):870-3.
Reexamining microRNA site accessibility in Drosophila: a population genomics study.
Chen K, Maaskola J, Siegal ML, Rajewsky N.
PLoS One. 2009 May 25;4(5):e5681.
Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data.
Wang YP, Li KB.
BMC Genomics. 2009 May 12;10:218.
Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data.
Jayaswal V, Lutherborrow M, Ma DD, Hwa Yang Y.
Nucleic Acids Res. 2009 May;37(8):e60.
Current tools for the identification of miRNA genes and their targets.
Mendes ND, Freitas AT, Sagot MF.
Nucleic Acids Res. 2009 May;37(8):2419-33.
MicroRNA target prediction by expression analysis of host genes.
Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S.
Genome Res. 2009 Mar;19(3):481-90.
Identifying the target mRNAs of microRNAs in colorectal cancer.
Kim S, Choi M, Cho KH.
Comput Biol Chem. 2009 Feb;33(1):94-9.
MicroRNA-like off-target transcript regulation by siRNAs is species specific.
Burchard J, Jackson AL, Malkov V, Needham RH, Tan Y, Bartz SR, Dai H, Sachs AB, Linsley PS.
RNA. 2009 Feb;15(2):308-15.
Predicting microRNA targets in time-series microarray experiments via functional data analysis.
Parker BJ, Wen J.
BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S32.
Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information.
Joung JG, Fei Z.
BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S34.
MicroRNAs: target recognition and regulatory functions.
Bartel DP.
Cell. 2009 Jan 23;136(2):215-33.
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.
Addo-Quaye C, Miller W, Axtell MJ.
Bioinformatics. 2009 Jan 1;25(1):130-1.
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function.
Taccioli C, Fabbri E, Visone R, Volinia S, Calin GA, Fong LY, Gambari R, Bottoni A, Acunzo M, Hagan J, Iorio MV, Piovan C, Romano G,
Croce CM.
Nucleic Acids Res. 2009 Jan;37(Database issue):D41-8.
Most mammalian mRNAs are conserved targets of microRNAs.
Friedman RC, Farh KK, Burge CB, Bartel DP.
Genome Res. 2009 Jan;19(1):92-105.
The database of experimentally supported targets: a functional update of TarBase.
Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG.
Nucleic Acids Res. 2009 Jan;37(Database issue):D155-8.
miRecords: an integrated resource for microRNA-target interactions.
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T.
Nucleic Acids Res. 2009 Jan;37(Database issue):D105-10.
An evolutionary perspective of animal microRNAs and their targets.
Shomron N, Golan D, Hornstein E.
J Biomed Biotechnol. 2009;2009:594738.
Computational challenges in miRNA target predictions: to be or not to be a true target?
Barbato C, Arisi I, Frizzo ME, Brandi R, Da Sacco L, Masotti A.
J Biomed Biotechnol. 2009;2009:803069.
Validating microRNA Target Transcripts Using Zebrafish Assays.
Pase L, Lieschke GJ.
Methods Mol Biol. 2009;546:227-40.
MiRTif: a support vector machine-based microRNA target interaction filter.
Yang Y, Wang YP, Li KB.
BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S4.
Identification of genes targeted by microRNAs.
Dalmay T.
Biochem Soc Trans. 2008 Dec;36(Pt 6):1194-6.
Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140.
Nicolas FE, Pais H, Schwach F, Lindow M, Kauppinen S, Moulton V, Dalmay T.
RNA. 2008 Dec;14(12):2513-20.
A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.
Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH.
RNA. 2008 Nov;14(11):2290-6.
A novel biochemical method to identify target genes of individual microRNAs: identification of a new Caenorhabditis elegans let-7 target.
Andachi Y.
RNA. 2008 Nov;14(11):2440-51.
CompMoby: comparative MobyDick for detection of cis-regulatory motifs.
Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.
BMC Bioinformatics. 2008 Oct 27;9:455.
mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts.
Hammell M, Long D, Zhang L, Lee A, Carmack CS, Han M, Ding Y, Ambros V.
Nat Methods. 2008 Sep;5(9):813-9.
Proteomics joins the search for microRNA targets.
Grosshans H, Filipowicz W.
Cell. 2008 Aug 22;134(4):560-2.
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.
German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C,
Schroth G, Meyers BC, Green PJ.
Nat Biotechnol. 2008 Aug;26(8):941-6.
Sequencing sliced ends reveals microRNA targets.
Henderson IR, Jacobsen SE.
Nat Biotechnol. 2008 Aug;26(8):881-2.
Construction of two mathematical models for prediction of bacterial sRNA targets.
Zhao Y, Li H, Hou Y, Cha L, Cao Y, Wang L, Ying X, Li W.
Biochem Biophys Res Commun. 2008 Jul 25;372(2):346-50.
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.
Linhart C, Halperin Y, Shamir R.
Genome Res. 2008 Jul;18(7):1180-9.
A computational screen for mouse signaling pathways targeted by microRNA clusters.
Xu J, Wong C.
RNA. 2008 Jul;14(7):1276-83.
On the relationship between GC content and the number of predicted microRNA binding sites by MicroInspector.
Davis N, Biddlecom N, Hecht D, Fogel GB.
Comput Biol Chem. 2008 Jun;32(3):222-6.
miRDB: a microRNA target prediction and functional annotation database with a wiki interface.
Wang X.
RNA. 2008 Jun;14(6):1012-7.
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance.
Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO.
PLoS ONE. 2008 May 7;3(5):e2126.
Characterization of microRNA-regulated protein-protein interaction network.
Hsu CW, Juan HF, Huang HC.
Proteomics. 2008 May;8(10):1975-9.
MicroRNA-target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis.
Tian Z, Greene AS, Pietrusz JL, Matus IR, Liang M.
Genome Res. 2008 Mar;18(3):404-11.
Prediction of both conserved and nonconserved microRNA targets in animals.
Wang X, El Naqa IM.
Bioinformatics. 2008 Feb 1;24(3):325-32.
Genome-wide computational analyses of microRNAs and their targets from Canis familiaris.
Zhou D, Li S, Wen J, Gong X, Xu L, Luo Y.
Comput Biol Chem. 2008 Feb;32(1):60-5.
Experimental validation of miRNA targets.
Kuhn DE, Martin MM, Feldman DS, Terry AV Jr, Nuovo GJ, Elton TS.
Methods. 2008 Jan;44(1):47-54.
miRGator: an integrated system for functional annotation of microRNAs.
Nam S, Kim B, Shin S, Lee S.
Nucleic Acids Res. 2008 Jan;36(Database issue):D159-64.
The microRNA.org resource: targets and expression.
Betel D, Wilson M, Gabow A, Marks DS, Sander C.
Nucleic Acids Res. 2008 Jan;36(Database issue):D149-53.
Chapter 17. Extension of endogenous primers as a tool to detect micro-RNA targets.
Vatolin S, Weil RJ.
Methods Enzymol. 2008;449:357-71.
Comparing sequence and expression for predicting microRNA targets using GenMiR3.
Huang JC, Frey BJ, Morris QD.
Pac Symp Biocomput. 2008;:52-63.
Analysis of microRNA-target interactions by a target structure based hybridization model.
Long D, Chan CY, Ding Y.
Pac Symp Biocomput. 2008;:64-74.
A biochemical approach to identifying microRNA targets.
Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ.
Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19291-6.
Using expression profiling data to identify human microRNA targets.
Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD.
Nat Methods. 2007 Dec;4(12):1045-9.
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila.
Gu J, Fu H, Zhang X, Li Y.
BMC Bioinformatics. 2007 Nov 8;8:432.
A universal framework for regulatory element discovery across all genomes and data types.
Elemento O, Slonim N, Tavazoie S.
Mol Cell. 2007 Oct 26;28(2):337-50.
Prediction and validation of microRNA targets in animal genomes.
Martin G, Schouest K, Kovvuru P, Spillane C.
J Biosci. 2007 Sep;32(6):1049-52.
MicroRNA targeting specificity in mammals: determinants beyond seed pairing.
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP.
Mol Cell. 2007 Jul 6;27(1):91-105.
Useful 'junk': Alu RNAs in the human transcriptome.
Hasler J, Samuelsson T, Strub K.
Cell Mol Life Sci. 2007 Jul;64(14):1793-800.
Identification of human microRNA targets from isolated argonaute protein complexes.
Beitzinger M, Peters L, Zhu JY, Kremmer E, Meister G.
RNA Biol. 2007 Jun;4(2):76-84.
Bayesian inference of MicroRNA targets from sequence and expression data.
Huang JC, Morris QD, Frey BJ.
J Comput Biol. 2007 Jun;14(5):550-63.
Prediction of microRNA targets.
Maziere P, Enright AJ.
Drug Discov Today. 2007 Jun;12(11-12):452-8.
Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions.
Cora D, Di Cunto F, Caselle M, Provero P.
BMC Bioinformatics. 2007 May 24;8:174.
Discovery of microRNA-mRNA modules via population-based probabilistic learning.
Joung JG, Hwang KB, Nam JW, Kim SJ, Zhang BT.
Bioinformatics. 2007 May 1;23(9):1141-7.
Abundance of microRNA target motifs in the 3'-UTRs of 20527 human genes.
Iwama H, Masaki T, Kuriyama S.
FEBS Lett. 2007 May 1;581(9):1805-10.
Bio-informatic trends for the determination of miRNA-target interactions in mammals.
Doran J, Strauss WM.
DNA Cell Biol. 2007 May;26(5):353-60.
Principles and limitations of computational microRNA gene and target finding.
Lindow M, Gorodkin J.
DNA Cell Biol. 2007 May;26(5):339-51.
MicroRNA detection and target prediction: integration of computational and experimental approaches.
Chaudhuri K, Chatterjee R.
DNA Cell Biol. 2007 May;26(5):321-37.
Improving the prediction of human microRNA target genes by using ensemble algorithm.
Yan X, Chao T, Tu K, Zhang Y, Xie L, Gong Y, Yuan J, Qiang B, Peng X.
FEBS Lett. 2007 Apr 17;581(8):1587-93.
Algorithms for mapping of mRNA targets for microRNA.
Ioshikhes I, Roy S, Sen CK.
DNA Cell Biol. 2007 Apr;26(4):265-72.
Inference of miRNA targets using evolutionary conservation and pathway analysis.
Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M.
BMC Bioinformatics. 2007 Mar 1;8:69.
ViTa: prediction of host microRNAs targets on viruses.
Hsu PW, Lin LZ, Hsu SD, Hsu JB, Huang HD.
Nucleic Acids Res. 2007 Jan;35(Database issue):D381-5.
Robust machine learning algorithms predict microRNA genes and targets.
Saetrom P, Snøve O Jr.
Methods Enzymol. 2007;427:25-49.
Computational methods for microRNA target prediction.
Watanabe Y, Tomita M, Kanai A.
Methods Enzymol. 2007;427:65-86.
MicroTar: predicting microRNA targets from RNA duplexes.
Thadani R, Tammi MT.
BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S20.
Computational identification of microRNAs and their targets.
Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA.
Comput Biol Chem. 2006 Dec;30(6):395-407.
A guide through present computational approaches for the identification of mammalian microRNA targets.
Sethupathy P, Megraw M, Hatzigeorgiou AG.
Nat Methods. 2006 Nov;3(11):881-6.
Alu elements within human mRNAs are probable microRNA targets.
Smalheiser NR, Torvik VI.
Trends Genet. 2006 Oct;22(10):532-6.
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.
Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I.
Cell. 2006 Sep 22;126(6):1203-17.
miTarget: microRNA target gene prediction using a support vector machine.
Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT.
BMC Bioinformatics. 2006 Sep 18;7:411.
Potential mRNA degradation targets of hsa-miR-200c, identified using informatics and qRT-PCR.
Hurteau GJ, Spivack SD, Brock GJ.
Cell Cycle. 2006 Sep;5(17):1951-6.
L(ou)sy miRNA targets?
Rajewsky N.
Nat Struct Mol Biol. 2006 Sep;13(9):754-5.
RNAhybrid: microRNA target prediction easy, fast and flexible.
Kruger J, Rehmsmeier M.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W451-4.
CRSD: a comprehensive web server for composite regulatory signature discovery.
Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W571-7.
microRNA target predictions in animals.
Rajewsky N.
Nat Genet. 2006 Jun;38 Suppl:S8-13.
Computational identification of microRNAs and their targets.
Yoon S, De Micheli G.
Birth Defects Res C Embryo Today. 2006 Jun;78(2):118-28.
A novel method to detect functional microRNA targets.
Vatolin S, Navaratne K, Weil RJ.
J Mol Biol. 2006 May 12;358(4):983-96.
Differential repression of alternative transcripts: a screen for miRNA targets.
Legendre M, Ritchie W, Lopez F, Gautheret D.
PLoS Comput Biol. 2006 May;2(5):e43.
Systematic identification of microRNA functions by combining target prediction and expression profiling.
Wang X, Wang X.
Nucleic Acids Res. 2006 Mar 20;34(5):1646-52.
A genome-wide map of conserved microRNA targets in C. elegans.
Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L,
Piano F, Rajewsky N.
Curr Biol. 2006 Mar 7;16(5):460-71.
Cell-type-specific signatures of microRNAs on target mRNA expression.
Sood P, Krek A, Zavolan M, Macino G, Rajewsky N.
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2746-51.
TarBase: A comprehensive database of experimentally supported animal microRNA targets.
Sethupathy P, Corda B, Hatzigeorgiou AG.
RNA. 2006 Feb;12(2):192-7.
Computational analysis of microRNA targets in Caenorhabditis elegans.
Watanabe Y, Yachie N, Numata K, Saito R, Kanai A, Tomita M.
Gene. 2006 Jan 3;365:2-10.
Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.
Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P.
Nucleic Acids Res. 2006;34(16):e107.
Prediction of microRNA targets.
Rehmsmeier M.
Methods Mol Biol. 2006;342:87-99.
Prediction of human microRNA targets.
John B, Sander C, Marks DS.
Methods Mol Biol. 2006;342:101-13.
Complications in mammalian microRNA target prediction.
Smalheiser NR, Torvik VI.
Methods Mol Biol. 2006;342:115-27.
MicroRNAs in search of a target.
Stefani G, Slack F.
Cold Spring Harb Symp Quant Biol. 2006;71:129-34.
Deep conservation of microRNA-target relationships and 3'UTR motifs in vertebrates, flies, and nematodes.
Chen K, Rajewsky N.
Cold Spring Harb Symp Quant Biol. 2006;71:149-56.
Physiological identification of human transcripts translationally regulated by a specific microRNA.
Nakamoto M, Jin P, O'Donnell WT, Warren ST.
Hum Mol Genet. 2005 Dec 15;14(24):3813-21.
Revealing posttranscriptional regulatory elements through network-level conservation.
Chan CS, Elemento O, Tavazoie S.
PLoS Comput Biol. 2005 Dec;1(7):e69.
Targets of microRNA regulation in the Drosophila oocyte proteome.
Nakahara K, Kim K, Sciulli C, Dowd SR, Minden JS, Carthew RW.
Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12023-8.
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence.
Rusinov V, Baev V, Minkov IN, Tabler M.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W696-700.
Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms.
Saetrom O, Snove O Jr, Saetrom P.
RNA. 2005 Jul;11(7):995-1003.
Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method.
Burgler C, Macdonald PM.
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