Fast and effective prediction of microRNA/target duplexes.

Keywords

Biology, microRNA, RNA, Computational biology, Base pair

References

• Prediction of plant microRNA targets.Matthew W. Rhoades, Brenda J. Reinhart, Lee P. Lim — 2002
• The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs.Juan E. Abrahante, Aric L. Daul, Ming Li — 2003
• A discipline of dynamic programming over sequence dataRobert Giegerich, Carsten Meyer, Steffen Peter — 2004
• Short-range cell interactions and cell survival in the Drosophila wing.Marco Milán, Lídia Pérez, Stephen M. Cohen — 2002
• Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.David H. Mathews, Jeffrey Sabina, Michael Zuker — 1999
• The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target.Shin-Yi Lin, Steven Johnson, Mary C. Abraham — 2003
• Optimal computer folding of large RNA sequences using thermodynamics and auxiliary informationMichael Zuker, Patrick Stiegler — 1981
• Rapid and accurate estimates of statistical significance for sequence data base searches.Michael S. Waterman, Martin Vingron — 1994
• Where is the ?c?Harry J. Lipkin, H.R. Rubinstein, Nathan Isgur — 1978
• bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila.Julius Brennecke, David R. Hipfner, Alexander Stark — 2003
• Identification of Drosophila MicroRNA TargetsAlexander Stark, Julius Brennecke, Robert B. Russell — 2003
• Computational identification of microRNA targetsNikolaus Rajewsky, Nicholas D. Socci — 2004
• Self-assembly of mesoscopically ordered chromatic polydiacetylene/silica nanocompositesYunfeng Lu, Yi Yang, Alan Sellinger — 2001
• Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulationEric C. Lai — 2002
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.Samuel Karlin, Stephen F. Altschul — 1990
• UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAsGraziano Pesole — 2000
• Vienna RNA secondary structure serverIvo L. Hofacker — 2003
• Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamicsJens Reeder, Robert Giegerich — 2004
• Developmental functions of the Distal-less/Dlx homeobox genes.Grace Panganiban, John L.R. Rubenstein — 2002
• Specificity of microRNA target selection in translational repression.John G. Doench, Phillip A. Sharp — 2004

Cited by

• Gene expression regulators —MicroRNAsFang Chen — 2005
• miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomesJoanne Wei Seen Teh — 2005
• Prediction of microRNA targets.Gaspar Aragón Osés — 2006
• RNAplex: a fast tool for RNA-RNA interaction searchLeyra Piñero de Paz, Ana Zorio‐Grima — 2008
• Overexpressed miR-494 down-regulates PTEN gene expression in cells transformed by anti-benzo(a)pyrene-trans-7,8-dihydrodiol-9,10-epoxide.Macario Santiago Kastner — 2010
• MAGIA, a web-based tool for miRNA and Genes Integrated AnalysisRoss Casley — 2010
• MicroRNAs 15a/16-1 function as tumor suppressor genes in multiple myeloma.Ramón Santos, Q Dominguez, Maritza Escalona — 2010
• Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis1[W][OA]施雪华 — 2011
• miR‐198 inhibits migration and invasion of hepatocellular carcinoma cells by targeting the HGF/c‐MET pathwayLesly Cardozo Fuentes — 2011
• MicroRNA-32 upregulation by 1,25-dihydroxyvitamin D3 in human myeloid leukemia cells leads to Bim targeting and inhibition of AraC-induced apoptosisHans van Veen — 2011
• Dynamic Modulation of Thymic MicroRNAs in Response to StressM. C. Wang, H. C. Chiang, S. T. Hsieh — 2011
• MicroRNA-125b/Lin28 Pathway Contributes to the Mesendodermal Fate Decision of Embryonic Stem CellsMarc Isern — 2012
• In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculusGiuseppe Tinelli — 2012
• Multiple microRNAs may regulate the DNA repair enzyme uracil-DNA glycosylase.Roberta Drehmer de Miranda — 2013
• Characterization and differential expression of microRNAs in the ovaries of pregnant and non-pregnant goats (Capra hircus)Ana Coelho, Matthew Schaller, Cory M. Hogaboam — 2013
• RNAplex a Fast and Flexible RNA-RNA Interaction Search ToolHakim Tafer — 2007
• CLIP-based prediction of mammalian microRNA binding sitesA. L. Cerdeira, A. W. Cole, Dawn S. Luthe — 2013
• Prediction of miRNA targets.Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi — 2015
• miR-638 Regulates Differentiation and Proliferation in Leukemic Cells by Targeting Cyclin-dependent Kinase 2*Yi Lin, Dengju Li, Qing Liang — 2014
• Knockdown of long non-coding RNA XIST exerts tumor-suppressive functions in human glioblastoma stem cells by up-regulating miR-152.王景武 — 2015

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