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Found 1346 results
2009
Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P.  2009.  Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach.. Nucleic Acids Res. 37(10):3276-87.
Appelt J-U, Giordano FA, Ecker M, Roeder I, Grund N, Hotz-Wagenblatt A, Opelz G, Zeller WJ, Allgayer H, Fruehauf S et al..  2009.  QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.. Gene Ther. 16(7):885-93.
Fan D, Bitterman PB, Larsson O.  2009.  Regulatory element identification in subsets of transcripts: comparison and integration of current computational methods.. RNA. 15(8):1469-82.
Bell GW, Lewitter F.  2009.  Resources for small regulatory RNAs.. Curr Protoc Mol Biol. Chapter 19:Unit19.8.
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR et al..  2009.  Rfam: updates to the RNA families database.. Nucleic Acids Res. 37(Database issue):D136-40.
Rieber N, Knapp B, Eils R, Kaderali L.  2009.  RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.. Bioinformatics. 25(5):678-9.
Wang X, Wang X, Varma RK, Beauchamp L, Magdaleno S, Sendera TJ.  2009.  Selection of hyperfunctional siRNAs with improved potency and specificity.. Nucleic Acids Res. 37(22):e152.
Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.  2009.  SHRiMP: accurate mapping of short color-space reads.. PLoS Comput Biol. 5(5):e1000386.
Naito Y, Yoshimura J, Morishita S, Ui-Tei K.  2009.  siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.. BMC Bioinformatics. 10:392.
Ren Y, Gong W, Zhou H, Wang Y, Xiao F, Li T.  2009.  siRecords: a database of mammalian RNAi experiments and efficacies.. Nucleic Acids Res. 37(Database issue):D146-9.
Xu Z, Taylor JA.  2009.  SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies.. Nucleic Acids Res. 37(Web Server issue):W600-5.
Pico AR, Smirnov IV, Chang JS, Yeh R-F, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M.  2009.  SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system.. Nucleic Acids Res. 37(Database issue):D803-9.
Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, Wang J.  2009.  SOAP2: an improved ultrafast tool for short read alignment.. Bioinformatics. 25(15):1966-7.
Huang H-Y, Chang H-Y, Chou C-H, Tseng C-P, Ho S-Y, Yang C-D, Ju Y-W, Da Huang H-.  2009.  sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.. Nucleic Acids Res. 37(Database issue):D150-4.
Kaczkowski B, Torarinsson E, Reiche K, Havgaard JHull, Stadler PF, Gorodkin J.  2009.  Structural profiles of human miRNA families from pairwise clustering.. Bioinformatics. 25(3):291-4.
Yousef M, Showe L, Showe M.  2009.  A study of microRNAs in silico and in vivo: bioinformatics approaches to microRNA discovery and target identification.. FEBS J. 276(8):2150-6.
Bandyopadhyay S, Mitra R.  2009.  TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.. Bioinformatics. 25(20):2625-31.
Jacobs GH, Chen A, Stevens SG, Stockwell PA, Black MA, Tate WP, Brown CM.  2009.  Transterm: a database to aid the analysis of regulatory sequences in mRNAs.. Nucleic Acids Res. 37(Database issue):D72-6.
Jenjaroenpun P, Kuznetsov VA.  2009.  TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.. BMC Genomics. 10 Suppl 3:S9.
Taccioli C, Fabbri E, Visone R, Volinia S, Calin GA, Fong LY, Gambari R, Bottoni A, Acunzo M, Hagan J et al..  2009.  UCbase & miRfunc: a database of ultraconserved sequences and microRNA function.. Nucleic Acids Res. 37(Database issue):D41-8.
Langmead B, Trapnell C, Pop M, Salzberg SL.  2009.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.. Genome Biol. 10(3):R25.
2008
Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q.  2008.  An analysis of human microRNA and disease associations.. PLoS One. 3(10):e3420.
Long D, Chan CYu, Ding Y.  2008.  Analysis of microRNA-target interactions by a target structure based hybridization model.. Pac Symp Biocomput. :64-74.
Park Y-K, Park S-M, Choi Y-C, Lee D, Won M, Kim YJoo.  2008.  AsiDesigner: exon-based siRNA design server considering alternative splicing.. Nucleic Acids Res. 36(Web Server issue):W97-103.
Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH.  2008.  A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.. RNA. 14(11):2290-6.

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