Computational prediction of microRNA genes.
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[1] Michelle S. Scott,et al. Identification of human miRNA precursors that resemble box C/D snoRNAs , 2011, Nucleic acids research.
[2] Peter F. Stadler,et al. Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures , 2009, PLoS Comput. Biol..
[3] Lydia Gramzow,et al. SplamiR - prediction of spliced miRNAs in plants , 2011, Bioinform..
[4] B. Cullen,et al. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. , 2004, RNA.
[5] M. Ivan,et al. microRNA: emerging therapeutic targets in acute ischemic diseases. , 2010, Pharmacology & therapeutics.
[6] Ana M. Aransay,et al. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments , 2009, Nucleic Acids Res..
[7] Bo Wei,et al. MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences , 2011, BMC Bioinformatics.
[8] Raymond K. Auerbach,et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. , 2011, Genome research.
[9] Anders Krogh,et al. Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants , 2007, PLoS Comput. Biol..
[10] D. Bartel,et al. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. , 2004, Molecular cell.
[11] F. Slack,et al. The let-7 family of microRNAs. , 2008, Trends in cell biology.
[12] A. Hatzigeorgiou,et al. The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function , 2010, PloS one.
[13] Kristin C. Gunsalus,et al. microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets , 2005, PLoS Comput. Biol..
[14] David W. Taylor,et al. A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity , 2010, Science.
[15] Tomohiro Miyoshi,et al. Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production , 2010, Molecular Genetics and Genomics.
[16] Sean R. Eddy,et al. Infernal 1.0: inference of RNA alignments , 2009, Bioinform..
[17] Robert Giegerich,et al. Abstract shapes of RNA. , 2004, Nucleic acids research.
[18] Bin Liu,et al. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs) , 2008, Proceedings of the National Academy of Sciences.
[19] Olivier Voinnet,et al. Revisiting the principles of microRNA target recognition and mode of action , 2009, Nature Reviews Molecular Cell Biology.
[20] Sean R. Eddy,et al. Rfam: an RNA family database , 2003, Nucleic Acids Res..
[21] Duangdao Wichadakul,et al. MicroPC (μPC): A comprehensive resource for predicting and comparing plant microRNAs , 2009, BMC Genomics.
[22] Byoung-Tak Zhang,et al. Human microRNA prediction through a probabilistic co-learning model of sequence and structure , 2005, Nucleic acids research.
[23] M. Levine,et al. miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data , 2010, Genome Biology.
[24] R. Berro,et al. HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR , 2007, BMC Molecular Biology.
[25] B. Cullen,et al. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. , 2003, Genes & development.
[26] Hui Zhou,et al. deepBase: a database for deeply annotating and mining deep sequencing data , 2009, Nucleic Acids Res..
[27] J. Mattick,et al. Small RNAs derived from snoRNAs. , 2009, RNA.
[28] T. Tuschl,et al. Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.
[29] G. Hannon,et al. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. , 2007, Genes & development.
[30] E. Lai,et al. The Mirtron Pathway Generates microRNA-Class Regulatory RNAs in Drosophila , 2007, Cell.
[31] V. Praz,et al. Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. , 2010, Genome research.
[32] B. Cullen,et al. Sequence requirements for micro RNA processing and function in human cells. , 2003, RNA.
[33] Baohong Zhang,et al. Plant microRNA: a small regulatory molecule with big impact. , 2006, Developmental biology.
[34] Mihaela Zavolan,et al. Identification of Clustered Micrornas Using an Ab Initio Prediction Method , 2022 .
[35] B. Cullen. Derivation and function of small interfering RNAs and microRNAs. , 2004, Virus research.
[36] C. Burge,et al. The microRNAs of Caenorhabditis elegans. , 2003, Genes & development.
[37] Peter F Stadler,et al. Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.
[38] David Osumi-Sutherland,et al. FlyBase: enhancing Drosophila Gene Ontology annotations , 2008, Nucleic Acids Res..
[39] Christoph Flamm,et al. The expansion of the metazoan microRNA repertoire , 2006, BMC Genomics.
[40] Gerhard Steger,et al. NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome , 2010, Journal of nucleic acids.
[41] L. Mao,et al. Evolution of plant microRNA gene families , 2007, Cell Research.
[42] Weixiong Zhang,et al. Multiple distinct small RNAs originate from the same microRNA precursors , 2010, Genome Biology.
[43] G. Ruvkun,et al. A uniform system for microRNA annotation. , 2003, RNA.
[44] I. K. Jordan,et al. Origin and Evolution of Human microRNAs From Transposable Elements , 2007, Genetics.
[45] L. Lim,et al. An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.
[46] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[47] Eric J Wagner,et al. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. , 2002, Molecular cell.
[48] Geoffrey J. Barton,et al. Human miRNA Precursors with Box H/ACA snoRNA Features , 2009, PLoS Comput. Biol..
[49] Eugene Berezikov,et al. Mammalian mirtron genes. , 2007, Molecular cell.
[50] D. Haussecker,et al. Human tRNA-derived small RNAs in the global regulation of RNA silencing. , 2010, RNA.
[51] Ashesh A. Saraiya,et al. snoRNA, a Novel Precursor of microRNA in Giardia lamblia , 2008, PLoS pathogens.
[52] S. Salzberg,et al. GeneSplicer: a new computational method for splice site prediction. , 2001, Nucleic acids research.
[53] A. Sandelin,et al. Hidden layers of human small RNAs , 2008, BMC Genomics.
[54] Gi-Ho Sung,et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana , 2004, Nature Genetics.
[55] Paul W. Sternberg,et al. WormBase: network access to the genome and biology of Caenorhabditis elegans , 2001, Nucleic Acids Res..
[56] Peter F. Stadler,et al. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data , 2006, ISMB.
[57] Benjamin M. Wheeler,et al. The deep evolution of metazoan microRNAs , 2009, Evolution & development.
[58] Sam Griffiths-Jones,et al. MicroRNA evolution by arm switching , 2011, EMBO reports.
[59] M. Jones-Rhoades. Prediction of plant miRNA genes. , 2010, Methods in molecular biology.
[60] Fei Li,et al. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine , 2005, BMC Bioinformatics.
[61] Sanghyuk Lee,et al. MicroRNA genes are transcribed by RNA polymerase II , 2004, The EMBO journal.
[62] Rui Shi,et al. Computational prediction of plant miRNA targets. , 2011, Methods in molecular biology.
[63] A. Adai,et al. Computational prediction of miRNAs in Arabidopsis thaliana. , 2005, Genome research.
[64] Shuigeng Zhou,et al. MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features , 2010, BMC Bioinformatics.
[65] N. Rajewsky,et al. Discovering microRNAs from deep sequencing data using miRDeep , 2008, Nature Biotechnology.
[66] D. Bartel,et al. MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.
[67] Nancy F. Hansen,et al. Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.
[68] G. Barton,et al. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. , 2009, RNA.
[69] Ben Berkhout,et al. A miRNA-tRNA mix-up: tRNA origin of proposed miRNA , 2010 .
[70] Gang Xu,et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing , 2010, Nucleic Acids Res..
[71] R. Bruskiewich,et al. Characterization of statistical features for plant microRNA prediction , 2011, BMC Genomics.
[72] Siu-Ming Yiu,et al. SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..
[73] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[74] P. Poirazi,et al. Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach , 2009, Nucleic acids research.
[75] Sam Griffiths-Jones,et al. The microRNA Registry , 2004, Nucleic Acids Res..
[76] Jiayu Wen,et al. Computational Prediction of Candidate miRNAs and their Targets from Medicago truncatula Non-Protein-Coding Transcripts , 2008, Silico Biol..
[77] P. Poirazi,et al. MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors , 2010, PloS one.
[78] F. Slack,et al. MicroRNAs as potential cancer therapeutics , 2008, Oncogene.
[79] Z. Lun,et al. Discoveries and functions of virus-encoded MicroRNAs , 2008 .
[80] Yuasa Takashi,et al. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. , 2005, RNA.
[81] R. Shiekhattar,et al. The Microprocessor complex mediates the genesis of microRNAs , 2004, Nature.
[82] J. Steitz,et al. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production , 2008, The Journal of cell biology.
[83] G. Hutvagner,et al. A microRNA in a Multiple-Turnover RNAi Enzyme Complex , 2002, Science.
[84] Panayiotis V. Benos,et al. HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models , 2009, BMC Bioinformatics.
[85] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[86] David P. Bartel,et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals , 2008, Nature.
[87] Johan T den Dunnen,et al. New methods for next generation sequencing based microRNA expression profiling , 2010, BMC Genomics.
[88] N. Rajewsky,et al. A human snoRNA with microRNA-like functions. , 2008, Molecular cell.
[89] Philip C. J. Donoghue,et al. MicroRNAs and the advent of vertebrate morphological complexity , 2008, Proceedings of the National Academy of Sciences.
[90] Jun Yu,et al. PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features , 2010, Artif. Intell. Medicine.
[91] Peter F. Stadler,et al. Non-coding RNA annotation of the genome of Trichoplax adhaerens , 2009, Nucleic acids research.
[92] Markus Brameier,et al. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs , 2010, Nucleic Acids Res..
[93] M. McPeek,et al. MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.
[94] M. Axtell,et al. Evolution of plant microRNAs and their targets. , 2008, Trends in plant science.
[95] Peter F. Stadler,et al. Prediction of locally stable RNA secondary structures for genome-wide surveys , 2004, Bioinform..
[96] Ana M. Aransay,et al. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments , 2011, Nucleic Acids Res..