A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing
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Hsien-Da Huang | Tzu-Hao Chang | Chih-Hung Chou | Sirjana Shrestha | Sheng-Da Hsu | Shun-Long Weng | Feng-Mao Lin | Jui-Hung Hung | Min-Te Chou | Chiung-Chih Hsiao | S. Shrestha | Chih-Hung Chou | Hsien-Da Huang | F. Lin | S. Weng | Tzu-Hao Chang | Jui-Hung Hung | Min-Te Chou | Sheng-Da Hsu | Chiung-Chih Hsiao | Shun-Long Weng
[1] Nectarios Koziris,et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support , 2011, Nucleic Acids Res..
[2] N. Rajewsky,et al. Discovering microRNAs from deep sequencing data using miRDeep , 2008, Nature Biotechnology.
[3] T. Tuschl,et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex , 2008, Nature.
[4] M. Esteller. Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.
[5] Hui Zhou,et al. deepBase: a database for deeply annotating and mining deep sequencing data , 2009, Nucleic Acids Res..
[6] M. Kiebler,et al. Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .
[7] C. Burge,et al. Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.
[8] Scott B. Dewell,et al. Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.
[9] Xavier Estivill,et al. SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells , 2009, Nucleic acids research.
[10] Mihaela Zavolan,et al. Inference of miRNA targets using evolutionary conservation and pathway analysis , 2007, BMC Bioinformatics.
[11] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[12] Ana M. Aransay,et al. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments , 2009, Nucleic Acids Res..
[13] Chi-Ying F. Huang,et al. miRTarBase: a database curates experimentally validated microRNA–target interactions , 2010, Nucleic Acids Res..
[14] K. Gunsalus,et al. Combinatorial microRNA target predictions , 2005, Nature Genetics.
[15] Gene W. Yeo,et al. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans , 2010, Nature Structural &Molecular Biology.
[16] Robert Homann,et al. Geoseq: a tool for dissecting deep-sequencing datasets , 2010, BMC Bioinformatics.
[17] D. Bartel. MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.
[18] Dominic Grün,et al. In vivo and transcriptome-wide identification of RNA binding protein target sites. , 2011, Molecular cell.
[19] D. Bartel,et al. Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs , 2011, Nature Structural &Molecular Biology.
[20] Uwe Ohler,et al. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. , 2011, Cell host & microbe.
[21] Rasko Leinonen,et al. The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..
[22] Christoph Dieterich,et al. doRiNA: a database of RNA interactions in post-transcriptional regulation , 2011, Nucleic Acids Res..
[23] W. Filipowicz,et al. The widespread regulation of microRNA biogenesis, function and decay , 2010, Nature Reviews Genetics.
[24] Hui Zhou,et al. starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data , 2010, Nucleic Acids Res..
[25] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[26] Grace X. Y. Zheng,et al. Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs , 2010, Nature Structural &Molecular Biology.
[27] Uwe Ohler,et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data , 2011, Genome Biology.
[28] Gang Xu,et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing , 2010, Nucleic Acids Res..
[29] Hsien-Da Huang,et al. miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression , 2009, BMC Bioinformatics.
[30] Sam Griffiths-Jones,et al. The microRNA Registry , 2004, Nucleic Acids Res..
[31] Mohsen Khorshid,et al. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins , 2010, Nucleic Acids Res..
[32] Chi-Ching Lee,et al. DSAP: deep-sequencing small RNA analysis pipeline , 2010, Nucleic Acids Res..
[33] Eran Halperin,et al. miRNAkey: a software for microRNA deep sequencing analysis , 2010, Bioinform..
[34] Ana Kozomara,et al. miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..
[35] Sebastian D. Mackowiak,et al. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.