Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

[1]  J. Kjems,et al.  Natural RNA circles function as efficient microRNA sponges , 2013, Nature.

[2]  Sebastian D. Mackowiak,et al.  Circular RNAs are a large class of animal RNAs with regulatory potency , 2013, Nature.

[3]  G. Hannon,et al.  The Structure of Human Argonaute-2 in Complex with miR-20a , 2012, Cell.

[4]  K. Zen,et al.  Mouse miRNA-709 directly regulates miRNA-15a/16-1 biogenesis at the posttranscriptional level in the nucleus: evidence for a microRNA hierarchy system , 2011, Cell Research.

[5]  Ivo Grosse,et al.  Functional microRNA targets in protein coding sequences , 2012, Bioinform..

[6]  S. Chi,et al.  An alternative mode of microRNA target recognition , 2012, Nature Structural &Molecular Biology.

[7]  Nectarios Koziris,et al.  TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support , 2011, Nucleic Acids Res..

[8]  Hanah Margalit,et al.  A wide repertoire of miRNA binding sites: prediction and functional implications , 2011, Bioinform..

[9]  Sean P Ryder,et al.  Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. , 2011, RNA.

[10]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

[11]  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.

[12]  R. Darnell,et al.  Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data , 2011, Nature Biotechnology.

[13]  Peter T. Nelson,et al.  Specific sequence determinants of miR-15/107 microRNA gene group targets , 2011, Nucleic acids research.

[14]  David Tollervey,et al.  Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast , 2011, Proceedings of the National Academy of Sciences.

[15]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[16]  S. Crooke,et al.  Depletion of key protein components of the RISC pathway impairs pre-ribosomal RNA processing , 2011, Nucleic acids research.

[17]  Yoshihide Hayashizaki,et al.  Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin , 2011, RNA biology.

[18]  Chi-Ying F. Huang,et al.  miRTarBase: a database curates experimentally validated microRNA–target interactions , 2010, Nucleic Acids Res..

[19]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[20]  V. Kim,et al.  Modifications of Small RNAs and Their Associated Proteins , 2010, Cell.

[21]  Shuang Huang,et al.  Ratio of miR-196s to HOXC8 messenger RNA correlates with breast cancer cell migration and metastasis. , 2010, Cancer research.

[22]  Mohsen Khorshid,et al.  PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins , 2010, Journal of visualized experiments : JoVE.

[23]  P. Pandolfi,et al.  A coding-independent function of gene and pseudogene mRNAs regulates tumour biology , 2010, Nature.

[24]  W. Filipowicz,et al.  Regulation of mRNA translation and stability by microRNAs. , 2010, Annual review of biochemistry.

[25]  Guanming Wu,et al.  A Viral microRNA Down-Regulates Multiple Cell Cycle Genes through mRNA 5′UTRs , 2010, PLoS pathogens.

[26]  Kyle Kai-How Farh,et al.  Expanding the microRNA targeting code: functional sites with centered pairing. , 2010, Molecular cell.

[27]  Peter T Nelson,et al.  Individual microRNAs (miRNAs) display distinct mRNA targeting “rules” , 2010, RNA biology.

[28]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[29]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[30]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

[31]  H. Grosshans,et al.  Active turnover modulates mature microRNA activity in Caenorhabditis elegans , 2009, Nature.

[32]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

[33]  Oliver Hofmann,et al.  miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements. , 2009, Molecular cell.

[34]  E. Chan,et al.  The C-terminal half of human Ago2 binds to multiple GW-rich regions of GW182 and requires GW182 to mediate silencing. , 2009, RNA.

[35]  Xiaozhong Wang,et al.  Essential and overlapping functions for mammalian Argonautes in microRNA silencing. , 2009, Genes & development.

[36]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[37]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[38]  Michael Zuker,et al.  UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.

[39]  Richard S. Rogers,et al.  Comprehensive analysis of diverse ribonucleoprotein complexes , 2007, Nature Methods.

[40]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[41]  L. Lim,et al.  MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.

[42]  T. Pederson,et al.  MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells , 2006, Proceedings of the National Academy of Sciences.

[43]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[44]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[45]  F. Slack,et al.  Architecture of a validated microRNA::target interaction. , 2004, Chemistry & biology.

[46]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[47]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[48]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[49]  J. M. Thomson,et al.  Argonaute2 Is the Catalytic Engine of Mammalian RNAi , 2004, Science.

[50]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[51]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[52]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[53]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[54]  G. Ruvkun,et al.  A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. , 1996, Genes & development.

[55]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[56]  AC Tose Cell , 1993, Cell.

[57]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[58]  F. Barré-Sinoussi,et al.  HIV‐1 reverse transcriptase specifically interacts with the anticodon domain of its cognate primer tRNA. , 1989, The EMBO journal.