Genome-wide identification of miRNA targets by PAR-CLIP.

[1]  Renato Paro,et al.  Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data , 2012, Nucleic acids research.

[2]  Norman E. Davey,et al.  Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins , 2012, Cell.

[3]  Siu-Ming Yiu,et al.  SOAP3: ultra-fast GPU-based parallel alignment tool for short reads , 2012, Bioinform..

[4]  Thomas Tuschl,et al.  Identification of RNA–protein interaction networks using PAR‐CLIP , 2012, Wiley interdisciplinary reviews. RNA.

[5]  Bo Peng,et al.  Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools , 2012, Bioinform..

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

[7]  Bryan R. Cullen,et al.  The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines , 2012, PLoS pathogens.

[8]  Eugene Berezikov,et al.  Evolution of microRNA diversity and regulation in animals , 2011, Nature Reviews Genetics.

[9]  C. Sander,et al.  Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. , 2011, Genes & development.

[10]  Chris Sander,et al.  RNA targets of wild-type and mutant FET family proteins , 2011, Nature Structural &Molecular Biology.

[11]  Uwe Ohler,et al.  PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data , 2011, Genome Biology.

[12]  Uwe Ohler,et al.  Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. , 2011, Molecular cell.

[13]  Patrick Callier,et al.  Germline deletion of the miR-1792 cluster causes growth and skeletal defects in humans , 2011 .

[14]  N. Rajewsky,et al.  Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. , 2011, Molecular cell.

[15]  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.

[16]  M. Zavolan,et al.  A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins , 2011, Nature Methods.

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

[18]  Volker Hovestadt,et al.  Molecular and Cellular Pathobiology MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing , 2011 .

[19]  Aaron R. Quinlan,et al.  BamTools: a C++ API and toolkit for analyzing and managing BAM files , 2011, Bioinform..

[20]  Anders Krogh,et al.  MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. , 2011, RNA.

[21]  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.

[22]  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.

[23]  Robert B Darnell,et al.  HITS‐CLIP: panoramic views of protein–RNA regulation in living cells , 2010, Wiley interdisciplinary reviews. RNA.

[24]  Anjali J. Koppal,et al.  Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010 .

[25]  C. Sander,et al.  Target mRNA abundance dilutes microRNA and siRNA activity , 2010, Molecular systems biology.

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

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

[28]  Sayan Mukherjee,et al.  Evidence-ranked motif identification , 2010, Genome Biology.

[29]  A. Mortazavi,et al.  Computation for ChIP-seq and RNA-seq studies , 2009, Nature Methods.

[30]  David G Hendrickson,et al.  Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA , 2009, PLoS biology.

[31]  David Tollervey,et al.  Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs , 2009, Proceedings of the National Academy of Sciences.

[32]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[33]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[34]  A. Brivanlou,et al.  The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. , 2009, Developmental cell.

[35]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[36]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[37]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[38]  Q. Cui,et al.  An Analysis of Human MicroRNA and Disease Associations , 2008, PloS one.

[39]  Tyson A. Clark,et al.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing , 2008, Nature.

[40]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[41]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[42]  Mihaela Zavolan,et al.  Computational analysis of small RNA cloning data. , 2008, Methods.

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

[44]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[45]  Erik van Nimwegen,et al.  PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny , 2005, PLoS Comput. Biol..

[46]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[47]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[48]  AC Tose Cell , 1993, Cell.