Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins inGiardia lamblia

(2012) Wei Li et al.   CELLULAR MICROBIOLOGY

Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway

(2012) Francisco Esteban Nicolas et al.   FEBS LETTERS

Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin

(2012) Thomas Schubert et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs

(2012) Zhihua Li et al.   NUCLEIC ACIDS RESEARCH

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

(2012) Marek Zywicki et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

From snoRNA to miRNA: Dual function regulatory non-coding RNAs

(2011) Michelle S. Scott et al.   BIOCHIMIE

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns

(2011) David Langenberger et al.   BIOINFORMATICS

Conserved generation of short products at piRNA loci

(2011) Philipp Berninger et al.   BMC GENOMICS

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human box C/D snoRNA processing conservation across multiple cell types

(2011) Michelle S. Scott et al.   NUCLEIC ACIDS RESEARCH

Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression

(2011) Manli Shen et al.   NUCLEIC ACIDS RESEARCH

Identification and Analysis of Intermediate Size Noncoding RNAs in the Human Fetal Brain

(2011) Dongsheng Yan et al.   PLoS One

Animal snoRNAs and scaRNAs with exceptional structures

(2011) Manja Marz et al.   RNA Biology

PLEXY: efficient target prediction for box C/D snoRNAs

(2010) Stephanie Kehr et al.   BIOINFORMATICS

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data

(2010) Chol-Hee Jung et al.   BMC GENOMICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing

(2010) Shivendra Kishore et al.   HUMAN MOLECULAR GENETICS

Box H/ACA Small Ribonucleoproteins

(2010) Tamás Kiss et al.   MOLECULAR CELL

Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs

(2010) Markus Brameier et al.   NUCLEIC ACIDS RESEARCH

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers

(2010) Jian-You Liao et al.   PLoS One

Spliceosomal snRNA modifications and their function

(2010) John Karijolich et al.   RNA Biology

Human tRNA-derived small RNAs in the global regulation of RNA silencing

(2010) D. Haussecker et al.   RNA

RNAsnoop: efficient target prediction for H/ACA snoRNAs

(2009) Hakim Tafer et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

(2009) Yong Sun Lee et al.   GENES & DEVELOPMENT

Angiogenin cleaves tRNA and promotes stress-induced translational repression

(2009) Satoshi Yamasaki et al.   JOURNAL OF CELL BIOLOGY

The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs

(2009) Helena Persson et al.   NATURE CELL BIOLOGY

Systematic identification and characterization of chicken ( Gallus gallus ) ncRNAs

(2009) Yong Zhang et al.   NUCLEIC ACIDS RESEARCH

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

(2009) C. Cole et al.   RNA

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Hidden layers of human small RNAs

(2008) Hideya Kawaji et al.   BMC GENOMICS

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing

(2007) Markus Hafner et al.   METHODS