The discovery potential of RNA processing profiles

Clustering by Fast Search and Find of Density Peaks with Data Field

(2016) Shuliang Wang et al.   CHINESE JOURNAL OF ELECTRONICS

tRFs: miRNAs in disguise

(2016) Thejaswini Venkatesh et al.   GENE

Re-evaluation of the roles ofDROSHA,Exportin 5, andDICERin microRNA biogenesis

(2016) Young-Kook Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational analysis of RNA structures with chemical probing data

(2015) Ping Ge et al.   METHODS

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

(2015) Yiliang Ding et al.   Nature Protocols

Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers

(2015) Shozo Honda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells

(2015) Valeria Bevilacqua et al.   RNA Biology

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

(2015) U. Sharma et al.   SCIENCE

Mining diverse small RNA species in the deep transcriptome

(2015) Kasey C. Vickers et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Landscape of long noncoding RNA classification

(2015) Georges St. Laurent et al.   TRENDS IN GENETICS

Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies

(2015) Aristeidis G. Telonis et al.   Oncotarget

Differential and coherent processing patterns from small RNAs

(2015) Sachin Pundhir et al.   Scientific Reports

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles

(2014) Pavankumar Videm et al.   BIOINFORMATICS

A Variety of Dicer Substrates in Human and C. elegans

(2014) Agnieszka Rybak-Wolf et al.   CELL

tRNA fragments in human health and disease

(2014) Paul Anderson et al.   FEBS LETTERS

Novel Long Noncoding RNAs (lncRNAs) in Myogenesis: amiR-31Overlapping lncRNA Transcript Controls Myoblast Differentiation

(2014) Monica Ballarino et al.   MOLECULAR AND CELLULAR BIOLOGY

A promoter-level mammalian expression atlas

(2014)   NATURE

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease

(2014) Sebastian Kirchner et al.   NATURE REVIEWS GENETICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

(2014) M. Allo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Evidence for the biogenesis of more than 1,000 novel human microRNAs

(2014) Marc R Friedländer et al.   GENOME BIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Small RNAs derived from structural non-coding RNAs

(2013) Chong-Jian Chen et al.   METHODS

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

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

SERE: Single-parameter quality control and sample comparison for RNA-Seq

(2012) Stefan K Schulze et al.   BMC GENOMICS

MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues

(2012) Sung-Chou Li et al.   BMC Systems Biology

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

(2012) Thomas Schubert et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

(2012) Sara Macias et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2012) Zhihua Li et al.   NUCLEIC ACIDS RESEARCH

MicroRNA Prediction Using a Fixed-Order Markov Model Based on the Secondary Structure Pattern

(2012) Wei Shen et al.   PLoS One

MicroRNA evolution by arm switching

(2011) Sam Griffiths-Jones et al.   EMBO REPORTS

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

(2011) Mario Fasold et al.   NUCLEIC ACIDS RESEARCH

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Shivendra Kishore et al.   HUMAN MOLECULAR GENETICS

Structural basis of microRNA length variety

(2010) Julia Starega-Roslan et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Markus Brameier et al.   NUCLEIC ACIDS RESEARCH

Evidence for human microRNA-offset RNAs in small RNA sequencing data

(2009) D. Langenberger et al.   BIOINFORMATICS

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

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

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

(2009) C. Cole et al.   RNA

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL