PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications

Ribosome heterogeneity in stem cells and development

(2020) Dan Li et al.   JOURNAL OF CELL BIOLOGY

Noncanonical Roles of tRNAs: tRNA Fragments and Beyond

(2020) Zhangli Su et al.   Annual Review of Genetics

A tRNA half modulates translation as stress response in Trypanosoma brucei

(2019) Roger Fricker et al.   Nature Communications

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma

(2019) Maria D Giraldez et al.   EMBO JOURNAL

Maternal overnutrition programs hedonic and metabolic phenotypes across generations through sperm tsRNAs

(2019) Gitalee Sarker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic expression of tRNA‐derived small RNAs define cellular states

(2019) Srikar Krishna et al.   EMBO REPORTS

Sperm RNA code programmes the metabolic health of offspring

(2019) Yunfang Zhang et al.   Nature Reviews Endocrinology

Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation

(2019) Bo Ren et al.   SCIENCE

Human sperm displays rapid responses to diet

(2019) Daniel Nätt et al.   PLOS BIOLOGY

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

Metabolism in Pluripotent Stem Cells and Early Mammalian Development

(2018) Jin Zhang et al.   Cell Metabolism

Modifications and functional genomics of human transfer RNA

(2018) Tao Pan   CELL RESEARCH

Iron-dependent cleavage of ribosomal RNA during oxidative stress in the yeastSaccharomyces cerevisiae.

(2018) Jessica A. Zinskie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs

(2018) Yunfang Zhang et al.   NATURE CELL BIOLOGY

Structural and evolutionary insights into ribosomal RNA methylation

(2018) Petr V Sergiev et al.   Nature Chemical Biology

Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response

(2018) Shiqi Luo et al.   NUCLEIC ACIDS RESEARCH

tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner

(2018) Canan Kuscu et al.   RNA

Downregulation of ribosome biogenesis during early forebrain development

(2018) Kevin F Chau et al.   eLife

SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs

(2018) Junchao Shi et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life

(2018) Naomi R. Genuth et al.   MOLECULAR CELL

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

tsRNAs: The Swiss Army Knife for Translational Regulation

(2018) Junchao Shi et al.   TRENDS IN BIOCHEMICAL SCIENCES

Generation of 2′,3′-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome

(2018) Megumi Shigematsu et al.   Frontiers in Genetics

A transfer-RNA-derived small RNA regulates ribosome biogenesis

(2017) Hak Kyun Kim et al.   NATURE

The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis

(2017) Paul Schimmel   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA modifications and structures cooperate to guide RNA–protein interactions

(2017) Cole J.T. Lewis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

tRNA-derived small RNAs target transposable element transcripts

(2017) German Martinez et al.   NUCLEIC ACIDS RESEARCH

A sequence of 28S rRNA-derived small RNAs is enriched in mature sperm and various somatic tissues and possibly associates with inflammation

(2017) Chen Chu et al.   Journal of Molecular Cell Biology

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

RNA interference–induced hepatotoxicity results from loss of the first synthesized isoform of microRNA-122 in mice

(2016) Paul N Valdmanis et al.   NATURE MEDICINE

Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications

(2016) Qi Chen et al.   NATURE REVIEWS GENETICS

A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress

(2016) Jennifer Gebetsberger et al.   RNA Biology

Small RNA Modifications: Integral to Function and Disease

(2016) Xudong Zhang et al.   TRENDS IN MOLECULAR MEDICINE

Small RNAs derived from tRNAs and rRNAs are highly enriched in exosomes from both old and new world Leishmania providing evidence for conserved exosomal RNA Packaging

(2015) Ulrike Lambertz et al.   BMC GENOMICS

Cdk5rap1-Mediated 2-Methylthio Modification of Mitochondrial tRNAs Governs Protein Translation and Contributes to Myopathy in Mice and Humans

(2015) Fan-Yan Wei et al.   Cell Metabolism

The histone chaperone CAF-1 safeguards somatic cell identity

(2015) Sihem Cheloufi et al.   NATURE

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

(2015) Aaron E Cozen et al.   NATURE METHODS

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

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

Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder

(2015) Q. Chen et al.   SCIENCE

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

(2015) U. Sharma et al.   SCIENCE

Rfam 12.0: updates to the RNA families database

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

A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs

(2014) T. Suzuki et al.   NUCLEIC ACIDS RESEARCH

Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryoteGiardia lamblia

(2014) Jian-You Liao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Extracellular vesicles shed by Trypanosoma cruzi are linked to small RNA pathways, life cycle regulation, and susceptibility to infection of mammalian cells

(2013) Maria R. Garcia-Silva et al.   PARASITOLOGY RESEARCH

Profiling and Identification of Small rDNA-Derived RNAs and Their Potential Biological Functions

(2013) Haibin Wei et al.   PLoS One

A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm

(2012) Hongying Peng et al.   CELL RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer

(2012) Xinan Yang et al.   PLoS Computational Biology

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Several RNase T2 enzymes function in induced tRNA and rRNA turnover in the ciliate Tetrahymena

(2011) Kasper L. Andersen et al.   MOLECULAR BIOLOGY OF THE CELL

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

tRNA biology charges to the front

(2010) E. M. Phizicky et al.   GENES & DEVELOPMENT

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Angiogenin cleaves tRNA and promotes stress-induced translational repression

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

A reprogrammable mouse strain from gene-targeted embryonic stem cells

(2009) Matthias Stadtfeld et al.   NATURE METHODS

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH

tRNA cleavage is a conserved response to oxidative stress in eukaryotes

(2008) D. M. Thompson et al.   RNA

Selective Blockade of MicroRNA Processing by Lin28

(2008) S. R. Viswanathan et al.   SCIENCE