tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers

Consequential considerations when mapping tRNA fragments

(2016) Aristeidis G. Telonis et al.   BMC BIOINFORMATICS

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

(2015) Peter Kerpedjiev et al.   BIOINFORMATICS

Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets

(2015) Spyros Karaiskos et al.   Biology Direct

tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data

(2015) Sara R. Selitsky et al.   BMC BIOINFORMATICS

Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement

(2015) Hani Goodarzi et al.   CELL

Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs

(2015) TB Rounge et al.   Molecular Cancer

Breast Cancer-Specific miR Signature Unique to Extracellular Vesicles Includes "microRNA-like" tRNA Fragments

(2015) N. Guzman et al.   MOLECULAR CANCER RESEARCH

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

(2015) Aaron E Cozen et al.   NATURE METHODS

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

(2015) Wen-Ju Sun et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

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

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

(2015) Aristeidis G. Telonis et al.   Oncotarget

Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C

(2015) Sara R. Selitsky et al.   Scientific Reports

Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets

(2014) Pankaj Kumar et al.   BMC BIOLOGY

Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions

(2014) L. Vojtech et al.   NUCLEIC ACIDS RESEARCH

The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells

(2014) Simon P. Keam et al.   NUCLEIC ACIDS RESEARCH

tRFdb: a database for transfer RNA fragments

(2014) Pankaj Kumar et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki 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

Transfer RNA and human disease

(2014) Jamie A. Abbott et al.   Frontiers in Genetics

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

(2013) Guilherme Loss-Morais et al.   Biology Direct

CLP1 links tRNA metabolism to progressive motor-neuron loss

(2013) Toshikatsu Hanada et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma

(2013) Roy L. Maute et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells

(2013) Andrew Sobala et al.   RNA Biology

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

(2012) Hongying Peng et al.   CELL RESEARCH

A Comprehensive Expression Profile of MicroRNAs and Other Classes of Non-Coding Small RNAs in Barley Under Phosphorous-Deficient and -Sufficient Conditions

(2012) M. Hackenberg et al.   DNA RESEARCH

Identification and Functional Characterization of tRNA-derived RNA Fragments (tRFs) in Respiratory Syncytial Virus Infection

(2012) Qingrong Wang et al.   MOLECULAR THERAPY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Zhihua Li et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

(2012) Esther N. M. Nolte-’t Hoen et al.   NUCLEIC ACIDS RESEARCH

tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA inHaloferax volcanii

(2012) Jennifer Gebetsberger et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa)

(2011) Lu Wang et al.   BMC GENOMICS

Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus

(2011) Chong-Jian Chen et al.   RNA Biology

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

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

(2010) D. Haussecker et al.   RNA

Stressing Out over tRNA Cleavage

(2009) Debrah M. Thompson et al.   CELL

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

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

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Angiogenin cleaves tRNA and promotes stress-induced translational repression

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

Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid

(2009) Man Lung Yeung et al.   NUCLEIC ACIDS RESEARCH

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

(2009) C. Cole et al.   RNA

tRNAs as regulators in gene expression

(2009) Yan Li et al.   Science in China. Series C, Life sciences / Chinese Academy of Sciences

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Hidden layers of human small RNAs

(2008) Hideya Kawaji et al.   BMC GENOMICS

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs

(2008) J. E. Babiarz et al.   GENES & DEVELOPMENT

Stress-induced tRNA-derived RNAs: a novel class of small RNAs in the primitive eukaryote Giardia lamblia

(2008) Yan Li et al.   NUCLEIC ACIDS RESEARCH

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

(2008) Christoph Jöchl et al.   NUCLEIC ACIDS RESEARCH

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

tRNA cleavage is a conserved response to oxidative stress in eukaryotes

(2008) D. M. Thompson et al.   RNA