High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes

(2020) Stephan Werner et al.   NUCLEIC ACIDS RESEARCH

The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity

(2020) Ketty Pernod et al.   NUCLEIC ACIDS RESEARCH

Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation

(2020) Otis Pinkard et al.   Nature Communications

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

(2019) Yuri Motorin et al.   Genes

Absolute quantification of noncoding RNA by microscale thermophoresis

(2019) Dominik Jacob et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

(2019) Adrian Gabriel Torres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance

(2019) Isao Masuda et al.   Cell Systems

Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction

(2019) Hengyi Xu et al.   Scientific Reports

Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA

(2019) Huiqing Zhou et al.   NATURE METHODS

Logomaker: beautiful sequence logos in Python

(2019) Ammar Tareen et al.   BIOINFORMATICS

Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway

(2018) Lu Han et al.   PLoS Genetics

Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds

(2018) Aldema Sas-Chen et al.   METHODS

Transcriptome-wide measurement of translation by ribosome profiling

(2017) Nicholas J. McGlincy et al.   METHODS

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Determination of tRNA aminoacylation levels by high-throughput sequencing

(2017) Molly E. Evans et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron

(2017) Chen Zhao et al.   RNA

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

(2017) Tasos Gogakos et al.   Cell Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

tRNA base methylation identification and quantification via high-throughput sequencing

(2016) Wesley C. Clark et al.   RNA

Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSerrequiresN6-isopentenylation of A37

(2016) Aneeshkumar G. Arimbasseri et al.   RNA

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

Inosine modifications in human tRNAs are incorporated at the precursor tRNA level

(2015) Adrian Gabriel Torres et al.   NUCLEIC ACIDS RESEARCH

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

High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases

(2015) Yidan Qin et al.   RNA

Maintenance of protein synthesis reading frame by EF-P and m1G37-tRNA

(2015) Howard B. Gamper et al.   Nature Communications

RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification

(2015) Aneeshkumar G. Arimbasseri et al.   PLoS Genetics

Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function

(2014) Ender Karaca et al.   CELL

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

(2014) Bianca M. Schmitt et al.   GENOME RESEARCH

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

(2014) Sebastian Kirchner et al.   NATURE REVIEWS GENETICS

An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments

(2014) Erin E. Heyer et al.   NUCLEIC ACIDS RESEARCH

Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5

(2014) G. E. Katibah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops

(2014) T. Maehigashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration

(2014) R. Ishimura et al.   SCIENCE

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

(2014) Yao-Cheng Lin et al.   Nature Communications

Infernal 1.1: 100-fold faster RNA homology searches

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

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

(2013) S. Mohr et al.   RNA

Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10

(2013) W. E. Swinehart et al.   RNA

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin et al.   RNA

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop

(2012) M. P. Guy et al.   RNA

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Optimal enzymes for amplifying sequencing libraries

(2011) Michael A Quail et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Do all modifications benefit all tRNAs?

(2009) Eric M. Phizicky et al.   FEBS LETTERS

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

(2009) H. Alexander Ebhardt et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

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