tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

R2DT is a framework for predicting and visualising RNA secondary structure using templates

(2021) Blake A. Sweeney et al.   Nature Communications

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders

(2019) Joan Pons et al.   BMC GENOMICS

Predicting transfer RNA gene activity from sequence and genome context

(2019) Bryan P. Thornlow et al.   GENOME RESEARCH

The unique tRNASec and its role in selenocysteine biosynthesis

(2018) Vitor Hugo Balasco Serrão et al.   AMINO ACIDS

DASHR 2.0: integrated database of human small non-coding RNA genes and mature products

(2018) Pavel P Kuksa et al.   BIOINFORMATICS

RNAcentral: a hub of information for non-coding RNA sequences

(2018) et al.   NUCLEIC ACIDS RESEARCH

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles

(2017) Anna Muszewska et al.   Genome Biology and Evolution

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals

(2016) Hidenori Nishihara et al.   Genome Biology and Evolution

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

(2016) Stefanie Mühlhausen et al.   GENOME RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

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

tRNA Biology in Mitochondria

(2015) Thalia Salinas-Giegé et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Convergent evolution of AUA decoding in bacteria and archaea

(2015) Tsutomu Suzuki et al.   RNA Biology

A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes)

(2014) Wei Shi et al.   BMC GENOMICS

Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors

(2014) Yoh-ichi Watanabe et al.   Frontiers in Genetics

Infernal 1.1: 100-fold faster RNA homology searches

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

The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens

(2013) Christopher J Gobler et al.   ISME Journal

Selenocysteine biosynthesis and insertion machinery in Naegleria gruberi

(2013) M.T.A. da Silva et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Tertiary structure of bacterial selenocysteine tRNA

(2013) Y. Itoh et al.   NUCLEIC ACIDS RESEARCH

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

Evolution of selenoproteins in the metazoan

(2012) Liang Jiang et al.   BMC GENOMICS

Composition and Evolution of the Vertebrate and Mammalian Selenoproteomes

(2012) Marco Mariotti et al.   PLoS One

Armless mitochondrial tRNAs in Enoplea (Nematoda)

(2012) Frank Jühling et al.   RNA Biology

Life without the essential bacterial tRNAIle2-lysidine synthetase TilS: a case of tRNA gene recruitment in Bacillus subtilis

(2011) Céline Fabret et al.   MOLECULAR MICROBIOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

(2011) Frank Jühling et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Discovery of permuted and recently split transfer RNAs in Archaea

(2011) Patricia P Chan et al.   GENOME BIOLOGY

Large-Scale tRNA Intron Transposition in the Archaeal Order Thermoproteales Represents a Novel Mechanism of Intron Gain

(2010) K. Fujishima et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

(2010) Sinead C. Leahy et al.   PLoS One

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios

(2009) Junichi Sugahara et al.   JOURNAL OF MOLECULAR EVOLUTION

Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea

(2009) Kosuke Fujishima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

(2008) C Gissi et al.   HEREDITY

Comprehensive Analysis of Archaeal tRNA Genes Reveals Rapid Increase of tRNA Introns in the Order Thermoproteales

(2008) Junichi Sugahara et al.   MOLECULAR BIOLOGY AND EVOLUTION

Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O -phosphoseryl-tRNA Sec kinase

(2008) R. Lynn Sherrer 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

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

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

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology