相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。The UCSC Genome Browser database: 2021 update
Jairo Navarro Gonzalez et al.
NUCLEIC ACIDS RESEARCH (2021)
R2DT is a framework for predicting and visualising RNA secondary structure using templates
Blake A. Sweeney et al.
NATURE COMMUNICATIONS (2021)
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
Blake A. Sweeney et al.
NUCLEIC ACIDS RESEARCH (2021)
Predicting transfer RNA gene activity from sequence and genome context
Bryan P. Thornlow et al.
GENOME RESEARCH (2020)
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
Pavel P. Kuksa et al.
BIOINFORMATICS (2019)
Arm-less mitochondrial tRNAs conserved for over 30 millions of years in spiders
Joan Pons et al.
BMC GENOMICS (2019)
RNAcentral: a hub of information for non-coding RNA sequences
Blake A. Sweeney et al.
NUCLEIC ACIDS RESEARCH (2019)
GenBank
Dennis A. Benson et al.
NUCLEIC ACIDS RESEARCH (2018)
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
Ioanna Kalvari et al.
NUCLEIC ACIDS RESEARCH (2018)
The unique tRNA(Sec) and its role in selenocysteine biosynthesis
Vitor Hugo Balasco Serrao et al.
AMINO ACIDS (2018)
Cut-and-Paste Transposons in Fungi with Diverse Lifestyles
Anna Muszewska et al.
GENOME BIOLOGY AND EVOLUTION (2017)
Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales
Raul Castanera et al.
BMC GENOMICS (2017)
Fungal Genomes and Insights into the Evolution of the Kingdom
Jason E. Stajich
MICROBIOLOGY SPECTRUM (2017)
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
Patricia P. Chan et al.
NUCLEIC ACIDS RESEARCH (2016)
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary et al.
NUCLEIC ACIDS RESEARCH (2016)
MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals
Hidenori Nishihara et al.
GENOME BIOLOGY AND EVOLUTION (2016)
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes
Stefanie Muehlhausen et al.
GENOME RESEARCH (2016)
NCBI prokaryotic genome annotation pipeline
Tatiana Tatusova et al.
NUCLEIC ACIDS RESEARCH (2016)
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
Todd M. Lowe et al.
NUCLEIC ACIDS RESEARCH (2016)
tRNA base methylation identification and quantification via high-throughput sequencing
Wesley C. Clark et al.
RNA (2016)
tRNA Biology in Mitochondria
Thalia Salinas-Giege et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2015)
Efficient and quantitative high-throughput tRNA sequencing
Guanqun Zheng et al.
NATURE METHODS (2015)
ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments
Aaron E. Cozen et al.
NATURE METHODS (2015)
Repbase Update, a database of repetitive elements in eukaryotic genomes
Weidong Bao et al.
MOBILE DNA (2015)
A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes)
Wei Shi et al.
BMC GENOMICS (2014)
Convergent evolution of AUA decoding in bacteria and archaea
Tsutomu Suzuki et al.
RNA BIOLOGY (2014)
Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors
Yoh-ichi Watanabe et al.
FRONTIERS IN GENETICS (2014)
Infernal 1.1: 100-fold faster RNA homology searches
Eric P. Nawrocki et al.
BIOINFORMATICS (2013)
The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens
Christopher J. Gobler et al.
ISME JOURNAL (2013)
Selenocysteine biosynthesis and insertion machinery in Naegleria gruberi
M. T. A. da Silva et al.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2013)
Tertiary structure of bacterial selenocysteine tRNA
Yuzuru Itoh et al.
NUCLEIC ACIDS RESEARCH (2013)
Horizontal gene transfer and the evolution of bacterial and archaeal population structure
Martin F. Polz et al.
TRENDS IN GENETICS (2013)
Evolution of selenoproteins in the metazoan
Liang Jiang et al.
BMC GENOMICS (2012)
Phytozome: a comparative platform for green plant genomics
David M. Goodstein et al.
NUCLEIC ACIDS RESEARCH (2012)
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
Frank Juehling et al.
NUCLEIC ACIDS RESEARCH (2012)
Composition and Evolution of the Vertebrate and Mammalian Selenoproteomes
Marco Mariotti et al.
PLOS ONE (2012)
Armless mitochondrial tRNAs in enoplea (nematoda)
Frank Juehling et al.
RNA BIOLOGY (2012)
Life without the essential bacterial tRNAIle2-lysidine synthetase TilS: a case of tRNA gene recruitment in Bacillus subtilis
Celine Fabret et al.
MOLECULAR MICROBIOLOGY (2011)
Accelerated Profile HMM Searches
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2011)
Discovery of permuted and recently split transfer RNAs in Archaea
Patricia P. Chan et al.
GENOME BIOLOGY (2011)
Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes
Henri Grosjean et al.
FEBS LETTERS (2010)
Large-Scale tRNA Intron Transposition in the Archaeal Order Thermoproteales Represents a Novel Mechanism of Intron Gain
Kosuke Fujishima et al.
MOLECULAR BIOLOGY AND EVOLUTION (2010)
The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions
Sinead C. Leahy et al.
PLOS ONE (2010)
Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes
Einat Hazkani-Covo et al.
PLOS GENETICS (2010)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios
Junichi Sugahara et al.
JOURNAL OF MOLECULAR EVOLUTION (2009)
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
Patricia P. Chan et al.
NUCLEIC ACIDS RESEARCH (2009)
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
Frank Juehling et al.
NUCLEIC ACIDS RESEARCH (2009)
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea
Kosuke Fujishima et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species
C. Gissi et al.
HEREDITY (2008)
Comprehensive Analysis of Archaeal tRNA Genes Reveals Rapid Increase of tRNA Introns in the Order Thermoproteales
Junichi Sugahara et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase
R. Lynn Sherrer et al.
NUCLEIC ACIDS RESEARCH (2008)
A probabilistic model of local sequence alignment that simplifies statistical significance estimation
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2008)
ARWEN:: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences
Dean Laslett et al.
BIOINFORMATICS (2008)
TFAM 1.0:: an online tRNA function classifier
Helena Taquist et al.
NUCLEIC ACIDS RESEARCH (2007)
Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life
Alexey V. Lobanov et al.
GENOME BIOLOGY (2007)
Differential annotation of tRNA genes with anticodon CAT in bacterial genomes
Francisco J. Silva et al.
NUCLEIC ACIDS RESEARCH (2006)
Identification of Leishmania selenoproteins and SECIS element
A. Cassago et al.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY (2006)
Methanococcus aeolicus sp nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments
Melissa M. Kendall et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2006)
The Plasmodium selenoproteome
AV Lobanov et al.
NUCLEIC ACIDS RESEARCH (2006)
TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase
DH Ardell et al.
NUCLEIC ACIDS RESEARCH (2006)
Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues
Yan Zhang et al.
GENOME BIOLOGY (2006)
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
Jonathan A. Eisen et al.
PLOS BIOLOGY (2006)
A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome
D San Mauro et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
A mutation in the anticodon of a single tRNAala is sufficient to confer auxin resistance in Arabidopsis
J Perry et al.
PLANT PHYSIOLOGY (2005)
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
P Schattner et al.
NUCLEIC ACIDS RESEARCH (2005)
The complete set of tRNA species in Nanoarchaeum equitans
L Randau et al.
FEBS LETTERS (2005)
A novel eukaryotic selenoprotein in the haptophyte alga Emiliania huxleyi
T Obata et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2005)
The genome of the social amoeba Dictyostelium discoideum
L Eichinger et al.
NATURE (2005)
Suppression of a mitotic mutant by tRNA-Ala anticodon mutations that produce a dominant defect in late mitosis
Y Kimata et al.
JOURNAL OF CELL SCIENCE (2004)
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
RA Gibbs et al.
NATURE (2004)
Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
EL Hendrickson et al.
JOURNAL OF BACTERIOLOGY (2004)
Automatic annotation of organellar genomes with DOGMA
SK Wyman et al.
BIOINFORMATICS (2004)
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
D Laslett et al.
NUCLEIC ACIDS RESEARCH (2004)
NUMTs in sequenced eukaryotic genomes
E Richly et al.
MOLECULAR BIOLOGY AND EVOLUTION (2004)
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications
C Marck et al.
RNA (2003)
tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features
C Marck et al.
RNA (2002)
Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii
SV Novoselov et al.
EMBO JOURNAL (2002)
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
AI Slesarev et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Horizontal gene transfer in prokaryotes: Quantification and classification
EV Koonin et al.
ANNUAL REVIEW OF MICROBIOLOGY (2001)
Search for characteristic structural features of mammalian mitochondrial tRNAs
M Helm et al.
RNA (2000)
Eukaryotic selenocysteine tRNA has the 9/4 secondary structure
T Mizutani et al.
FEBS LETTERS (2000)
分享论文
