Published in Bioinformatics on August 01, 2002
tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Res (2006) 1.63
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS One (2007) 1.60
Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli. EMBO J (2003) 1.51
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations. PLoS One (2011) 1.44
Identification of stop codon readthrough genes in Saccharomyces cerevisiae. Nucleic Acids Res (2003) 1.42
Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.40
Mechanisms and implications of programmed translational frameshifting. Wiley Interdiscip Rev RNA (2012) 1.34
Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol (2005) 1.28
Preferred and avoided codon pairs in three domains of life. BMC Genomics (2008) 1.19
A programmed -1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element. Nucleic Acids Res (2004) 1.18
Predicting genes expressed via -1 and +1 frameshifts. Nucleic Acids Res (2004) 1.18
Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast. Nucleic Acids Res (2010) 1.09
A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol Biol Evol (2011) 1.08
ICDS database: interrupted CoDing sequences in prokaryotic genomes. Nucleic Acids Res (2006) 1.04
Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli. J Bacteriol (2005) 1.00
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. RNA (2011) 0.91
FELINES: a utility for extracting and examining EST-defined introns and exons. Nucleic Acids Res (2003) 0.90
Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning. Nat Rev Genet (2015) 0.88
Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res (2013) 0.86
Slipping and sliding: frameshift mutations in herpes simplex virus thymidine kinase and drug-resistance. Drug Resist Updat (2011) 0.86
Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation. Virol J (2010) 0.85
Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs. BMC Bioinformatics (2008) 0.83
On programmed ribosomal frameshifting: the alternative proteomes. Front Genet (2012) 0.82
FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots. Nucleic Acids Res (2009) 0.82
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res (2016) 0.82
Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol (2014) 0.81
The gateway pDEST17 expression vector encodes a -1 ribosomal frameshifting sequence. Nucleic Acids Res (2007) 0.81
Codon-triplet context unveils unique features of the Candida albicans protein coding genome. BMC Genomics (2007) 0.79
Recoding: translational bifurcations in gene expression. Gene (2002) 2.72
An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci U S A (2008) 2.54
Deletion of selenoprotein P alters distribution of selenium in the mouse. J Biol Chem (2003) 2.27
Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res (2011) 2.16
A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting. Virol J (2009) 1.69
Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res (2007) 1.68
Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production. J Gen Virol (2011) 1.61
Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res (2007) 1.55
Screening the SPO11 and EIF5A2 genes in a population of infertile men. Fertil Steril (2005) 1.51
Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli. EMBO J (2003) 1.51
Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res (2012) 1.50
NS1' of flaviviruses in the Japanese encephalitis virus serogroup is a product of ribosomal frameshifting and plays a role in viral neuroinvasiveness. J Virol (2009) 1.50
Readthrough of dystrophin stop codon mutations induced by aminoglycosides. Ann Neurol (2004) 1.47
P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA (2004) 1.46
RECODE 2003. Nucleic Acids Res (2003) 1.46
Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J (2005) 1.45
Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element. Nucleic Acids Res (2011) 1.44
Recoding in bacteriophages and bacterial IS elements. Trends Genet (2006) 1.43
Pyrrolysine and selenocysteine use dissimilar decoding strategies. J Biol Chem (2005) 1.43
Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. Virol J (2008) 1.33
Programmed ribosomal frameshifting in decoding the SARS-CoV genome. Virology (2005) 1.33
Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression. Genome Biol (2005) 1.33
uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs. Proc Natl Acad Sci U S A (2008) 1.33
Release factor 2 frameshifting sites in different bacteria. EMBO Rep (2002) 1.29
Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1). Proc Natl Acad Sci U S A (2010) 1.24
The selenium-rich C-terminal domain of mouse selenoprotein P is necessary for the supply of selenium to brain and testis but not for the maintenance of whole body selenium. J Biol Chem (2007) 1.22
Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein. Proc Natl Acad Sci U S A (2012) 1.22
Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. RNA (2004) 1.21
Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons. Nucleic Acids Res (2002) 1.18
Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res (2011) 1.18
Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs. EMBO J (2003) 1.16
Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res (2009) 1.15
A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. J Biol Chem (2006) 1.11
Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA (2003) 1.10
Maintenance of the correct open reading frame by the ribosome. EMBO Rep (2003) 1.09
A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol Biol Evol (2011) 1.08
Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses. Virology (2010) 1.08
Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression. RNA (2002) 1.08
A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation. Nucleic Acids Res (2009) 1.07
Production of selenoprotein P (Sepp1) by hepatocytes is central to selenium homeostasis. J Biol Chem (2012) 1.06
Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species. J Mol Biol (2004) 1.04
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics (2013) 1.04
Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site. Proc Natl Acad Sci U S A (2012) 1.03
Identification of polymorphisms in the Hrb, GOPC, and Csnk2a2 genes in two men with globozoospermia. J Androl (2006) 1.01
Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli. J Bacteriol (2005) 1.00
Epitopes derived by incidental translational frameshifting give rise to a protective CTL response. J Immunol (2006) 0.99
Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome. Proc Natl Acad Sci U S A (2011) 0.98
Frameshifting in alphaviruses: a diversity of 3' stimulatory structures. J Mol Biol (2010) 0.96
Artificial neural network prediction of antisense oligodeoxynucleotide activity. Nucleic Acids Res (2002) 0.95
Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice. J Biol Chem (2004) 0.95
Polyamine sensing during antizyme mRNA programmed frameshifting. Biochem Biophys Res Commun (2005) 0.93
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting. Bioinformatics (2006) 0.92
Molecular biology. Translation goes global. Science (2011) 0.91
Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA. EMBO J (2008) 0.90
Translation: duality in the genetic code. Nature (2007) 0.90
Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses. Virol J (2009) 0.89
Evaluation of recombinant caspase specificity by competitive substrates. Anal Biochem (2009) 0.88
A TRPC1 protein-dependent pathway regulates osteoclast formation and function. J Biol Chem (2013) 0.88
Sequence requirements for ribosome stalling by the arginine attenuator peptide. J Biol Chem (2010) 0.88
Identification of novel polymorphisms in the nuclear protein genes and their relationship with human sperm protamine deficiency and severe male infertility. Fertil Steril (2006) 0.87
The stringency of start codon selection in the filamentous fungus Neurospora crassa. J Biol Chem (2013) 0.86
Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses. Virol J (2009) 0.86
Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res (2013) 0.86
Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons. Biol Direct (2006) 0.85
Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene. Arch Virol (2008) 0.84
Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory function. J Mol Evol (2010) 0.84
Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene. Virol J (2008) 0.84
Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs. BMC Bioinformatics (2008) 0.83
Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL. Nucleic Acids Res (2010) 0.83