PubRank

John F Atkins

Author PubWeight™ 97.15‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Recoding: translational bifurcations in gene expression. Gene 2002 2.72
2 An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci U S A 2008 2.54
3 Deletion of selenoprotein P alters distribution of selenium in the mouse. J Biol Chem 2003 2.27
4 Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 2011 2.16
5 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
6 Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res 2007 1.68
7 Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production. J Gen Virol 2011 1.61
8 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
9 Screening the SPO11 and EIF5A2 genes in a population of infertile men. Fertil Steril 2005 1.51
10 Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli. EMBO J 2003 1.51
11 Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res 2012 1.50
12 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
13 Readthrough of dystrophin stop codon mutations induced by aminoglycosides. Ann Neurol 2004 1.47
14 P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA 2004 1.46
15 RECODE 2003. Nucleic Acids Res 2003 1.46
16 Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J 2005 1.45
17 Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element. Nucleic Acids Res 2011 1.44
18 Recoding in bacteriophages and bacterial IS elements. Trends Genet 2006 1.43
19 Pyrrolysine and selenocysteine use dissimilar decoding strategies. J Biol Chem 2005 1.43
20 Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. Virol J 2008 1.33
21 Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression. Genome Biol 2005 1.33
22 Programmed ribosomal frameshifting in decoding the SARS-CoV genome. Virology 2005 1.33
23 uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs. Proc Natl Acad Sci U S A 2008 1.33
24 A case for "StopGo": reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go). RNA 2007 1.31
25 Release factor 2 frameshifting sites in different bacteria. EMBO Rep 2002 1.29
26 Computational identification of putative programmed translational frameshift sites. Bioinformatics 2002 1.25
27 Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1). Proc Natl Acad Sci U S A 2010 1.24
28 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
29 Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein. Proc Natl Acad Sci U S A 2012 1.22
30 Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides. RNA 2004 1.21
31 Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons. Nucleic Acids Res 2002 1.18
32 Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5. Nucleic Acids Res 2011 1.18
33 Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs. EMBO J 2003 1.16
34 Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res 2009 1.15
35 A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. J Biol Chem 2006 1.11
36 Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA 2003 1.10
37 Maintenance of the correct open reading frame by the ribosome. EMBO Rep 2003 1.09
38 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
39 Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses. Virology 2010 1.08
40 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
41 A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation. Nucleic Acids Res 2009 1.07
42 Production of selenoprotein P (Sepp1) by hepatocytes is central to selenium homeostasis. J Biol Chem 2012 1.06
43 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
44 rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics 2013 1.04
45 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
46 Identification of polymorphisms in the Hrb, GOPC, and Csnk2a2 genes in two men with globozoospermia. J Androl 2006 1.01
47 Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli. J Bacteriol 2005 1.00
48 Epitopes derived by incidental translational frameshifting give rise to a protective CTL response. J Immunol 2006 0.99
49 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
50 Frameshifting in alphaviruses: a diversity of 3' stimulatory structures. J Mol Biol 2010 0.96
51 Artificial neural network prediction of antisense oligodeoxynucleotide activity. Nucleic Acids Res 2002 0.95
52 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
53 Polyamine sensing during antizyme mRNA programmed frameshifting. Biochem Biophys Res Commun 2005 0.93
54 Comparative studies of frameshifting and nonframeshifting RNA pseudoknots: a mutational and NMR investigation of pseudoknots derived from the bacteriophage T2 gene 32 mRNA and the retroviral gag-pro frameshift site. RNA 2002 0.93
55 ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting. Bioinformatics 2006 0.92
56 Molecular biology. Translation goes global. Science 2011 0.91
57 Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA. EMBO J 2008 0.90
58 Translation: duality in the genetic code. Nature 2007 0.90
59 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
60 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
61 Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res 2013 0.86
62 Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses. Virol J 2009 0.86
63 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
64 Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene. Arch Virol 2008 0.84
65 Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory function. J Mol Evol 2010 0.84
66 Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene. Virol J 2008 0.84
67 Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs. BMC Bioinformatics 2008 0.83
68 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
69 The distinction between recoding and codon reassignment. Genetics 2010 0.82
70 Novel antizyme gene in Danio rerio expressed in brain and retina. Gene 2006 0.82
71 Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning. Virol J 2010 0.81
72 Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics 2004 0.81
73 Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). RNA Biol 2011 0.81
74 Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3' UTR. Proc Natl Acad Sci U S A 2014 0.80
75 The interplay of mRNA stimulatory signals required for AUU-mediated initiation and programmed -1 ribosomal frameshifting in decoding of transposable element IS911. J Bacteriol 2011 0.80
76 Versatile dual reporter gene systems for investigating stop codon readthrough in plants. PLoS One 2009 0.80
77 P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation. J Mol Biol 2005 0.80
78 Sequencing and haplotype analysis of the activator of CREM in the testis (ACT) gene in populations of fertile and infertile males. Mol Hum Reprod 2006 0.80
79 Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3. BMC Med Genet 2006 0.80
80 Evolutionary specialization of recoding: frameshifting in the expression of S. cerevisiae antizyme mRNA is via an atypical antizyme shift site but is still +1. RNA 2006 0.79
81 -1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222. J Bacteriol 2004 0.79
82 The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases. RNA 2006 0.78
83 A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product. Virol J 2009 0.77
84 Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene. Virol J 2009 0.76
85 Polyamine analogs with xylene rings induce antizyme frameshifting, reduce ODC activity, and deplete cellular polyamines. J Biochem 2006 0.75
86 Foot and Mouth's Achilles' heel? Nat Biotechnol 2008 0.75
87 Nailing fingerprints in the stars. Nature 2013 0.75
88 A cryptic lysis gene near the start of the Qbeta replicase gene in the +1 frame. Genes Cells 2004 0.75