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List of works by John F Atkins

-1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222

scientific article

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA

scientific article published on 21 May 2015

A [Cu]rious Ribosomal Profiling Pattern Leads to the Discovery of Ribosomal Frameshifting in the Synthesis of a Copper Chaperone.

scientific article published in January 2017

A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product

scientific article published on 08 September 2009

A case for trans translation.

scientific article published in February 1996

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

scientific article

A cryptic lysis gene near the start of the Qbeta replicase gene in the +1 frame.

scientific article

A dual-luciferase reporter system for studying recoding signals ⬇️

scientific article published on April 1, 1998

A functional mutant of tRNA(2Arg) with ten extra nucleotides in its TFC arm.

scientific article

A map of the restriction targets in yeast 2 micron plasmid DNA cloned on bacteriophage lambda

scientific article published on 01 November 1976

A nickel complex cleaves uridine in folded RNA structures: application to E. coli tmRNA and related engineered molecules

scientific article published on 01 June 1998

A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment

scientific article

A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation.

scientific article

A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures ⬇️

scientific article published on December 15, 1997

A three-way junction and constituent stem-loops as the stimulator for programmed -1 frameshifting in bacterial insertion sequence IS911.

scientific article published in March 1999

ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.

scientific article

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?

scientific article published on 16 October 2017

Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site

scientific article published on 13 January 2012

An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting

scientific article published on 5 July 2016

An overlapping essential gene in the Potyviridae

scholarly article

Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

scientific article

Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses

scientific article published on 17 March 2009

Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA.

scientific article published in June 2001

Attenuation of an amino-terminal premature stop codon mutation in the ATRX gene by an alternative mode of translational initiation.

scientific article published in December 2004

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

scientific article published on 11 August 2015

Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme

scientific journal article

Avoidance of reporter assay distortions from fused dual reporters

scientific article published on 25 April 2017

Bacteriophage T3 and T7 early RNAs are translated by eukaryotic 80S ribosomes: active phage T3 coded S-adenosylmethionine cleaving enzyme is synthesized ⬇️

scientific article published on August 1, 1976

Bacteriophages T7 and T3 as model systems for RNA synthesis and processing.

scientific article published on January 1976

Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function

scientific article

Biochemistry. The 22nd amino acid

scientific article

Bioinformatic analysis suggests that a conserved ORF in the waikaviruses encodes an overlapping gene

scientific article published on 6 June 2008

Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene

scientific article published on 20 May 2008

Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses

scientific article

Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning

scientific article

Cell-free synthesis of adenovirus 2 proteins programmed by fractionated messenger RNA: a comparison of polypeptide products and messenger RNA lengths.

scientific article published on July 1974

Characterization of ribosomal frameshift events by protein sequence analysis.

scientific article

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.

scientific article

Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

scientific article published on 10 April 2007

Control of Epistaxis in Patients with Hereditary Hemorrhagic Telangiectasia ⬇️

scientific article published on November 1, 1991

Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

scientific article

Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3' UTR.

scientific article published on 31 March 2014

Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation

scientific article published in August 1993

Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production

scientific article

Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma

scientific article

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

scientific article

Does Disparate Occurrence of Autoregulatory Programmed Frameshifting in Decoding the Release Factor 2 Gene Reflect an Ancient Origin with Loss in Independent Lineages? ⬇️

scientific article published on July 1, 1998

Does antizyme exist in Escherichia coli?

scientific article published on 01 September 1998

Doublet translocation at GGA is mediated directly by mutant tRNA(2Gly) ⬇️

scientific article published on June 1, 1992

Drop-off during ribosome hopping.

scientific article published on August 2001

E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent

scientific article published on 01 November 1989

Effects of 3'-terminal phosphates in RNA produced by ribozyme cleavage

scientific article published in June 1998

Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein

scientific article

Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides

scientific article

Electrophoresis, autoradiography and electroblotting of peptides: T4 gene 60 hopping

scientific article published on 01 October 1992

Enhanced differential synthesis of proteins in a mammalian cell-free system by addition of polyamines ⬇️

scientific article published on July 25, 1975

Epitopes derived by incidental translational frameshifting give rise to a protective CTL response

scientific article published in June 2006

Eubacterial tmRNAs: everywhere except the alpha-proteobacteria?

scientific article published on 01 July 1999

Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene

scientific article

Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses

scientific article

Evidence of efficient stop codon readthrough in four mammalian genes

scientific article

Evolution of DNA base compositions in microorganisms

scientific article published on 01 March 1972

Evolutionary specialization of recoding: frameshifting in the expression of S. cerevisiae antizyme mRNA is via an atypical antizyme shift site but is still +1.

scientific article published on 23 January 2006

External suppression of a frameshift mutant in salmonella.

scientific article

Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice

scientific article published on 05 January 2004

Flexibility of the nascent polypeptide chain within the ribosome--contacts from the peptide N-terminus to a specific region of the 30S subunit

scientific article

Foot and Mouth's Achilles' heel?

scientific article published on 01 December 2008

Frameshifting in alphaviruses: a diversity of 3' stimulatory structures

scientific article

Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA.

scientific article published in February 1999

Functional tRNAs with altered 3' ends

scientific article

Further mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments

article

Genetic instability associated with the aroC321 allele in Salmonella typhimurium involves genetic duplication.

scientific article published on January 1983

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

scientific article published on 21 July 2014

Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding

scientific article

Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements

scientific article

Identification of a New Antizyme mRNA +1 Frameshifting Stimulatory Pseudoknot in a Subset of Diverse Invertebrates and its Apparent Absence in Intermediate Species

article published in 2004

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

scientific article

Identification of novel polymorphisms in the nuclear protein genes and their relationship with human sperm protamine deficiency and severe male infertility

scientific article published on 20 September 2006

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

scientific article published on 16 March 2006

Identification of polymorphisms in the Hrb, GOPC, and Csnk2a2 genes in two men with globozoospermia.

scientific article

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome

scientific article

Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression.

scientific article

Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1) ⬇️

scientific article published on October 4, 2010

Intricacies of ribosomal frameshifting

scientific article published on 01 March 1999

Is UAA or UGA part of the recognition signal for ribosomal initiation? ⬇️

scientific article published on October 25, 1979

Location and identification of the genes for adenovirus type 2 early polypeptides

scientific article

Location of identification of the genes for adenovirus type 2 polypeptides

scientific article

Low Activity of β-Galactosidase in Frameshift Mutants of Escherichia coli ⬇️

scientific article published on May 1, 1972

Mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments ⬇️

scientific article published on April 1, 1975

Molecular biology. Translation goes global.

scientific article

Molecular biology: Antibiotic re-frames decoding

scientific article published in November 2013

Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P.

scientific article published on 23 October 2017

Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough.

scientific article

Mutants of translational components that alter reading frame by two steps forward or one step back

scientific article published in December 1988

Mutations which alter the elbow region of tRNA2Gly reduce T4 gene 60 translational bypassing efficiency.

scientific article published on May 1999

NS1' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness

scientific article

Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting

scientific article published on February 2000

Normal tRNAs promote ribosomal frameshifting ⬇️

scientific article published on December 1, 1979

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum

scientific article

Novel antizyme gene in Danio rerio expressed in brain and retina.

scientific article published on 30 August 2006

Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures.

scientific article published on January 1995

ODNBase--a web database for antisense oligonucleotide effectiveness studies. Oligodeoxynucleotides

scientific article published on 01 September 2000

Observation of dually decoded regions of the human genome using ribosome profiling data

scientific article

One protein from two open reading frames: mechanism of a 50 nt translational bypass.

scientific article

Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs

scientific article

Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression.

scientific article

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

scientific article published in January 2005

P-site tRNA is a crucial initiator of ribosomal frameshifting.

scientific article published on February 2004

Polyamine analogs with xylene rings induce antizyme frameshifting, reduce ODC activity, and deplete cellular polyamines.

scientific article

Polyamine sensing during antizyme mRNA programmed frameshifting

scientific article published on 27 October 2005

Position-dependent termination and widespread obligatory frameshifting in Euplotes translation.

scientific article

Prediction of antisense oligonucleotide efficacy by in vitro methods

scientific article published on 01 December 1998

Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons.

scientific article

Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches ⬇️

scientific article published on June 1, 1998

Production of selenoprotein P (Sepp1) by hepatocytes is central to selenium homeostasis

scientific article

Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators

scientific article published on 6 April 2015

Programmed frameshifting in the synthesis of mammalian antizyme is +1 in mammals, predominantly +1 in fission yeast, but −2 in budding yeast ⬇️

scientific article published on October 1, 1998

Programmed ribosomal frameshifting in decoding the SARS-CoV genome

scientific article

Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC).

scientific article

Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2

scientific article

Quadruplet codons: implications for code expansion and the specification of translation step size

scientific article published in April 2000

RECODE 2003.

scientific article published on January 2003

Reading two bases twice: mammalian antizyme frameshifting in yeast.

scientific article published in March 1996

Recode-2: new design, new search tools, and many more genes

scientific article

Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons.

scientific article

Recoding in bacteriophages and bacterial IS elements.

scientific article

Recoding: dynamic reprogramming of translation.

scientific article published on January 1996

Recoding: reprogrammed genetic decoding

scientific article published on 01 September 1992

Recoding: translational bifurcations in gene expression.

scientific article

Recurrent Emergence of Catalytically Inactive Ornithine Decarboxylase Homologous Forms That Likely Have Regulatory Function

article

Release factor 2 frameshifting sites in different bacteria.

scientific article published on 15 March 2002

Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe.

scientific article

Reported translational bypass in a trpR'-lacZ' fusion is accounted for by unusual initiation and +1 frameshifting.

scientific article published in August 1997

Resolution of the discrepancy between a gene translation--termination codon and the deduced sequence for release of the encoded polypeptide

scientific article published on 01 December 1983

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

scientific article (publication date: 6 September 2016)

Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome ⬇️

scientific article published on October 24, 2011

Ribosomal protein L9 interactions with 23 S rRNA: the use of a translational bypass assay to study the effect of amino acid substitutions.

scientific article

Screening the SPO11 and EIF5A2 genes in a population of infertile men.

scientific article

Sepp1(UF) forms are N-terminal selenoprotein P truncations that have peroxidase activity when coupled with thioredoxin reductase-1

scientific article published on 14 January 2014

Sequence of E.coli K12 valU operon which contains 3 genes for tRNA(Val1) and 1 gene for tRNA(Lys)

scientific article published in February 1990

Sequence specificity of aminoglycoside-induced stop condon readthrough: potential implications for treatment of Duchenne muscular dystrophy

scientific article published on 01 August 2000

Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli.

scientific article

Seven, eight and nine-membered anticodon loop mutants of tRNA(2Arg) which cause +1 frameshifting. Tolerance of DHU arm and other secondary mutations

scientific article published in December 1992

Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting

scientific article published on 01 January 1987

Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis

scientific article

Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage

scientific article

Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element

scientific article

Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5

scientific article

Structural organization of Escherichia coli tmRNA.

scientific article

Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%

scientific article

Structural studies of the RNA pseudoknot required for readthrough of the gag-termination codon of murine leukemia virus

scientific article published in May 1999

Structure of human ornithine decarboxylase antizyme 2 gene.

scientific article

Suppression of a -1 frameshift mutation by a recessive tRNA suppressor which causes doublet decoding.

scientific article

Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform

scientific article published on 25 May 2016

The distinction between recoding and codon reassignment

scientific article published on August 2010

The energy landscape of -1 ribosomal frameshifting

scientific article published on 01 January 2020

The forms of tRNATrp found in avian sarcoma virus and uninfected chicken cells have structural identity but functional distinctions

scientific article published in October 1980

The interplay of mRNA stimulatory signals required for AUU-mediated initiation and programmed -1 ribosomal frameshifting in decoding of transposable element IS911.

scientific article

The nucleotide sequence of the first externally suppressible--1 frameshift mutant, and of some nearby leaky frameshift mutants.

scientific article published in January 1983

The origin and destiny of adenovirus proteins

scientific article published in January 1975

The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases

scientific article

The role of EF-Tu and other translation components in determining translocation step size

scientific article published in August 1990

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

scientific article published on 20 February 2007

The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons

scientific article published in March 1991

The synthetase gene of the RNA phages R17, MS2 and f2 has a single UAG terminator codon

scientific article published in August 1975

The twenty-first amino acid

scientific article published in Nature

Theiler's murine encephalomyelitis virus contrasts with encephalomyocarditis and foot-and-mouth disease viruses in its functional utilization of the StopGo non-standard translation mechanism.

scientific article published on 24 October 2012

Thermodynamic calculations and statistical correlations for oligo-probes design.

scientific article

Transcription initiation in the histidine operon of Salmonella typhimurium.

scientific article

Transcriptional frameshifting rescues Citrobacter rodentium type VI secretion by the production of two length variants from the prematurely interrupted tssM gene

scientific article

Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression

scientific article

Transcriptional slippage in the positive-sense RNA virus family Potyviridae

scientific article

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity

scientific article

Translation: Duality in the genetic code

scientific article published in Nature

Translational recoding signals between gag and pol in diverse LTR retrotransposons.

scientific article published on December 2003

UGA and non-triplet suppressor reading of the genetic code

scientific article published in June 1974

Uninterrupted translation through putative 12-nucleotide coding gap in sequence of carA: business as usual.

scientific article published on January 1994

Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF

scientific article published on 21 September 2020

Utilization of selenocysteyl-tRNA[Ser]Sec and seryl-tRNA[Ser]Sec in protein synthesis.

scientific article published in November 1994

Versatile dual reporter gene systems for investigating stop codon readthrough in plants

scientific article

mRNA readout at 40.

scientific article

rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift

scientific article

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

scientific article published on 19 April 2013

tRNA and mRNA both in the same molecule

scientific article published on 01 June 1996

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