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John F. Atkins

University of Utah · US
Area of research
Molecular Biology · Genetics
Research interest
Research interests include RNA and protein synthesis mechanisms, RNA modifications and cancer, Bacterial Genetics and Biotechnology, and Bacteriophages and microbial interactions.
h-index
81
citations
20,395
works
330
NIH funding
primary concept
email

Recent publications

Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)
Nature Structural & Molecular Biology 2025cited by 25position: middledoi
Translon: a single term for translated regions
Nature Methods 2025cited by 10position: middledoi
Evaluating ribosomal frameshifting in CCR5 mRNA decoding
Nature 2022cited by 34position: lastdoi
Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding
Molecular Cell 2022cited by 16position: middledoi
Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts
Nucleic Acids Research 2022cited by 12position: middledoi
Tissue-specific dynamic codon redefinition in <i>Drosophila</i>
Proceedings of the National Academy of Sciences 2021cited by 21position: middledoi
The energy landscape of −1 ribosomal frameshifting
Science Advances 2020cited by 61position: middledoi
AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation
Nature 2018cited by 100position: middledoi
Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response
Journal of Biological Chemistry 2018cited by 80position: lastdoi
Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion
Emerging Topics in Life Sciences 2018cited by 38position: middledoi
Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection
PLoS ONE 2018cited by 34position: middledoi
Avoidance of reporter assay distortions from fused dual reporters
RNA 2017cited by 100position: lastdoi
Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity
mBio 2017cited by 31position: middledoi
Systematic analysis of the <i>PTEN</i> 5′ leader identifies a major AUU initiated proteoform
Open Biology 2016cited by 49position: middledoi
Transcriptional slippage in the positive‐sense RNA virus family Potyviridae
EMBO Reports 2015cited by 240position: middledoi
Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions
Cell 2015cited by 53position: middledoi
A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA
Journal of Biological Chemistry 2015cited by 27position: lastdoi
Evidence of efficient stop codon readthrough in four mammalian genes
Nucleic Acids Research 2014cited by 247position: lastdoi
Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3′ UTR
Proceedings of the National Academy of Sciences 2014cited by 56position: middledoi
Sepp1UF forms are N-terminal selenoprotein P truncations that have peroxidase activity when coupled with thioredoxin reductase-1
Free Radical Biology and Medicine 2014cited by 49position: middledoi
High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide
Nature Communications 2014cited by 41position: middledoi
Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli
Nucleic Acids Research 2014cited by 40position: middledoi
Discontinuous Triplet Decoding with or without Re-Pairing by Peptidyl tRNA
ASM Press eBooks 2014cited by 25position: firstdoi
rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
Bioinformatics 2013cited by 55position: middledoi
An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response
Science 2012cited by 638position: middledoi
Production of Selenoprotein P (Sepp1) by Hepatocytes Is Central to Selenium Homeostasis
Journal of Biological Chemistry 2012cited by 161position: middledoi
Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the +1 direction
Open Biology 2012cited by 86position: lastdoi
Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site
Proceedings of the National Academy of Sciences 2012cited by 64position: middledoi

Grants

1979 Science Faculty Professional Development Program
NSF7914933$15,3381979–1982PIRePORTER

Frequent collaborators

· 10 papers (2014–2022) · 9 papers (2012–2022)Pavel V. Baranov · University College Cork8 papers (2013–2022)Ivaylo P. Ivanov · National Institutes of Health5 papers (2014–2018)Norma M. Wills · University of Utah4 papers (2012–2021) · 3 papers (2015–2018) · 3 papers (2016–2018)Yousuf A. Khan · Howard Hughes Medical Institute2 papers (2022–2022)Amy K. Motley · Vanderbilt University Medical Center2 papers (2012–2014) · 2 papers (2012–2014) · 2 papers (2018–2022)Irwin Jungreis · Massachusetts Institute of Technology2 papers (2014–2018)Jeffery K. Taubenberger · Tulane University2 papers (2012–2012)Sen Wu · Jiangnan University2 papers (2012–2014) · 2 papers (2016–2018)Patrick B. F. O’Connor · University College Cork2 papers (2013–2018) · 2 papers (2015–2020)Brett W. Jagger · National Institute of Allergy and Infectious Diseases2 papers (2012–2012)Matthew S. Sachs · University of Illinois Chicago2 papers (2015–2017)Paul Digard · University of Edinburgh2 papers (2012–2012)