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J

John F. Atkins

University College Cork

83H-index
378Paper Count
2.2WCitation Count
Published Papers 111
Publication Date
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Comprehensive analysis of yeast+1 ribosomal frameshifting unveils a novel stimulator supporting two distinct frameshifting mechanisms
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-12-11
err0
PREAI
errFenton, Darren A.; Bozko, Maria; Swirski, Michal, I; Loughran, Gary; Yordanova, Martina M.; Kufel, Joanna; Atkins, John F.; Baranov, Pavel, V
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Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function
errScience Advances
IF12.5
err2025-10-24
err0
PREAI
errGary Loughran; Raffaella De Pace; Ningyu Ding; Jianchao Zhang; Irwin Jungreis; Gionmattia Carancini; Jonathan M. Mudge; Ji Wang; Manolis Kellis; John F. Atkins; Pavel V. Baranov; Andrew E. Firth; Xiaowei Li; Juan S. Bonifacino; Yousuf A. Khan
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errSave
Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing
errRNA BIOLOGY
IF3.4
err2023-11-15
err0
errOAAI
errAntonov, Ivan V.; O'Loughlin, Sinead; Gorohovski, Alessandro N.; O'Connor, Patrick B. F.; Baranov, Pavel V.; Atkins, John F.
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errSave
Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease?
errFRONTIERS IN PHYSIOLOGY
IF3.4
err2023-06-30
err4
errOAAI
errVila-Sanjurjo, Anton; Mallo, Natalia; Atkins, John F.; Elson, Joanna L.; Smith, Paul M.
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errSave
Nontriplet feature of genetic code in Euplotes ciliates is a result of neutral evolution
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2023-05-22
err8
errOAAI
errGaydukova, Sofya A.; Moldovan, Mikhail A.; Vallesi, Adriana; Heaphy, Stephen M.; Atkins, John F.; Gelfand, Mikhail S.; V. Baranov, Pavel
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errSave
The Drosophila gene for antizyme requires ribosomal frameshifting for expression and contains an intronic gene for snRNP Sm D3 on the opposite strand
errMOLECULAR AND CELLULAR BIOLOGY
IF2.7
err2023-03-28
err41
errOAAI
errIvanov, IP; Simin, K; Letsou, A; Atkins, JF; Gesteland, RF
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errSave
The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services
errNATURE COMMUNICATIONS
IF15.7
err2023-02-25
err23
errOAAI
errFromm, Simon A. A.; O'Connor, Kate M. M.; Purdy, Michael; Bhatt, Pramod R. R.; Loughran, Gary; Atkins, John F. F.; Jomaa, Ahmad; Mattei, Simone
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errSave
Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts
errNUCLEIC ACIDS RESEARCH
IF13.1
err2022-12-19
err3
errOAAI
errLoughran, Gary; Li, Xiang; O'Loughlin, Sinead; Atkins, John F.; Baranov, Pavel, V
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errSave
Lack of evidence for ribosomal frameshifting in ATP7B mRNA decoding
errMOLECULAR CELL
IF16.6
err2022-10-01
err5
errOAAI
errLoughran, Gary; Fedorova, Alla D.; Khan, Yousuf A.; Atkins, John F.; Baranov, Pavel, V
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errSave
Maximum depth sequencing reveals an ON/OFF replication slippage switch and apparent in vivo selection for bifidobacterial pilus expression
errSCIENTIFIC REPORTS
IF3.9
err2022-06-10
err2
errOAAI
errPenno, Christophe; Motherway, Mary O'Connell; Fu, Yuan; Sharma, Virag; Crispie, Fiona; Cotter, Paul D.; Houeix, Benoit; Joshi, Lokesh; Bottacini, Francesca; O'Dwyer, Aoife; Loughran, Gary; Atkins, John F.; van Sinderen, Douwe
errShare
errSave
Immune cells alter genetic decoding in cancer
errNATURE
IF48.5
err2022-03-09
err0
PREAI
errBaranov, Pavel V.; Atkins, John F.
errShare
errSave
From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion
errVIRUSES-BASEL
IF3.5
err2021-06-27
err2
errOAAI
errAtkins, John F.; O'Connor, Kate M.; Bhatt, Pramod R.; Loughran, Gary
errShare
errSave
Tissue-specific dynamic codon redefinition in Drosophila
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2021-01-26
err11
errOAAI
errHudson, Andrew M.; Loughran, Gary; Szabo, Nicholas L.; Wills, Norma M.; Atkins, John F.; Cooley, Lynn
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errSave
Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2020-09-21
err25
errOAAI
errLoughran, Gary; Zhdanov, Alexander V.; Mikhaylova, Maria S.; Rozov, Fedor N.; Datskevich, Petr N.; Kovalchuk, Sergey I.; Serebryakova, Marina V.; Kiniry, Stephen J.; Michel, Audrey M.; O'Connor, Patrick B. F.; Papkovsky, Dmitri B.; Atkins, John F.; Baranov, Pavel V.; Shatsky, Ivan N.; Andreev, Dmitry E.
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errSave
The energy landscape of-1 ribosomal frameshifting
errSCIENCE ADVANCES
IF12.5
err2020-01-03
err43
errOAAI
errChoi, Junhong; O'Loughlin, Sinead; Atkins, John F.; Puglisi, Joseph D.
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errSave
Culmination of a half-century quest reveals insight into mutant tRNA-mediated frameshifting after tRNA departure from the decoding site
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2018-10-19
err2
errOAAI
errAtkins, John F.
errShare
errSave
Polyamine Control of Translation Elongation Regulates Start Site Selection on Antizyme Inhibitor mRNA via Ribosome Queuing
errMOLECULAR CELL
IF16.6
err2018-04-01
err102
errOAAI
errIvanov, Ivaylo P.; Shin, Byung-Sik; Loughran, Gary; Tzani, Ioanna; Young-Baird, Sara K.; Cao, Chune; Atkins, John F.; Dever, Thomas E.
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errSave
Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response
errJOURNAL OF BIOLOGICAL CHEMISTRY
IF3.9
err2018-03-01
err56
errOAAI
errLoughran, Gary; Jungreis, Irwin; Tzani, Ioanna; Power, Michael; Dmitriev, Ruslan I.; Ivanov, Ivaylo P.; Kellis, Manolis; Atkins, John F.
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errSave
Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P
errNUCLEIC ACIDS RESEARCH
IF13.1
err2017-10-23
err21
errOAAI
errMariotti, Marco; Shetty, Sumangala; Baird, Lisa; Wu, Sen; Loughran, Gary; Copeland, Paul R.; Atkins, John F.; Howard, Michael T.
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errSave
ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?
errBIOLOGY DIRECT
IF4.9
err2017-10-16
err13
errOAAI
errDinan, Adam M.; Atkins, John F.; Firth, Andrew E.
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errSave

Research Directions

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Co-authors
Cooperation Journals
R
Richard Smith
H-index: 160 · Papers: 4.8W
M
Manolis Kellis
H-index: 139 · Papers: 1.1K
V
Vadim N. Gladyshev
H-index: 123 · Papers: 786
J
Juan S. Bonifacino
H-index: 117 · Papers: 404
P
Paul D. Cotter
H-index: 113 · Papers: 729
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