Senior Research Fellow
Biochemistry
University College Cork
Cork
Ireland

T: +353-21-490-3000
E: j.atkins@ucc.ie

John went from Dunmanway Co. Cork to obtain his degrees from the Department of Genetics in Trinity College Dublin (where he is an Honorary Professor). He is engaged in doing research full time though there have been brief periods when he also lectured (in UCC's Biochem. Dept.) or was also an administrator (the first Director for Life Sciences in Science Foundation Ireland). Apart from the excitement of the dramatic technical and conceptual advances in molecular biology, John gets pleasure from interacting with some great outside collaborators and UCC lab members several of whom are benefiting from his ongoing work in the Department of Human Genetics in the University of Utah. Our lab in UCC is part of the BioSciences Institute and John is a member of both the Biochemistry and Microbiology Departments. Other memberships include EMBO, RIA and the RNA Society.

Research Interests

Genetic decoding is dynamic. It can be altered in an mRNA- or site-specific manner and in a remarkable variety of ways. The meaning of individual codons can be redefined in response to signals in mRNA. A proportion of translating ribosomes can be diverted at a specific site to a different reading frame. They can also be directed to bypass a block of nucleotides - at least up to 50 - or even to resume on a different mRNA. We are studying these "recoding" phenomena to determine where they occur, understand their functional significance, elucidate the mechanisms involved, and where desirable plot intervention strategies.


Recoding is used for a subset of mRNAs in probably all organisms with some types being most prevalent in the decoding of viral genomes and mobile elements. In some cases it is exploited for regulatory purposes. In others it yields an extra product with distinctive functions at a set ratio to the product of standard decoding (as in HIV decoding). One class of codon redefinition involves UGA specifying the 21st encoded amino acid, selenocysteine rather than termination (our studies of this aspect are focused on the mammalian selenoprotein P mRNA coding sequence where there are 10 UGA codons, all of them specifying selenocysteine).


A variety of recoding signals are used to reprogram the ribosomes. Some are mRNA signals 5' of the recoding site, others are specific nascent peptide signals encoded 5' of the recoding site, that interact with the ribosome peptide exit tunnel to cause conformational alterations. Yet others are 3' of the recoding site - and only some of these are a variety of specific intra-mRNA structure. Synthetic trans-acting small RNAs can mimic the effect of certain recoding signals to ameliorate mutant phenotypes, but whether any natural small RNAs act in trans as recoding signals is unknown but ripe for investigation. With increasing structural knowledge of ribosome conformational changes, the prospect of at last understanding how ribosomes sense and respond to recoding signals is approaching.


The most immediately exciting prospects are being able to systematically find where recoding is utilized. The deluge of DNA sequence information and its analysis is facilitating this. However, a recently developed technique that permits identification of the location and framing of all ribosomes promises to be a bonanza and allow the realization of a dream that for a long time seemed distant. In a broader perspective we interested in the multiple unrecognized types of RNA with diverse roles in gene expression that are being discovered and characterized. The implications of the roles of some RNAs in present day organisms for hypotheses of the origin of protein synthesis and an ancient RNA World are fascinating.

Books

YearPublication
(2011)RNA Worlds: From life’s origins to diversity in gene regulation.
J.F. Atkins, R.F. Gesteland and T.R. Cech (eds). (2011) RNA Worlds: From life’s origins to diversity in gene regulation. New York: Cold Spring Harbor Laboratory Press. [Details]
(2010)Recoding: Expansion of Decoding rules enriches gene expression.
J.F. Atkins and R.F. Gesteland. (2010) Recoding: Expansion of Decoding rules enriches gene expression. New York: Springer. [Details]
(2006)The RNA World. The Nature of modern RNA suggests a prebiotic RNA World.
R.F. Gesteland, T.R. Cech and J.F. Atkins. (2006) The RNA World. The Nature of modern RNA suggests a prebiotic RNA World. Cold Spring Harbor, New York: Cold Spring Harbor Lab. Press. Globe icon [Details]
(2000)Bringing RNA into view: RNA and its roles in biology.
J.F. Atkins, A. Ellington, B.E. Friedman, R.F. Gesteland, H.F. Noller, S.M. Pasquale, R.D. Storey, O.C. Uhlenbeck and A.M. Weiner. (2000) Bringing RNA into view: RNA and its roles in biology. Colorado Springs: Colorado Springs. Globe icon [Details]
(1999)Dynamics of the Genetic Code. in The RNA World. 2nd edition. (eds. R.F. Gesteland, T.R. Cech and J.F. Atkins).
J.F. Atkins, A. Böck, S. Matsufuji and R.F. Gesteland. (1999) Dynamics of the Genetic Code. in The RNA World. 2nd edition. (eds. R.F. Gesteland, T.R. Cech and J.F. Atkins). Cold Spring Harbor: Cold Spring Harbor Laboratory Press. [Details]
(1993)The RNA World. The Nature of modern RNA suggests a prebiotic RNA World.
R.F. Gesteland and J.F. Atkins, eds. (1993) The RNA World. The Nature of modern RNA suggests a prebiotic RNA World. New York: Cold Spring Harbor Laboratory Press. Globe icon [Details]

Book Chapters

YearPublication
(2010)'Complementary studies in the histidine operon and on frameshifting: A compliment to what Roth has wrought'
J.F. Atkins. (2010) 'Complementary studies in the histidine operon and on frameshifting: A compliment to what Roth has wrought' In: The Lure of Bacterial Genetics: a Tribute to John Roth. S. Maloy, K. Hughes and J. Casadesus (eds.). Washington D.C: ASM press. [Details]
(2006)'The shapely mRNA: Knotting ventured, knotting gained'
J.F. Atkins, R.F. Gesteland, R.J. Jackson and N.M. Wills. (2006) 'The shapely mRNA: Knotting ventured, knotting gained' In: The RNA World, 3rd Ed. R.F. Gesteland, T.R. Cech & J.F. Atkins, eds. Cold Spring Harbor, New York: Cold Spring Harbor Lab. Press. [Details]
(2006)'Major update of article on “Frameshifting”'
J.F. Atkins and R.F. Gesteland. (2006) 'Major update of article on “Frameshifting”' In: Encyclopedia of Life Sciences. North America: John Wiley & Sons, Ltd. [Details]
(2003)'Recoding: Site- or mRNA-specific alteration of genetic readout utilized for gene expression'
I. P. Ivanov, O.L. Gurvich, R.F. Gesteland and J.F. Atkins. (2003) 'Recoding: Site- or mRNA-specific alteration of genetic readout utilized for gene expression' In: Translation Mechanisms eds J. Lapointe and L. Brakier-Gingras. New York: Kluwer Academic /Plenum Publishers. [Details]
(2000)'Poking a hole in the sanctity of the triplet code: Inferences for framing'
J. F. Atkins, A.J. Herr, C. Massiere, M. O’Connor, I. Ivanov and R.F. Gesteland. (2000) 'Poking a hole in the sanctity of the triplet code: Inferences for framing' In: The Ribosome. Structure, Function, Antibiotics and Cellular Interactions.(eds R.A. Garrett, S.R. Douthwaite, A. Liljas, A.T. Matheson, P.B. Moore and H.F. Noller). Washington D.C: ASM press. [Details]
(1999)'The RNA World'
J.F. Atkins, A. Böck, S. Matsufuji and R.F. Gesteland. (1999) 'The RNA World' In: Dynamics of the Genetic Code. Cold Spring Harbor: Cold Spring Harbor Laboratory Press. [Details]
(1995)'Discontinuous triplet decoding with, or without, pairing by peptidyl tRNA'
J.F. Atkins and R.F. Gesteland. (1995) 'Discontinuous triplet decoding with, or without, pairing by peptidyl tRNA' In: Transfer RNA (eds. D. Söll and U. RajBhandary). Washington D.C: ASM Publications. [Details]
(1993)'“Stop Codons”'
J.F. Atkins and R.F. Gesteland. (1993) '“Stop Codons”' In: The Encyclopedia of Molecular Biology (ed. T.E. Creighton). New York: Wiley Publishers. [Details]
(1993)'“Start Codons”'
J.F. Atkins and R.F. Gesteland. (1993) '“Start Codons”' In: The Encyclopedia of Molecular Biology (ed. T.E. Creighton). New York: Wiley Publishers. [Details]
(1993)'Nonsense Codons and Unassigned Codons'
J.F. Atkins, K. Watanabe and S. Yokobori. (1993) 'Nonsense Codons and Unassigned Codons' In: The Encyclopedia of Molecular Biology (ed. T.E. Creighton). New York: Wiley Publishers. [Details]
(1993)'“The Genetic Code”'
J.F. Atkins, R.F. Gesteland and K. Watanabe. (1993) '“The Genetic Code”' In: The Encyclopedia of Molecular Biology (ed. T.E. Creighton). New York: Wiley Publishers. [Details]
(1993)'“Degeneracy of the Genetic Code”'
J.F. Atkins and R.F. Gesteland. (1993) '“Degeneracy of the Genetic Code”' In: The Encyclopedia of Molecular Biology (ed. T.E. Creighton). New York: Wiley Publishers. [Details]
(1993)'“Wobble Pairing”'
K. Watanabe, T. Ueda and J.F. Atkins. (1993) '“Wobble Pairing”' In: The Encyclopedia of Molecular Biology (ed. T.E. Creighton). New York: Wiley Publishers. [Details]

Abstract

YearPublication
(1984)REPLACEMENT OF ANTICODON-LOOP NUCLEOTIDES TO PRODUCE FUNCTIONAL TRANSFER-RNAS.
BRUCE, AG,ATKINS, JF,WILLS, N,BARE, L,UHLENBECK, O,GESTELAND, RF (1984) REPLACEMENT OF ANTICODON-LOOP NUCLEOTIDES TO PRODUCE FUNCTIONAL TRANSFER-RNAS. Abstract [Details]

Audiovisual material

YearPublication
(2008)Recoding. Getting more out of the message by shifting reading frame and redefining codon meaning. in Steitz, T. (ed.).
J.F. Atkins and R.F. Gesteland. (2008) Recoding. Getting more out of the message by shifting reading frame and redefining codon meaning. in Steitz, T. (ed.). Audiovisual material Globe icon [Details]

Peer Reviewed Journals

YearPublication
(2015)'A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA'
Yordanova MM, Wu C, Andreev DE, Sachs MS, Atkins JF (2015) 'A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA'. The Journal of Biological Chemistry, 290 (29):17863-17878 [DOI] [Details]
(2015)'Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators'
Penno, Christophe,Sharma, Virag,Coakley, Arthur,Motherway, Mary O'Connell,van Sinderen, Douwe,Lubkowska, Lucyna,Kireeva, Maria L.,Kashlev, Mikhail,Baranov, Pavel V.,Atkins, John F. (2015) 'Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators'. Proceedings of the National Academy of Sciences of the United States of America, 112 (1616) Globe icon [Details]
(2014)'Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding'
Kwun, Hyun Jin,Toptan, Tuna,da Silva, Suzane Ramos,Atkins, John F.,Moore, Patrick S.,Chang, Yuan (2014) 'Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding'. Proceedings of the National Academy of Sciences of the United States of America, 111 (4141) Globe icon [Details]
(2014)'Transcriptional Frameshifting Rescues Citrobacter rodentium Type VI Secretion by the Production of Two Length Variants from the Prematurely Interrupted tssM Gene'
Gueguen, Erwan,Wills, Norma M.,Atkins, John F.,Cascales, Eric (2014) 'Transcriptional Frameshifting Rescues Citrobacter rodentium Type VI Secretion by the Production of Two Length Variants from the Prematurely Interrupted tssM Gene'. Plos Genetics, 10 (1212) Globe icon [Details]
(2014)'Evidence of efficient stop codon readthrough in four mammalian genes'
Loughran G, Chou MY, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV, Atkins JF (2014) 'Evidence of efficient stop codon readthrough in four mammalian genes'. Nucleic acids research, 42 (14):8928-8938 [DOI] [Details]
(2014)'High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide'
Samatova, E,Konevega, AL,Wills, NM,Atkins, JF,Rodnina, MV (2014) 'High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide'. Nature Communications, 5 [DOI] [Details]
(2014)'Sepp1UF is a truncated N-terminal form of selenoprotein P that has peroxidase activity when coupled with thioredoxin reductase-1'
S. Kurokawa, S. Eriksson, K.L. Rose, S. Wu, A.K. Motley, S. Hill, V.P. Winfrey, W.H. McDonald, M.R. Capecchi, J.F. Atkins, E.S.J. Arnér, K.E. Hill and R.F. Burk. (2014) 'Sepp1UF is a truncated N-terminal form of selenoprotein P that has peroxidase activity when coupled with thioredoxin reductase-1'. Free Radical Biology & Medicine, (69):67-76 [Details]
(2014)'Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli'
Sharma V, Prère MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O (2014) 'Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli'. Nucleic acids research, [DOI] [Details]
(2014)'Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding'
Kwun, HJ,Toptan, T,da Silva, SR,Atkins, JF,Moore, PS,Chang, Y (2014) 'Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding'. Proceedings of The National Academy of Sciences of The United States of America, 111 :4342-4349 [DOI] [Details]
(2014)'Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3 ' UTR'
Goodenough, E,Robinson, TM,Zook, MB,Flanigan, KM,Atkins, JF,Howard, MT,Eisenlohr, LC (2014) '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 of The United States of America, 111 :5670-5675 [DOI] [Details]
(2013)'Molecular biology: Antibiotic re-frames decoding'
Atkins JF, Baranov PV (2013) 'Molecular biology: Antibiotic re-frames decoding'. Nature, 503 (7477):478-479 [DOI] [Details]
(2013)'rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments'
O'Connor, PBF,Li, GW,Weissman, JS,Atkins, JF,Baranov, PV (2013) 'rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments'. Bioinformatics (Oxford, England), 29 :1488-1491 [DOI] [Details]
(2013)'Identification of the nature of reading frame transitions observed in prokaryotic genomes'
Antonov, I,Coakley, A,Atkins, JF,Baranov, PV,Borodovsky, M (2013) 'Identification of the nature of reading frame transitions observed in prokaryotic genomes'. Nucleic Acids Research, 41 :6514-6530 [DOI] [Details]
(2013)'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'
Loughran, G,Libbey, JE,Uddowla, S,Scallan, MF,Ryan, MD,Fujinami, RS,Rieder, E,Atkins, JF (2013) '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'. The Journal of General Virology, 94 :348-353 [DOI] [Details]
(2012)'Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site'
Ren, Q,Wang, QS,Firth, AE,Chan, MMY,Gouw, JW,Guarna, MM,Foster, LJ,Atkins, JF,Jan, E (2012) 'Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site'. Proceedings of The National Academy of Sciences of The United States of America, 109 :630-639 [DOI] [Details]
(2012)'Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the+1 direction'
Firth, AE,Jagger, BW,Wise, HM,Nelson, CC,Parsawar, K,Wills, NM,Napthine, S,Taubenberger, JK,Digard, P,Atkins, JF (2012) 'Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the+1 direction'. Open Biology, 2 [DOI] [Details]
(2012)'Observation of dually decoded regions of the human genome using ribosome profiling data'
Michel, AM,Choudhury, KR,Firth, AE,Ingolia, NT,Atkins, JF,Baranov, PV (2012) 'Observation of dually decoded regions of the human genome using ribosome profiling data'. Genome Research, 22 :2219-2229 [DOI] [Details]
(2012)'Efficient-2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein'
Fang, Y,Treffers, EE,Li, YH,Tas, A,Sun, Z,van der Meer, Y,de Ru, AH,van Veelen, PA,Atkins, JF,Snijder, EJ,Firth, AE (2012) 'Efficient-2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein'. Proceedings of The National Academy of Sciences of The United States of America, 109 :2920-2928 [DOI] [Details]
(2012)'The Biological Higgs'
H. Ledford. (2012) 'The Biological Higgs'. Nature, :528-530 [Details]
(2012)'Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5'
Loughran, G,Sachs, MS,Atkins, JF,Ivanov, IP (2012) 'Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5'. Nucleic Acids Research, 40 :2898-2906 [DOI] [Details]
(2012)'An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response'
Jagger, BW,Wise, HM,Kash, JC,Walters, KA,Wills, NM,Xiao, YL,Dunfee, RL,Schwartzman, LM,Ozinsky, A,Bell, GL,Dalton, RM,Lo, A,Efstathiou, S,Atkins, JF,Firth, AE,Taubenberger, JK,Digard, P (2012) 'An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response'. Science (New York, N.Y.), 337 :199-204 [DOI] [Details]
(2012)'Production of Selenoprotein P (Sepp1) by Hepatocytes Is Central to Selenium Homeostasis'
Hill, KE,Wu, S,Motley, AK,Stevenson, TD,Winfrey, VP,Capecchi, MR,Atkins, JF,Burk, RF (2012) 'Production of Selenoprotein P (Sepp1) by Hepatocytes Is Central to Selenium Homeostasis'. The Journal of Biological Chemistry, 287 :40414-40424 [DOI] [Details]
(2011)'A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment'
Sharma V, Firth AE, Antonov I, Fayet O, Atkins JF, Borodovsky M, Baranov PV (2011) 'A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment'. Molecular Biology and Evolution, 28 (11):3195-3211 [DOI] [Details]
(2011)'Stimulation of stop codon readthrough: frequent presence of an extended 3 ' RNA structural element'
Firth, AE,Wills, NM,Gesteland, RF,Atkins, JF; (2011) 'Stimulation of stop codon readthrough: frequent presence of an extended 3 ' RNA structural element'. Nucleic Acids Research, 39 :6679-6691 [DOI] [Details]
(2011)'Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)'
Baranov, PV,Wills, NM,Barriscale, KA,Firth, AE,Jud, MC,Letsou, A,Manning, G,Atkins, JF; (2011) 'Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC)'. RNA biology, 8 :637-647 [DOI] [Details]
(2011)'Translation goes global'
R.B. Weiss and J.F. Atkins. (2011) 'Translation goes global'. Science, 334 :1509-1510 [Details]
(2011)'Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production'
Firth, AE,Zevenhoven-Dobbe, JC,Wills, NM,Go, YY,Balasuriya, UBR,Atkins, JF,Snijder, EJ,Posthuma, CC; (2011) 'Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production'. The Journal of General Virology, 92 :1097-1106 [DOI] [Details]
(2011)'Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL'
Gurvich, OL,Nasvall, SJ,Baranov, PV,Bjork, GR,Atkins, JF; (2011) 'Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL'. Nucleic Acids Research, 39 :3079-3092 [DOI] [Details]
(2011)'The Interplay of mRNA Stimulatory Signals Required for AUU-Mediated Initiation and Programmed-1 Ribosomal Frameshifting in Decoding of Transposable Element IS911'
Prere, MF,Canal, I,Wills, NM,Atkins, JF,Fayet, O; (2011) 'The Interplay of mRNA Stimulatory Signals Required for AUU-Mediated Initiation and Programmed-1 Ribosomal Frameshifting in Decoding of Transposable Element IS911'. Journal of Bacteriology, 193 :2735-2744 [DOI] [Details]
(2011)'Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences'
Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV (2011) 'Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences'. Nucleic Acids Research, 39 (10):4220-4234 [DOI] [Details]
(2011)'Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome'
Loughran, G,Firth, AE,Atkins, JF (2011) 'Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome'. Proceedings of The National Academy of Sciences of The United States of America, 108 :1111-1119 [DOI] [Details]
(2011)'Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences'
Ivanov, IP,Firth, AE,Michel, AM,Atkins, JF,Baranov, PV; (2011) 'Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences'. Nucleic Acids Research, 39 :4220-4234 [DOI] [Details]
(2010)'NS1 ' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness'
Melian, EB,Hinzman, E,Nagasaki, T,Firth, AE,Wills, NM,Nouwens, AS,Blitvich, BJ,Leung, J,Funk, A,Atkins, JF,Hall, R,Khromykh, AA; (2010) 'NS1 ' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness'. Journal of Virology, 84 :1641-1647 [DOI] [Details]
(2010)'Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for+1 frame overlapping genes accessed by leaky scanning'
Firth, AE,Atkins, JF; (2010) 'Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for+1 frame overlapping genes accessed by leaky scanning'. Virology Journal, 7 [DOI] [Details]
(2010)'Frameshifting in Alphaviruses: A Diversity of 3 ' Stimulatory Structures'
Chung, BYW,Firth, AE,Atkins, JF; (2010) 'Frameshifting in Alphaviruses: A Diversity of 3 ' Stimulatory Structures'. Journal of Molecular Biology, 397 :448-456 [DOI] [Details]
(2010)'Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses'
Firth, AE,Blitvich, BJ,Wills, NM,Miller, CL,Atkins, JF; (2010) 'Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses'. Virology, 399 :153-166 [DOI] [Details]
(2010)'Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1)'
Ivanov, IP,Loughran, G,Sachs, MS,Atkins, JF; (2010) 'Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1)'. Science, 107 :18056-18060 [DOI] [Details]
(2010)'Recurrent Emergence of Catalytically Inactive Ornithine Decarboxylase Homologous Forms That Likely Have Regulatory Function'
Ivanov, IP,Firth, AE,Atkins, JF; (2010) 'Recurrent Emergence of Catalytically Inactive Ornithine Decarboxylase Homologous Forms That Likely Have Regulatory Function'. Journal of Molecular Evolution, 70 :289-302 [DOI] [Details]
(2010)'The distinction between recoding and codon reassignment'
Atkins JF, Baranov PV (2010) 'The distinction between recoding and codon reassignment'. Genetics, 185 (4):1535-1536 [DOI] [Details]
(2010)'Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses'
Firth, AE; Blitvich, BJ; Wills, NM; Miller, CL; Atkins, JF; (2010) 'Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses'. Virology, 399 (1):153-166 [DOI] [Details]
(2010)'A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation'
Ivanov, IP; Atkins, JF; Michael, AJ; (2010) 'A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation'. Nucleic Acids Research, 38 (2):353-359 [DOI] [Details]
(2010)'Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning'
Firth, AE; Atkins, JF; (2010) 'Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning'. Virology Journal, 7 [DOI] [Details]
(2010)'Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory function'
Ivanov, IP; Firth, AE; Atkins, JF; (2010) 'Recurrent emergence of catalytically inactive ornithine decarboxylase homologous forms that likely have regulatory function'. Journal of Molecular Evolution, 70 (3):289-302 [DOI] [Details]
(2010)'Recode-2: new design, new search tools, and many more genes'
Bekaert, M; Firth, AE; Zhang, Y; Gladyshev, VN; Atkins, JF; Baranov, PV; (2010) 'Recode-2: new design, new search tools, and many more genes'. Nucleic acids research, [DOI] [Details]
(2009)'Versatile dual reporter gene systems for investigating stop codon readthrough in plants'
Lao, NT; Maloney, AP; Atkins, JF; Kavanagh, TA; (2009) 'Versatile dual reporter gene systems for investigating stop codon readthrough in plants'. Plos One, 4 (10) [DOI] [Details]
(2009)'A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment'
Atkins JF, Björk GR; (2009) 'A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment'. Microbiology and Molecular Biology Reviews, 73 (1):178-210 [DOI] [Details]
(2009)'Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses'
Firth, AE; Wang, QS; Jan, E; Atkins, JF; (2009) 'Bioinformatic evidence for a stem-loop structure 5'-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses'. Virology Journal, 6 (6) [DOI] [Details]
(2009)'Evidence for a novel coding sequence overlapping the 5 '-terminal similar to 90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene'
Firth, AE,Atkins, JF; (2009) 'Evidence for a novel coding sequence overlapping the 5 '-terminal similar to 90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene'. Virology Journal, 6 [DOI] [Details]
(2009)'A Conserved Predicted Pseudoknot In The Ns2a-Encoding Sequence of West Nile and Japanese Encephalitis Flaviviruses Suggests Ns1 ' May Derive From Ribosomal Frameshifting'
Firth, AE, Atkins, JF; (2009) 'A Conserved Predicted Pseudoknot In The Ns2a-Encoding Sequence of West Nile and Japanese Encephalitis Flaviviruses Suggests Ns1 ' May Derive From Ribosomal Frameshifting'. Virology Journal, 6 (NA) [DOI] [Details]
(2009)'Bioinformatic evidence for a stem-loop structure 5 '-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses'
Firth, AE,Wang, QS,Jan, E,Atkins, JF; (2009) 'Bioinformatic evidence for a stem-loop structure 5 '-adjacent to the IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses'. Virology Journal, 6 [DOI] [Details]
(2009)'Analysis of The Coding Potential of The Partially Overlapping 3 ' Orf In Segment 5 of The Plant Fijiviruses'
Firth, AE, Atkins, JF; (2009) 'Analysis of The Coding Potential of The Partially Overlapping 3 ' Orf In Segment 5 of The Plant Fijiviruses'. Virology Journal, 6 (NA) [DOI] [Details]
(2009)'A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product'
Firth AE, Atkins JF; (2009) 'A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product'. Virology Journal, 6 [DOI] [Details]
(2008)'Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene'
A.E. Firth. (2008) 'Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene'. Journal of Virology, 5 (48) [Details]
(2008)'Translational Bypassing Without Peptidyl-Trna Anticodon Scanning of Coding Gap Mrna'
Wills, NM, O'Connor, M, Nelson, CC, Rettberg, CC, Huang, WM, Gesteland, RF, Atkins, JF; (2008) 'Translational Bypassing Without Peptidyl-Trna Anticodon Scanning of Coding Gap Mrna'. The Embo Journal, 27 (19):2533-2544 [DOI] [Details]
(2008)'Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs'
Bekaert, M,Ivanov, IP,Atkins, JF,Baranov, PV; (2008) 'Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs'. BMC Bioinformatics, 9 [DOI] [Details]
(2008)'Bioinformatic Analysis Suggests That A Conserved Orf In The Waikaviruses Encodes An Overlapping Gene'
Firth, AE, Atkins, JF; (2008) 'Bioinformatic Analysis Suggests That A Conserved Orf In The Waikaviruses Encodes An Overlapping Gene'. Archives of Virology, 153 (7):1379-1383 [DOI] [Details]
(2008)'Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma'
Firth, AE,Chung, BYW,Fleeton, MN,Atkins, JF; (2008) 'Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma'. Virology Journal, 5 [DOI] [Details]
(2008)'uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs'
Ivanov, IP,Loughran, G,Atkins, JF; (2008) 'uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs'. Proceedings of The National Academy of Sciences of The United States of America, 105 :10079-10084 [DOI] [Details]
(2008)'An overlapping essential gene in the Potyviridae'
Chung, BYW,Miller, WA,Atkins, JF,Firth, AE; (2008) 'An overlapping essential gene in the Potyviridae'. Proceedings of The National Academy of Sciences of The United States of America, 105 :5897-5902 [DOI] [Details]
(2008)'Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene'
Firth, AE,Atkins, JF; (2008) 'Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene'. Virology Journal, 5 [DOI] [Details]
(2008)'Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma'
Firth AE, Chung BY, Fleeton MN, Atkins JF; (2008) 'Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma'. Virology Journal, 5 [DOI] [Details]
(2008)'Foot and Mouth's Achilles' heel?'
Atkins JF, Ryan MD; (2008) 'Foot and Mouth's Achilles' heel?'. Nature Biotechnology, 26 (12):1335-1336 [DOI] [Details]
(2007)'Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation'
Ivanov IP, Atkins JF; (2007) 'Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation'. Nucleic Acids Research, 35 (6):1842-1858 [DOI] [Details]
(2007)'Comparison of approaches for rational siRNA design leading to a new efficient and transparent method'
Matveeva O, Nechipurenko Y, Rossi L, Moore B, Saetrom P, Ogurtsov AY, Atkins JF, Shabalina SA; (2007) 'Comparison of approaches for rational siRNA design leading to a new efficient and transparent method'. Nucleic Acids Research, 35 (8) [DOI] [Details]
(2007)'Translation: duality in the genetic code'
Atkins JF, Baranov PV; (2007) 'Translation: duality in the genetic code'. Nature, 448 (7157):1004-1005 [DOI] [Details]
(2007)'Comparison of Approaches For Rational Sirna Design Leading to A New Efficient and Transparent Method'
Matveeva, O, Nechipurenko, Y, Rossi, L, Moore, B, Saetrom, P, Ogurtsov, AY, Atkins, JF, Shabalina, SA; (2007) 'Comparison of Approaches For Rational Sirna Design Leading to A New Efficient and Transparent Method'. Nucleic Acids Research, 35 (8) [DOI] [Details]
(2007)'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'
Hill, KE, Zhou, JD, Austin, LM, Motley, AK, Ham, AJL, Olson, GE, Atkins, JF, Gesteland, RF, Burk, RF; (2007) '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'. The Journal of Biological Chemistry, 282 (15):10972-10980 [DOI] [Details]
(2007)'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)'
Atkins, JF,Wills, NM,Loughran, G,Wu, CY,Parsawar, K,Ryan, MD,Wang, CH,Nelson, CC; (2007) '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-A Publication of The Rna Society, 13 :803-810 [DOI] [Details]
(2007)'Comparison of approaches for rational siRNA design leading to a new efficient and transparent method'
Matveeva, O,Nechipurenko, Y,Rossi, L,Moore, B,Saetrom, P,Ogurtsov, AY,Atkins, JF,Shabalina, SA; (2007) 'Comparison of approaches for rational siRNA design leading to a new efficient and transparent method'. Nucleic Acids Research, 35 [DOI] [Details]
(2007)'Novel Antizyme Gene In Danio Rerio Expressed In Brain and Retina'
Ivanov, IP, Pittman, AJ, Chien, CB, Gesteland, RF, Atkins, JF; (2007) 'Novel Antizyme Gene In Danio Rerio Expressed In Brain and Retina'. Gene, 387 (1-2):87-92 [DOI] [Details]
(2006)'ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting'
Bekaert M, Atkins JF, Baranov PV; (2006) 'ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting'. Bioinformatics (Oxford, England), 22 (20):2463-2465 [DOI] [Details]
(2006)'Polyamine analogs with xylene rings induce antizyme frameshifting, reduce ODC activity, and deplete cellular polyamines'
Petros LM, Graminski GF, Robinson S, Burns MR, Kisiel N, Gesteland RF, Atkins JF, Kramer DL, Howard MT, Weeks RS; (2006) 'Polyamine analogs with xylene rings induce antizyme frameshifting, reduce ODC activity, and deplete cellular polyamines'. Journal of Biochemistry, 140 (5):657-666 [DOI] [Details]
(2006)'Epitopes derived by incidental translational frameshifting give rise to a protective CTL response'
Zook MB, Howard MT, Sinnathamby G, Atkins JF, Eisenlohr LC; (2006) 'Epitopes derived by incidental translational frameshifting give rise to a protective CTL response'. Journal of Immunology, 176 (11):6928-6934 [Details]
(2006)'Identification of novel polymorphisms in the nuclear protein genes and their relationship with human sperm protamine deficiency and severe male infertility'
Aoki VW, Christensen GL, Atkins JF, Carrell DT; (2006) 'Identification of novel polymorphisms in the nuclear protein genes and their relationship with human sperm protamine deficiency and severe male infertility'. Fertility and Sterility, 86 (5):1416-1422 [DOI] [Details]
(2006)'Recoding in bacteriophages and bacterial IS elements'
Baranov PV, Fayet O, Hendrix RW, Atkins JF; (2006) 'Recoding in bacteriophages and bacterial IS elements'. Trends Genetics, 22 (3):174-181 [DOI] [Details]
(2006)'Sequencing and haplotype analysis of the activator of CREM in the testis (ACT) gene in populations of fertile and infertile males'
Christensen GL, Wooding SP, Ivanov IP, Atkins JF, Carrell DT; (2006) 'Sequencing and haplotype analysis of the activator of CREM in the testis (ACT) gene in populations of fertile and infertile males'. Human Reproduction, 12 (4):257-262 [DOI] [Details]
(2006)'Identification of polymorphisms in the Hrb, GOPC, and Csnk2a2 genes in two men with globozoospermia'
Christensen GL, Ivanov IP, Atkins JF, Campbell B, Carrell DT; (2006) 'Identification of polymorphisms in the Hrb, GOPC, and Csnk2a2 genes in two men with globozoospermia'. Journal of Andrology, 27 (1):11-15 [DOI] [Details]
(2006)'The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases'
Wills NM, Atkins JF; (2006) 'The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases'. Rna-A Publication of The Rna Society, 12 (7):1149-1153 [DOI] [Details]
(2006)'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'
Baranov PV, Vestergaard B, Hamelryck T, Gesteland RF, Nyborg J, Atkins JF; (2006) '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'. Biology Direct, 1 [DOI] [Details]
(2006)'A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene'
Wills NM, Moore B, Hammer A, Gesteland RF, Atkins JF; (2006) 'A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene'. The Journal of Biological Chemistry, 281 (11):7082-7088 [DOI] [Details]
(2006)'Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3'
Christensen GL, Ivanov IP, Wooding SP, Atkins JF, Mielnik A, Schlegel PN, Carrell DT; (2006) 'Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3'. Gene, 7 [DOI] [Details]
(2006)'Epitopes derived by incidental translational frameshifting give rise to a protective CTL response'
Zook, MB,Howard, MT,Sinnathamby, G,Atkins, JF,Eisenlohr, LC; (2006) 'Epitopes derived by incidental translational frameshifting give rise to a protective CTL response'. Journal of Immunology, 176 :6928-6934 [Details]
(2006)'The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases'
Wills, NM,Atkins, JF; (2006) 'The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases'. Rna-A Publication of The Rna Society, 12 :1149-1153 [DOI] [Details]
(2006)'Evolutionary specialization of recoding: frameshifting in the expression of S. cerevisiae antizyme mRNA is via an atypical antizyme shift site but is still +1'
Ivanov IP, Gesteland RF, Atkins JF; (2006) '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-A Publication of The Rna Society, 12 (3):332-337 [DOI] [Details]
(2006)'Arfa: A Program For Annotating Bacterial Release Factor Genes, Including Prediction of Programmed Ribosomal Frameshifting'
Bekaert, M, Atkins, JF, Baranov, PV; (2006) 'Arfa: A Program For Annotating Bacterial Release Factor Genes, Including Prediction of Programmed Ribosomal Frameshifting'. Bioinformatics (Oxford, England), 22 (20):2463-2465 [DOI] [Details]
(2006)'Evolutionary specialization of recoding: Frameshifting in the expression of S-cerevisiae antizyme mRNA is via an atypical antizyme shift site but is still+1'
Ivanov, IP,Gesteland, RF,Atkins, JF; (2006) '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-A Publication of The Rna Society, 12 :332-337 [DOI] [Details]
(2005)'Polyamine sensing during antizyme mRNA programmed frameshifting'
Petros LM, Howard MT, Gesteland RF, Atkins JF; (2005) 'Polyamine sensing during antizyme mRNA programmed frameshifting'. Biochemical and Biophysical Research Communications, 338 (3):1478-1489 [DOI] [Details]
(2005)'Screening the SPO11 and EIF5A2 genes in a population of infertile men'
Christensen GL, Ivanov IP, Atkins JF, Mielnik A, Schlegel PN, Carrell DT; (2005) 'Screening the SPO11 and EIF5A2 genes in a population of infertile men'. Fertility and Sterility, 84 (3):758-760 [DOI] [Details]
(2005)'Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons'
Howard MT, Aggarwal G, Anderson CB, Khatri S, Flanigan KM, Atkins JF; (2005) 'Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons'. The Embo Journal, 24 (8):1596-1607 [DOI] [Details]
(2005)'Pyrrolysine and selenocysteine use dissimilar decoding strategies'
Zhang Y, Baranov PV, Atkins JF, Gladyshev VN; (2005) 'Pyrrolysine and selenocysteine use dissimilar decoding strategies'. The Journal of Biological Chemistry, 280 (21):20740-20751 [DOI] [Details]
(2005)'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'
Bucklin DJ, Wills NM, Gesteland RF, Atkins JF; (2005) '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'. Journal of Molecular Biology, 345 (1):39-49 [DOI] [Details]
(2005)'Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression'
Baranov PV, Hammer AW, Zhou J, Gesteland RF, Atkins JF; (2005) 'Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression'. Genome Canada, 6 (3) [DOI] [Details]
(2005)'Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli'
Gurvich OL, Baranov PV, Gesteland RF, Atkins JF; (2005) 'Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli'. Journal of Bacteriology, 187 (12):4023-4032 [DOI] [Details]
(2005)'Programmed ribosomal frameshifting in decoding the SARS-CoV genome'
Baranov, P.V. et al; (2005) 'Programmed ribosomal frameshifting in decoding the SARS-CoV genome'. Virology, (332):498-510 [Details]
(2005)'Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons'
Howard, MT,Aggarwal, G,Anderson, CB,Khatri, S,Flanigan, KM,Atkins, JF; (2005) 'Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons'. The Embo Journal, 24 :1596-1607 [DOI] [Details]
(2005)'Programmed ribosomal frameshifting in decoding the SARS-CoV genome'
Baranov, PV,Henderson, CM,Anderson, CB,Gesteland, RF,Atkins, JF,Howard, MT; (2005) 'Programmed ribosomal frameshifting in decoding the SARS-CoV genome'. Virology, 332 :498-510 [DOI] [Details]
(2005)'Polyamine sensing during antizyme mRNA programmed frameshifting'
Petros, LM,Howard, MT,Gesteland, RF,Atkins, JF (2005) 'Polyamine sensing during antizyme mRNA programmed frameshifting'. Biochemical and Biophysical Research Communications, 338 :1478-1489 [DOI] [Details]
(2005)'Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression'
Baranov, PV,Hammer, AW,Zhou, JD,Gesteland, RF,Atkins, JF; (2005) 'Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression'. Genome Biology, 6 [DOI] [Details]
(2005)'Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli'
Gurvich, OL,Baranov, PV,Gesteland, RF,Atkins, JF; (2005) 'Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli'. Journal of Bacteriology, 187 :4023-4032 [DOI] [Details]
(2005)'Pyrrolysine and selenocysteine use dissimilar decoding strategies'
Zhang, Y,Baranov, PV,Atkins, JF,Gladyshev, VN; (2005) 'Pyrrolysine and selenocysteine use dissimilar decoding strategies'. The Journal of Biological Chemistry, 280 :20740-20751 [DOI] [Details]
(2004)'Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice'
Herr AJ, Wills NM, Nelson CC, Gesteland RF, Atkins JF; (2004) 'Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice'. The Journal of Biological Chemistry, 279 (12):11081-11087 [DOI] [Details]
(2004)'A cryptic lysis gene near the start of the Q beta replicase gene in the+1 frame'
Nishihara, T,Morisawa, H,Ohta, N,Atkins, JF,Nishimura, Y (2004) 'A cryptic lysis gene near the start of the Q beta replicase gene in the+1 frame'. Genes To Cells, 9 :877-889 [DOI] [Details]
(2004)'A cryptic lysis gene near the start of the Qbeta replicase gene in the +1 frame'
Nishihara T, Morisawa H, Ohta N, Atkins JF, Nishimura Y; (2004) 'A cryptic lysis gene near the start of the Qbeta replicase gene in the +1 frame'. Cell, 9 (10):877-889 [DOI] [Details]
(2004)'P-site tRNA is a crucial initiator of ribosomal frameshifting'
Baranov PV, Gesteland RF, Atkins JF; (2004) 'P-site tRNA is a crucial initiator of ribosomal frameshifting'. Rna-A Publication of The Rna Society, 10 (2):221-230 [Details]
(2004)'Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides'
Howard MT, Gesteland RF, Atkins JF; (2004) 'Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides'. Rna-A Publication of The Rna Society, 10 (10):1653-1661 [DOI] [Details]
(2004)'Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species'
Ivanov IP, Anderson CB, Gesteland RF, Atkins JF; (2004) 'Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species'. Journal of Molecular Biology, 339 (3):495-504 [DOI] [Details]
(2004)'Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome'
Matveeva OV, Foley BT, Nemtsov VA, Gesteland RF, Matsufuji S, Atkins JF, Ogurtsov AY, Shabalina SA; (2004) 'Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome'. BMC Bioinformatics, 5 [DOI] [Details]
(2004)'Readthrough of dystrophin stop codon mutations induced by aminoglycosides'
Howard MT, Anderson CB, Fass U, Khatri S, Gesteland RF, Atkins JF, Flanigan KM; (2004) 'Readthrough of dystrophin stop codon mutations induced by aminoglycosides'. Annals of Neurology, 55 (3):422-426 [DOI] [Details]
(2004)'-1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222'
Mejlhede N, Licznar P, Prère MF, Wills NM, Gesteland RF, Atkins JF, Fayet O; (2004) '-1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222'. Journal of Bacteriology, 186 (10):3274-3277 [Details]
(2004)'Attenuation of an amino-terminal premature stop codon mutation in the ATRX gene by an alternative mode of translational initiation'
Howard MT, Malik N, Anderson CB, Voskuil JL, Atkins JF, Gibbons RJ; (2004) 'Attenuation of an amino-terminal premature stop codon mutation in the ATRX gene by an alternative mode of translational initiation'. Gene, 41 (12):951-956 [DOI] [Details]
(2004)'Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome'
Matveeva, OV,Foley, BT,Nemtsov, VA,Gesteland, RF,Matsufuji, S,Atkins, JF,Ogurtsov, AY,Shabalina, SA; (2004) 'Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome'. BMC Bioinformatics, 5 [DOI] [Details]
(2003)'Thermodynamic criteria for high hit rate antisense oligonucleotide design'
Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF, Freier SM; (2003) 'Thermodynamic criteria for high hit rate antisense oligonucleotide design'. Nucleic Acids Research, 31 (17):4989-4994 [Details]
(2003)'RECODE 2003'
Baranov PV, Gurvich OL, Hammer AW, Gesteland RF, Atkins JF; (2003) 'RECODE 2003'. Nucleic Acids Research, 31 (1):87-89 [Details]
(2003)'Maintenance of the correct open reading frame by the ribosome'
Hansen TM, Baranov PV, Ivanov IP, Gesteland RF, Atkins JF; (2003) 'Maintenance of the correct open reading frame by the ribosome'. Embo Reports, 4 (5):499-504 [DOI] [Details]
(2003)'Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs'
Licznar P, Mejlhede N, Prère MF, Wills N, Gesteland RF, Atkins JF, Fayet O; (2003) 'Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs'. The Embo Journal, 22 (18):4770-4778 [DOI] [Details]
(2003)'Translational recoding signals between gag and pol in diverse LTR retrotransposons'
Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF; (2003) 'Translational recoding signals between gag and pol in diverse LTR retrotransposons'. Rna-A Publication of The Rna Society, 9 (12):1422-1430 [Details]
(2003)'Thermodynamic calculations and statistical correlations for oligo-probes design'
Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF; (2003) 'Thermodynamic calculations and statistical correlations for oligo-probes design'. Nucleic Acids Research, 31 (14):4211-4217 [Details]
(2003)'Deletion of selenoprotein P alters distribution of selenium in the mouse'
Hill KE, Zhou J, McMahan WJ, Motley AK, Atkins JF, Gesteland RF, Burk RF; (2003) 'Deletion of selenoprotein P alters distribution of selenium in the mouse'. The Journal of Biological Chemistry, 278 (16):13640-13646 [DOI] [Details]
(2003)'Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli'
Gurvich OL, Baranov PV, Zhou J, Hammer AW, Gesteland RF, Atkins JF; (2003) 'Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli'. The Embo Journal, 22 (21):5941-5950 [DOI] [Details]
(2002)'Artificial neural network prediction of antisense oligodeoxynucleotide activity'
Giddings MC, Shah AA, Freier S, Atkins JF, Gesteland RF, Matveeva OV; (2002) 'Artificial neural network prediction of antisense oligodeoxynucleotide activity'. Nucleic Acids Research, 30 (19):4295-4304 [Details]
(2002)'Recoding: translational bifurcations in gene expression'
Baranov PV, Gesteland RF, Atkins JF; (2002) 'Recoding: translational bifurcations in gene expression'. Gene, 286 (2):187-201 [Details]
(2002)'Computational identification of putative programmed translational frameshift sites'
Shah AA, Giddings MC, Parvaz JB, Gesteland RF, Atkins JF, Ivanov IP; (2002) 'Computational identification of putative programmed translational frameshift sites'. Bioinformatics (Oxford, England), 18 (8):1046-1053 [Details]
(2002)'Release factor 2 frameshifting sites in different bacteria'
Baranov PV, Gesteland RF, Atkins JF; (2002) 'Release factor 2 frameshifting sites in different bacteria'. Embo Reports, 3 (4):373-377 [DOI] [Details]
(2002)'Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression'
Bertrand C, Prère MF, Gesteland RF, Atkins JF, Fayet O; (2002) 'Influence of the stacking potential of the base 3' of tandem shift codons on -1 ribosomal frameshifting used for gene expression'. Rna-A Publication of The Rna Society, 8 (1):16-28 [Details]
(2002)'Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons'
Harrell L, Melcher U, Atkins JF; (2002) 'Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons'. Nucleic Acids Research, 30 (9):2011-2017 [Details]
(2002)'Biochemistry. The 22nd amino acid'
Atkins JF, Gesteland R; (2002) 'Biochemistry. The 22nd amino acid'. Science, 296 (5572):1409-1410 [DOI] [Details]
(2002)'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'
Wang Y, Wills NM, Du Z, Rangan A, Atkins JF, Gesteland RF, Hoffman DW; (2002) '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-A Publication of The Rna Society, 8 (8):981-996 [Details]
(2001)'Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature'
Felden B, Massire C, Westhof E, Atkins JF, Gesteland RF; (2001) 'Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature'. Nucleic Acids Research, 29 (7):1602-1607 [Details]
(2001)'Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA'
Herr AJ, Nelson CC, Wills NM, Gesteland RF, Atkins JF; (2001) 'Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA'. Journal of Molecular Biology, 309 (5):1029-1048 [DOI] [Details]
(2001)'RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression'
Baranov PV, Gurvich OL, Fayet O, Prère MF, Miller WA, Gesteland RF, Atkins JF, Giddings MC; (2001) 'RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression'. Nucleic Acids Research, 29 (1):264-267 [Details]
(2001)'Genetic Code: Readout at 40'
Atkins JF, Gesteland RF; (2001) 'Genetic Code: Readout at 40'. Nature, 414 (693) [DOI] [Details]
(2001)'Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes'
Howard MT, Shirts BH, Zhou J, Carlson CL, Matsufuji S, Gesteland RF, Weeks RS, Atkins JF; (2001) 'Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes'. Cell, 6 (11):931-941 [Details]
(2001)'Drop-off during ribosome hopping'
Herr AJ, Wills NM, Nelson CC, Gesteland RF, Atkins JF; (2001) 'Drop-off during ribosome hopping'. Journal of Molecular Biology, 311 (3):445-452 [DOI] [Details]
(2001)'Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression'
Atkins JF, Baranov PV, Fayet O, Herr AJ, Howard MT, Ivanov IP, Matsufuji S, Miller WA, Moore B, Prère MF, Wills NM, Zhou J, Gesteland RF; (2001) 'Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression'. Cold Spring Harbor Symposia On Quantitative Biology, 66 :217-232 [Details]
(2000)'The twenty-first amino acid'
Atkins JF, Gesteland RF; (2000) 'The twenty-first amino acid'. Nature, 407 (6803) [DOI] [Details]
(2000)'Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity'
Matveeva OV, Tsodikov AD, Giddings M, Freier SM, Wyatt JR, Spiridonov AN, Shabalina SA, Gesteland RF, Atkins JF; (2000) 'Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity'. Nucleic Acids Research, 28 (15):2862-2865 [Details]
(2000)'Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit'
Ivanov IP, Gesteland RF, Atkins JF; (2000) 'Antizyme expression: a subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit'. Nucleic Acids Research, 28 (17):3185-3196 [Details]
(2000)'The 23 S rRNA environment of ribosomal protein L9 in the 50 S ribosomal subunit'
Lieberman KR, Firpo MA, Herr AJ, Nguyenle T, Atkins JF, Gesteland RF, Noller HF; (2000) 'The 23 S rRNA environment of ribosomal protein L9 in the 50 S ribosomal subunit'. Journal of Molecular Biology, 297 (5):1129-1143 [DOI] [Details]
(2000)'Decoding of tandem quadruplets by adjacent tRNAs with eight-base anticodon loops'
Moore B, Nelson CC, Persson BC, Gesteland RF, Atkins JF; (2000) 'Decoding of tandem quadruplets by adjacent tRNAs with eight-base anticodon loops'. Nucleic Acids Research, 28 (18):3615-3624 [Details]
(2000)'Conservation of polyamine regulation by translational frameshifting from yeast to mammals'
Ivanov IP, Matsufuji S, Murakami Y, Gesteland RF, Atkins JF; (2000) 'Conservation of polyamine regulation by translational frameshifting from yeast to mammals'. The Embo Journal, 19 (8):1907-1917 [DOI] [Details]
(2000)'Discovery of a spermatogenesis stage-specific ornithine decarboxylase antizyme: antizyme 3'
Ivanov IP, Rohrwasser A, Terreros DA, Gesteland RF, Atkins JF; (2000) 'Discovery of a spermatogenesis stage-specific ornithine decarboxylase antizyme: antizyme 3'. Proceedings of The National Academy of Sciences of The United States of America, 97 (9):4808-4813 [DOI] [Details]
(2000)'ODNBase--a web database for antisense oligonucleotide effectiveness studies. Oligodeoxynucleotides'
Giddings MC, Matveeva OV, Atkins JF, Gesteland RF; (2000) 'ODNBase--a web database for antisense oligonucleotide effectiveness studies. Oligodeoxynucleotides'. Bioinformatics (Oxford, England), 16 (9):843-844 [Details]
(2000)'Quadruplet codons: implications for code expansion and the specification of translation step size'
Moore B, Persson BC, Nelson CC, Gesteland RF, Atkins JF; (2000) 'Quadruplet codons: implications for code expansion and the specification of translation step size'. Journal of Molecular Biology, 298 (2):195-209 [DOI] [Details]
(2000)'One protein from two open reading frames: mechanism of a 50 nt translational bypass'
Herr AJ, Gesteland RF, Atkins JF; (2000) 'One protein from two open reading frames: mechanism of a 50 nt translational bypass'. The Embo Journal, 19 (11):2671-2680 [DOI] [Details]
(2000)'Coupling of open reading frames by translational bypassing'
Herr AJ, Atkins JF, Gesteland RF; (2000) 'Coupling of open reading frames by translational bypassing'. Annual Review of Biochemistry, 69 :343-372 [DOI] [Details]
(2000)'Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting'
Larsen B, Wills NM, Nelson C, Atkins JF, Gesteland RF; (2000) 'Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting'. Proceedings of The National Academy of Sciences of The United States of America, 97 (4):1683-1688 [Details]
(2000)'Sequence specificity of aminoglycoside-induced stop condon readthrough: potential implications for treatment of Duchenne muscular dystrophy'
Howard MT, Shirts BH, Petros LM, Flanigan KM, Gesteland RF, Atkins JF; (2000) 'Sequence specificity of aminoglycoside-induced stop condon readthrough: potential implications for treatment of Duchenne muscular dystrophy'. Annals of Neurology, 48 (2):164-169 [Details]
(1999)'Structure of human ornithine decarboxylase antizyme 2 gene'
Zhou J, Atkins JF, Gesteland RF; (1999) 'Structure of human ornithine decarboxylase antizyme 2 gene'. Gene, 232 (2):165-171 [Details]
(1999)'A three-way junction and constituent stem-loops as the stimulator for programmed -1 frameshifting in bacterial insertion sequence IS911'
Rettberg CC, Prère MF, Gesteland RF, Atkins JF, Fayet O; (1999) 'A three-way junction and constituent stem-loops as the stimulator for programmed -1 frameshifting in bacterial insertion sequence IS911'. Journal of Molecular Biology, 286 (5):1365-1378 [DOI] [Details]
(1999)'Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA'
Nameki N, Felden B, Atkins JF, Gesteland RF, Himeno H, Muto A; (1999) 'Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA'. Journal of Molecular Biology, 286 (3):733-744 [Details]
(1999)'Mutations which alter the elbow region of tRNA2Gly reduce T4 gene 60 translational bypassing efficiency'
Herr AJ, Atkins JF, Gesteland RF; (1999) 'Mutations which alter the elbow region of tRNA2Gly reduce T4 gene 60 translational bypassing efficiency'. The Embo Journal, 18 (10):2886-2896 [DOI] [Details]
(1999)'Structural studies of the RNA pseudoknot required for readthrough of the gag- termination codon of Murine Leukemia Virus'
S. L. Alam, N.M. Wills, J.A. Ingram, J.F. Atkins and R.F. Gesteland. (1999) 'Structural studies of the RNA pseudoknot required for readthrough of the gag- termination codon of Murine Leukemia Virus'. Journal of Molecular Biology, 288 :837-852 [Details]
(1999)'Eubacterial tmRNAs: everywhere except the alpha-proteobacteria?'
Felden B, Gesteland RF, Atkins JF; (1999) 'Eubacterial tmRNAs: everywhere except the alpha-proteobacteria?'. Biochimica Et Biophysica Acta, 1446 (1-2):145-148 [Details]
(1999)'Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG'
Mejlhede N, Atkins JF, Neuhard J; (1999) 'Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG'. Journal of Bacteriology, 181 (9):2930-2937 [Details]
(1999)'Ribosomal –1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG'
N. Mejlhede, J.F. Atkins and J. Neuhard. (1999) 'Ribosomal –1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG'. The Journal of Bacteriology, 181 :2930-2937 [Details]
(1999)'Intricacies of ribosomal frameshifting'
Atkins JF, Gesteland RF; (1999) 'Intricacies of ribosomal frameshifting'. Nature Structural Biology, 6 (3):206-207 [DOI] [Details]
(1999)'Structural studies of the RNA pseudoknot required for readthrough of the gag-termination codon of murine leukemia virus'
Alam SL, Wills NM, Ingram JA, Atkins JF, Gesteland RF; (1999) 'Structural studies of the RNA pseudoknot required for readthrough of the gag-termination codon of murine leukemia virus'. Journal of Molecular Biology, 288 (5):837-852 [DOI] [Details]
(1999)'Programmed ribosomal frameshifting: much ado about knotting!'
Alam SL, Atkins JF, Gesteland RF; (1999) 'Programmed ribosomal frameshifting: much ado about knotting!'. Proceedings of The National Academy of Sciences of The United States of America, 96 (25):14177-14179 [Details]
(1998)'Prediction of antisense oligonucleotide efficacy by in vitro methods'
Matveeva O, Felden B, Tsodikov A, Johnston J, Monia BP, Atkins JF, Gesteland RF, Freier SM; (1998) 'Prediction of antisense oligonucleotide efficacy by in vitro methods'. Nature Biotechnology, 16 (13):1374-1375 [DOI] [Details]
(1998)'A nickel complex cleaves uridine in folded RNA structures: application to E. coli tmRNA and related engineered molecules'
Hickerson RP, Watkins-Sims CD, Burrows CJ, Atkins JF, Gesteland RF, Felden B; (1998) 'A nickel complex cleaves uridine in folded RNA structures: application to E. coli tmRNA and related engineered molecules'. Journal of Molecular Biology, 279 (3):577-587 [DOI] [Details]
(1998)'A second mammalian antizyme: conservation of programmed ribosomal frameshifting'
Ivanov IP, Gesteland RF, Atkins JF; (1998) 'A second mammalian antizyme: conservation of programmed ribosomal frameshifting'. Genomics, 52 (2):119-129 [DOI] [Details]
(1998)'Efficiency of T4 gene 60 translational bypassing'
R. Maldonado and A.J. Herr. (1998) 'Efficiency of T4 gene 60 translational bypassing'. The Journal of Bacteriology, 180 :1822-1830 [Details]
(1998)'The Drosophila gene for antizyme requires ribosomal frameshifting for expression and contains an intronic gene for snRNP Sm D3 on the opposite strand'
Ivanov IP, Simin K, Letsou A, Atkins JF, Gesteland RF; (1998) 'The Drosophila gene for antizyme requires ribosomal frameshifting for expression and contains an intronic gene for snRNP Sm D3 on the opposite strand'. Molecular and Cellular Biology, 18 (3):1553-1561 [Details]
(1998)'Does antizyme exist in Escherichia coli?'
Ivanov IP, Gesteland RF, Atkins JF; (1998) 'Does antizyme exist in Escherichia coli?'. Molecular Microbiology, 29 (6):1521-1522 [Details]
(1998)'Flexibility of the nascent polypeptide chain within the ribosome--contacts from the peptide N-terminus to a specific region of the 30S subunit'
Choi KM, Atkins JF, Gesteland RF, Brimacombe R; (1998) 'Flexibility of the nascent polypeptide chain within the ribosome--contacts from the peptide N-terminus to a specific region of the 30S subunit'. European Journal of Biochemistry, 255 (2):409-413 [Details]
(1998)'Does disparate occurrence of autoregulatory programmed frameshifting in decoding the release factor 2 gene reflect an ancient origin with loss in independent lineages?'
Persson BC, Atkins JF; (1998) 'Does disparate occurrence of autoregulatory programmed frameshifting in decoding the release factor 2 gene reflect an ancient origin with loss in independent lineages?'. Journal of Bacteriology, 180 (13):3462-3466 [Details]
(1998)'A dual-luciferase reporter system for studying recoding signals'
Grentzmann G, Ingram JA, Kelly PJ, Gesteland RF, Atkins JF; (1998) 'A dual-luciferase reporter system for studying recoding signals'. Rna-A Publication of The Rna Society, 4 (4):479-486 [Details]
(1998)'Programmed frameshifting in the synthesis of mammalian antizyme is +1 in mammals, predominantly +1 in fission yeast, but -2 in budding yeast'
Ivanov IP, Gesteland RF, Matsufuji S, Atkins JF; (1998) 'Programmed frameshifting in the synthesis of mammalian antizyme is +1 in mammals, predominantly +1 in fission yeast, but -2 in budding yeast'. Rna-A Publication of The Rna Society, 4 (10):1230-1238 [Details]
(1998)'Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches'
Felden B, Hanawa K, Atkins JF, Himeno H, Muto A, Gesteland RF, McCloskey JA, Crain PF; (1998) 'Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches'. The Embo Journal, 17 (11):3188-3196 [DOI] [Details]
(1998)'Effects of 3'-terminal phosphates in RNA produced by ribozyme cleavage'
Alam SL, Nelson CC, Felden B, Atkins JF, Gesteland RF; (1998) 'Effects of 3'-terminal phosphates in RNA produced by ribozyme cleavage'. Rna-A Publication of The Rna Society, 4 (6):607-612 [Details]
(1997)'Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%'
Larsen B, Gesteland RF, Atkins JF; (1997) 'Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%'. Journal of Molecular Biology, 271 (1):47-60 [DOI] [Details]
(1997)'A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures'
Matveeva O, Felden B, Audlin S, Gesteland RF, Atkins JF; (1997) 'A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures'. Nucleic Acids Research, 25 (24):5010-5016 [Details]
(1997)'Probing the structure of the Escherichia coli 10Sa RNA (tmRNA)'
Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF; (1997) 'Probing the structure of the Escherichia coli 10Sa RNA (tmRNA)'. Rna-A Publication of The Rna Society, 3 (1):89-103 [Details]
(1997)'Reported translational bypass in a trpR'-lacZ' fusion is accounted for by unusual initiation and +1 frameshifting'
Wills NM, Ingram JA, Gesteland RF, Atkins JF; (1997) 'Reported translational bypass in a trpR'-lacZ' fusion is accounted for by unusual initiation and +1 frameshifting'. Journal of Molecular Biology, 271 (4):491-498 [DOI] [Details]
(1996)'Regulatory Recoding. in Translational Control (eds. J. Hershey, M. Mathews and N. Sonenberg)'
J.F. Atkins and R.F. Gesteland. (1996) 'Regulatory Recoding. in Translational Control (eds. J. Hershey, M. Mathews and N. Sonenberg)'. Cold Spring Harbor Symposia On Quantitative Biology, :653-684 [Details]
(1996)'Structural organization of Escherichia coli tmRNA'
Felden B, Himeno H, Muto A, Atkins JF, Gesteland RF; (1996) 'Structural organization of Escherichia coli tmRNA'. Biochimie, 78 (11-12):979-983 [Details]
(1996)'A case for trans translation'
Atkins JF, Gesteland RF; (1996) 'A case for trans translation'. Nature, 379 (6568):769-771 [DOI] [Details]
(1996)'Reading two bases twice: mammalian antizyme frameshifting in yeast'
Matsufuji S, Matsufuji T, Wills NM, Gesteland RF, Atkins JF; (1996) 'Reading two bases twice: mammalian antizyme frameshifting in yeast'. The Embo Journal, 15 (6):1360-1370 [Details]
(1996)'Recoding: dynamic reprogramming of translation'
Gesteland RF, Atkins JF; (1996) 'Recoding: dynamic reprogramming of translation'. Annual Review of Biochemistry, 65 :741-768 [DOI] [Details]
(1996)'tRNA and mRNA both in the same molecule'
Felden B, Atkins JF, Gesteland RF; (1996) 'tRNA and mRNA both in the same molecule'. Nature Structural Biology, 3 (6) [Details]
(1996)'Gifted Public Servants'
Atkins JF; (1996) 'Gifted Public Servants'. Science, 272 (5264) [DOI] [Details]
(1996)'Assignment of the human antizyme gene (OAZ) to chromosome 19p13.3 by fluorescence in situ hybridization'
Matsufuji S, Inazawa J, Hayashi T, Miyazaki Y, Ichiba T, Furusaka A, Matsufuji T, Atkins JF, Gesteland RF, Murakami Y, Hayashi S; (1996) 'Assignment of the human antizyme gene (OAZ) to chromosome 19p13.3 by fluorescence in situ hybridization'. Genomics, 38 (1):102-104 [Details]
(1996)'Ribosomal protein L9 interactions with 23 S rRNA: the use of a translational bypass assay to study the effect of amino acid substitutions'
Adamski FM, Atkins JF, Gesteland RF; (1996) 'Ribosomal protein L9 interactions with 23 S rRNA: the use of a translational bypass assay to study the effect of amino acid substitutions'. Journal of Molecular Biology, 261 (3):357-371 [DOI] [Details]
(1995)'Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures'
Olsthoorn RC, Garde G, Dayhuff T, Atkins JF, Van Duin J; (1995) 'Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures'. Virology, 206 (1):611-625 [Details]
(1995)'Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme'
Matsufuji S, Matsufuji T, Miyazaki Y, Murakami Y, Atkins JF, Gesteland RF, Hayashi S; (1995) 'Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme'. Cell, 80 (1):51-60 [Details]
(1995)'NUCLEOTIDE-SEQUENCE OF A SINGLE-STRANDED RNA PHAGE FROM PSEUDOMONAS-AERUGINOSA - KINSHIP TO COLIPHAGES AND CONSERVATION OF REGULATORY RNA STRUCTURES'
OLSTHOORN, RCL,GARDE, G,DAYHUFF, T,ATKINS, JF,VANDUIN, J; (1995) 'NUCLEOTIDE-SEQUENCE OF A SINGLE-STRANDED RNA PHAGE FROM PSEUDOMONAS-AERUGINOSA - KINSHIP TO COLIPHAGES AND CONSERVATION OF REGULATORY RNA STRUCTURES'. Virology, 206 :611-625 [Details]
(1995)'Upstream stimulators for recoding'
Larsen B, Peden J, Matsufuji S, Matsufuji T, Brady K, Maldonado R, Wills NM, Fayet O, Atkins JF, Gesteland RF; (1995) 'Upstream stimulators for recoding'. Cell, 73 (11-12):1123-1129 [Details]
(1994)'A functional mutant of tRNA(2Arg) with ten extra nucleotides in its TFC arm'
Tuohy TM, Li Z, Atkins JF, Deutscher MP; (1994) 'A functional mutant of tRNA(2Arg) with ten extra nucleotides in its TFC arm'. Journal of Molecular Biology, 235 (5):1369-1376 [Details]
(1994)'Utilization of selenocysteyl-tRNA[Ser]Sec and seryl-tRNA[Ser]Sec in protein synthesis'
Jung JE, Karoor V, Sandbaken MG, Lee BJ, Ohama T, Gesteland RF, Atkins JF, Mullenbach GT, Hill KE, Wahba AJ; (1994) 'Utilization of selenocysteyl-tRNA[Ser]Sec and seryl-tRNA[Ser]Sec in protein synthesis'. The Journal of Biological Chemistry, 269 (47):29739-29745 [Details]
(1994)'rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift'
Larsen B, Wills NM, Gesteland RF, Atkins JF; (1994) 'rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift'. Journal of Bacteriology, 176 (22):6842-6851 [Details]
(1994)'Uninterrupted translation through putative 12-nucleotide coding gap in sequence of carA: business as usual'
Tuohy TM, Kidd T, Gesteland RF, Atkins JF; (1994) 'Uninterrupted translation through putative 12-nucleotide coding gap in sequence of carA: business as usual'. Journal of Bacteriology, 176 (1):265-267 [Details]
(1994)'Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2'
Wills NM, Gesteland RF, Atkins JF; (1994) 'Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2'. The Embo Journal, 13 (17):4137-4144 [Details]
(1993)'Mutants of tRNA, ribosomes and mRNA affecting frameshifting, hopping or stop-codon readthrough. in The Translation Apparatus (eds. K.H. Nierhaus, A.R. Subramanian, V.A. Erdmann, F. Franceschi and B. Wittman-Liebold)'
J.F. Atkins, K. Herbst, M. O'Connor, T.M.F. Tuohy, R.B. Weiss, N.M. Wills & R.F. Gesteland. (1993) 'Mutants of tRNA, ribosomes and mRNA affecting frameshifting, hopping or stop-codon readthrough. in The Translation Apparatus (eds. K.H. Nierhaus, A.R. Subramanian, V.A. Erdmann, F. Franceschi and B. Wittman-Liebold)'. Plenum Publishing, :371-374 [Details]
(1993)'Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation'
Hagervall TG, Tuohy TM, Atkins JF, Björk GR; (1993) 'Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation'. Journal of Molecular Biology, 232 (3):756-765 [DOI] [Details]
(1993)'Functional tRNAs with altered 3' ends'
O'Connor M, Willis NM, Bossi L, Gesteland RF, Atkins JF; (1993) 'Functional tRNAs with altered 3' ends'. The Embo Journal, 12 (6):2559-2566 [Details]
(1993)'Contemporary RNA genomes. in The RNA World (eds R.F. Gesteland and J.F. Atkins)'
J.F. Atkins. (1993) 'Contemporary RNA genomes. in The RNA World (eds R.F. Gesteland and J.F. Atkins)'. Cold Spring Harbor Symposium on Quantatitive Biology, :535-556 [Details]
(1993)'Functional aspects of three modified nucleosides, Ψ, ms2io6A and m1G, present in the anticodon loop of tRNA in The Translation Apparatus (eds. K.H. Nierhaus, A.R. Subramanian, V.A. Erdmann, F. Franceschi and B. Wittman-Liebold)'
T.G. Hagervall, B. Esberg, J.-n. Li, T.M.F. Tuohy, J.F. Atkins, J.F. Curran and G.R. Björk. (1993) 'Functional aspects of three modified nucleosides, Ψ, ms2io6A and m1G, present in the anticodon loop of tRNA in The Translation Apparatus (eds. K.H. Nierhaus, A.R. Subramanian, V.A. Erdmann, F. Franceschi and B. Wittman-Liebold)'. Plenum Publishing, :66-78 [Details]
(1992)'Seven, eight and nine-membered anticodon loop mutants of tRNA(2Arg) which cause +1 frameshifting. Tolerance of DHU arm and other secondary mutations'
Tuohy TM, Thompson S, Gesteland RF, Atkins JF; (1992) 'Seven, eight and nine-membered anticodon loop mutants of tRNA(2Arg) which cause +1 frameshifting. Tolerance of DHU arm and other secondary mutations'. Journal of Molecular Biology, 228 (4):1042-1054 [Details]
(1992)'Recoding: reprogrammed genetic decoding'
Gesteland RF, Weiss RB, Atkins JF; (1992) 'Recoding: reprogrammed genetic decoding'. Science, 257 (5077):1640-1641 [Details]
(1992)'Doublet translocation at GGA is mediated directly by mutant tRNA(2Gly)'
Pagel FT, Tuohy TM, Atkins JF, Murgola EJ; (1992) 'Doublet translocation at GGA is mediated directly by mutant tRNA(2Gly)'. Journal of Bacteriology, 174 (12):4179-4182 [Details]
(1992)'Electrophoresis, autoradiography and electroblotting of peptides: T4 gene 60 hopping'
Dayhuff TJ, Gesteland RF, Atkins JF; (1992) 'Electrophoresis, autoradiography and electroblotting of peptides: T4 gene 60 hopping'. Biotechniques, 13 (4):499-41 [Details]
(1991)'Frameshifting in gene 10 of bacteriophage T7'
Condron BG, Atkins JF, Gesteland RF; (1991) 'Frameshifting in gene 10 of bacteriophage T7'. Journal of Bacteriology, 173 (21):6998-7003 [Details]
(1991)'The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons'
Skuzeski JM, Nichols LM, Gesteland RF, Atkins JF; (1991) 'The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons'. Journal of Molecular Biology, 218 (2):365-373 [Details]
(1991)'Control of epistaxis in patients with hereditary hemorrhagic telangiectasia'
Siegel MB, Keane WM, Atkins JF Jr, Rosen MR; (1991) 'Control of epistaxis in patients with hereditary hemorrhagic telangiectasia'. Otolaryngology - Head and Neck Surgery, 105 (5):675-679 [Details]
(1991)'An analysis of sequences stimulating frameshifting in the decoding of gene 10 of bacteriophage T7'
Condron BG, Gesteland RF, Atkins JF; (1991) 'An analysis of sequences stimulating frameshifting in the decoding of gene 10 of bacteriophage T7'. Nucleic Acids Research, 19 (20):5607-5612 [Details]
(1991)'Towards a genetic dissection of the basis of triplet decoding, and its natural subversion: programmed reading frame shifts and hops'
Atkins JF, Weiss RB, Thompson S, Gesteland RF; (1991) 'Towards a genetic dissection of the basis of triplet decoding, and its natural subversion: programmed reading frame shifts and hops'. Gene, 25 :201-228 [DOI] [Details]
(1991)'Studies of frameshifting in gene 10 of bacteriophage T7'
B.G. Condron, J.F. Atkins and R.F. Gesteland. (1991) 'Studies of frameshifting in gene 10 of bacteriophage T7'. The Journal of Bacteriology, (173):6998-7003 [Details]
(1991)'Evidence that a downstream pseudoknot is required for translational read-through of the Moloney murine leukemia virus gag stop codon'
Wills NM, Gesteland RF, Atkins JF; (1991) 'Evidence that a downstream pseudoknot is required for translational read-through of the Moloney murine leukemia virus gag stop codon'. Proceedings of The National Academy of Sciences of The United States of America, 88 (16):6991-6995 [Details]
(1991)'The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons'
J.M. Skuzeski, L.M. Nichols, R.F. Gesteland and J.F. Atkins. (1991) 'The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons'. Journal of Molecular Biology, (218):365-373 [Details]
(1990)'Ribosomal frameshifting from -2 to +50 nucleotides'
Weiss RB, Dunn DM, Atkins JF, Gesteland RF; (1990) 'Ribosomal frameshifting from -2 to +50 nucleotides'. Progress In Nucleic Acid Research and Molecular Biology, Vol 81, 39 :159-183 [Details]
(1990)'Ribosome gymnastics--degree of difficulty 9.5, style 10.0'
Atkins JF, Weiss RB, Gesteland RF; (1990) 'Ribosome gymnastics--degree of difficulty 9.5, style 10.0'. Cell, 62 (3):413-423 [Details]
(1990)'Sequence of E.coli K12 valU operon which contains 3 genes for tRNA(Val1) and 1 gene for tRNA(Lys)'
O'Connor M, Gesteland RF, Atkins JF; (1990) 'Sequence of E.coli K12 valU operon which contains 3 genes for tRNA(Val1) and 1 gene for tRNA(Lys)'. Nucleic Acids Research, 18 (3) [Details]
(1990)'The ribosome's rubbish.in The Translation Apparatus (eds. K.H. Nierhaus, A.R. Subramanian, V.A. Erdmann, F. Franceschi and B. Wittman-Liebold)'
.B. Weiss, D.M. Dunn, J.F. Atkins and R.F. Gesteland. (1990) 'The ribosome's rubbish.in The Translation Apparatus (eds. K.H. Nierhaus, A.R. Subramanian, V.A. Erdmann, F. Franceschi and B. Wittman-Liebold)'. American Society For Microbiology, :534-540 [Details]
(1990)'The role of EF-Tu and other translation components in determining translocation step size'
Tuohy TM, Thompson S, Gesteland RF, Hughes D, Atkins JF; (1990) 'The role of EF-Tu and other translation components in determining translocation step size'. Biochimica Et Biophysica Acta, 1050 (1-3):274-278 [Details]
(1989)'GLYCINE TRANSFER-RNA MUTANTS WITH NORMAL ANTICODON LOOP SIZE CAUSE - 1 FRAMESHIFTING'
OMAHONY, DJ,MIMS, BH,THOMPSON, S,MURGOLA, EJ,ATKINS, JF; (1989) 'GLYCINE TRANSFER-RNA MUTANTS WITH NORMAL ANTICODON LOOP SIZE CAUSE - 1 FRAMESHIFTING'. Proceedings of The National Academy of Sciences of The United States of America, 86 :7979-7983 [Details]
(1989)'E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent'
Weiss RB, Dunn DM, Shuh M, Atkins JF, Gesteland RF; (1989) 'E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent'. The New Biologist, 1 (2):159-169 [Details]
(1989)'tRNA hopping: enhancement by an expanded anticodon'
O'Connor M, Gesteland RF, Atkins JF; (1989) 'tRNA hopping: enhancement by an expanded anticodon'. The Embo Journal, 8 (13):4315-4323 [Details]
(1989)'Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting'
O'Mahony DJ, Mims BH, Thompson S, Murgola EJ, Atkins JF; (1989) 'Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting'. Proceedings of The National Academy of Sciences of The United States of America, 86 (20):7979-7983 [Details]
(1989)'Suppression of a -1 frameshift mutation by a recessive tRNA suppressor which causes doublet decoding'
O'Mahony DJ, Hughes D, Thompson S, Atkins JF; (1989) 'Suppression of a -1 frameshift mutation by a recessive tRNA suppressor which causes doublet decoding'. Journal of Bacteriology, 171 (7):3824-3830 [Details]
(1989)'GENETIC-CHARACTERIZATION OF FRAMESHIFT SUPPRESSORS WITH NEW DECODING PROPERTIES'
HUGHES, D,THOMPSON, S,OCONNOR, M,TUOHY, T,NICHOLS, BP,ATKINS, JF; (1989) 'GENETIC-CHARACTERIZATION OF FRAMESHIFT SUPPRESSORS WITH NEW DECODING PROPERTIES'. Journal of Bacteriology, 171 :1028-1034 [Details]
(1989)'SUPPRESSION OF A -1-FRAMESHIFT MUTATION BY A RECESSIVE TRANSFER-RNA SUPPRESSOR WHICH CAUSES DOUBLET DECODING'
OMAHONY, DJ,HUGHES, D,THOMPSON, S,ATKINS, JF; (1989) 'SUPPRESSION OF A -1-FRAMESHIFT MUTATION BY A RECESSIVE TRANSFER-RNA SUPPRESSOR WHICH CAUSES DOUBLET DECODING'. Journal of Bacteriology, 171 :3824-3830 [Details]
(1989)'TRANSFER-RNA HOPPING - ENHANCEMENT BY AN EXPANDED ANTICODON'
OCONNOR, M,GESTELAND, RF,ATKINS, JF; (1989) 'TRANSFER-RNA HOPPING - ENHANCEMENT BY AN EXPANDED ANTICODON'. The Embo Journal, 8 :4315-4323 [Details]
(1989)'Genetic characterization of frameshift suppressors with new decoding properties'
Hughes D, Thompson S, O'Connor M, Tuohy T, Nichols BP, Atkins JF; (1989) 'Genetic characterization of frameshift suppressors with new decoding properties'. Journal of Bacteriology, 171 (2):1028-1034 [Details]
(1988)'Mutants of translational components that alter reading frame by two steps forward or one step back'
Falahee MB, Weiss RB, O'Connor M, Doonan S, Gesteland RF, Atkins JF; (1988) 'Mutants of translational components that alter reading frame by two steps forward or one step back'. The Journal of Biological Chemistry, 263 (34):18099-18103 [Details]
(1988)'Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli'
Weiss RB, Dunn DM, Dahlberg AE, Atkins JF, Gesteland RF; (1988) 'Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli'. The Embo Journal, 7 (5):1503-1507 [Details]
(1988)'MUTANTS OF TRANSLATIONAL COMPONENTS THAT ALTER READING FRAME BY 2 STEPS FORWARD OR ONE-STEP BACK'
FALAHEE, MB,WEISS, RB,OCONNOR, M,DOONAN, S,GESTELAND, RF,ATKINS, JF; (1988) 'MUTANTS OF TRANSLATIONAL COMPONENTS THAT ALTER READING FRAME BY 2 STEPS FORWARD OR ONE-STEP BACK'. The Journal of Biological Chemistry, 263 :18099-18103 [Details]
(1988)'READING FRAME SWITCH CAUSED BY BASE-PAIR FORMATION BETWEEN THE 3' END OF 16S RIBOSOMAL-RNA AND THE MESSENGER-RNA DURING ELONGATION OF PROTEIN-SYNTHESIS IN ESCHERICHIA-COLI'
WEISS, RB,DUNN, DM,DAHLBERG, AE,ATKINS, JF,GESTELAND, RF; (1988) 'READING FRAME SWITCH CAUSED BY BASE-PAIR FORMATION BETWEEN THE 3' END OF 16S RIBOSOMAL-RNA AND THE MESSENGER-RNA DURING ELONGATION OF PROTEIN-SYNTHESIS IN ESCHERICHIA-COLI'. The Embo Journal, 7 :1503-1507 [Details]
(1987)'Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough'
Hughes D, Atkins JF, Thompson S; (1987) 'Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough'. The Embo Journal, 6 (13):4235-4239 [Details]
(1987)'MUTANTS OF ELONGATION-FACTOR TU PROMOTE RIBOSOMAL FRAMESHIFTING AND NONSENSE READTHROUGH'
HUGHES, D,ATKINS, JF,THOMPSON, S; (1987) 'MUTANTS OF ELONGATION-FACTOR TU PROMOTE RIBOSOMAL FRAMESHIFTING AND NONSENSE READTHROUGH'. The Embo Journal, 6 :4235-4239 [Details]
(1987)'SLIPPERY RUNS, SHIFTY STOPS, BACKWARD STEPS, AND FORWARD HOPS - -2, -1, +1, +2, +5, AND +6 RIBOSOMAL FRAMESHIFTING'
WEISS, RB,DUNN, DM,ATKINS, JF,GESTELAND, RF; (1987) 'SLIPPERY RUNS, SHIFTY STOPS, BACKWARD STEPS, AND FORWARD HOPS - -2, -1, +1, +2, +5, AND +6 RIBOSOMAL FRAMESHIFTING'. Spring, 52 :687-693 [Details]
(1987)'Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting'
Weiss RB, Dunn DM, Atkins JF, Gesteland RF; (1987) 'Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting'. Cold Spring Harbor Symposia On Quantitative Biology, 52 :687-693 [Details]
(1986)'TRANSFER-RNA ANTICODON REPLACEMENT EXPERIMENTS SHOW THAT RIBOSOMAL FRAMESHIFTING CAN BE CAUSED BY DOUBLET DECODING'
BRUCE, AG,ATKINS, JF,GESTELAND, RF; (1986) 'TRANSFER-RNA ANTICODON REPLACEMENT EXPERIMENTS SHOW THAT RIBOSOMAL FRAMESHIFTING CAN BE CAUSED BY DOUBLET DECODING'. Proceedings of The National Academy of Sciences of The United States of America, 83 :5062-5066 [Details]
(1986)'tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding'
Bruce AG, Atkins JF, Gesteland RF; (1986) 'tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding'. Proceedings of The National Academy of Sciences of The United States of America, 83 (14):5062-5066 [Details]
(1986)'CHARACTERIZATION OF RIBOSOMAL FRAMESHIFT EVENTS BY PROTEIN-SEQUENCE ANALYSIS'
DAYHUFF, TJ,ATKINS, JF,GESTELAND, RF; (1986) 'CHARACTERIZATION OF RIBOSOMAL FRAMESHIFT EVENTS BY PROTEIN-SEQUENCE ANALYSIS'. The Journal of Biological Chemistry, 261 :7491-7500 [Details]
(1986)'Characterization of ribosomal frameshift events by protein sequence analysis'
Dayhuff TJ, Atkins JF, Gesteland RF; (1986) 'Characterization of ribosomal frameshift events by protein sequence analysis'. The Journal of Biological Chemistry, 261 (16):7491-7500 [Details]
(1983)'GENETIC INSTABILITY ASSOCIATED WITH THE AROC321 ALLELE IN SALMONELLA-TYPHIMURIUM INVOLVES GENETIC DUPLICATION'
HOFFMANN, GR,WALKOWICZ, MJ,MASON, JM,ATKINS, JF; (1983) 'GENETIC INSTABILITY ASSOCIATED WITH THE AROC321 ALLELE IN SALMONELLA-TYPHIMURIUM INVOLVES GENETIC DUPLICATION'. Molecular & General Genetics, 190 :183-188 [Details]
(1983)'Phage MS2 lysis protein does not require coat protein to mediate cell lysis'
J. Coleman, M. Inouye and J.F. Atkins. (1983) 'Phage MS2 lysis protein does not require coat protein to mediate cell lysis'. The Journal of Bacteriology, (153):1098-1100 [Details]
(1983)'Resolution of the discrepancy between a gene translation--termination codon and the deduced sequence for release of the encoded polypeptide'
Atkins JF, Gesteland RF; (1983) 'Resolution of the discrepancy between a gene translation--termination codon and the deduced sequence for release of the encoded polypeptide'. European Journal of Biochemistry, 137 (3):509-516 [Details]
(1983)'Genetic instability associated with the aroC321 allele in Salmonella typhimurium involves genetic duplication'
Hoffman GR, Walkowicz MJ, Mason JM, Atkins JF; (1983) 'Genetic instability associated with the aroC321 allele in Salmonella typhimurium involves genetic duplication'. Molecular & General Genetics, 190 (2):183-188 [Details]
(1983)'The nucleotide sequence of the first externally suppressible--1 frameshift mutant, and of some nearby leaky frameshift mutants'
Atkins JF, Nichols BP, Thompson S; (1983) 'The nucleotide sequence of the first externally suppressible--1 frameshift mutant, and of some nearby leaky frameshift mutants'. The Embo Journal, 2 (8):1345-1350 [Details]
(1983)'RESOLUTION OF THE DISCREPANCY BETWEEN A GENE TRANSLATION - TERMINATION CODON AND THE DEDUCED SEQUENCE FOR RELEASE OF THE ENCODED POLYPEPTIDE'
ATKINS, JF,GESTELAND, RF; (1983) 'RESOLUTION OF THE DISCREPANCY BETWEEN A GENE TRANSLATION - TERMINATION CODON AND THE DEDUCED SEQUENCE FOR RELEASE OF THE ENCODED POLYPEPTIDE'. European Journal of Biochemistry, 137 :509-516 [Details]
(1983)'THE NUCLEOTIDE-SEQUENCE OF THE 1ST EXTERNALLY SUPPRESSIBLE .1. FRAMESHIFT MUTANT, AND OF SOME NEARBY LEAKY FRAMESHIFT MUTANTS'
ATKINS, JF,NICHOLS, BP,THOMPSON, S; (1983) 'THE NUCLEOTIDE-SEQUENCE OF THE 1ST EXTERNALLY SUPPRESSIBLE .1. FRAMESHIFT MUTANT, AND OF SOME NEARBY LEAKY FRAMESHIFT MUTANTS'. The Embo Journal, 2 :1345-1350 [Details]
(1982)'Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe'
Bruce AG, Atkins JF, Wills N, Uhlenbeck O, Gesteland RF; (1982) 'Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe'. Proceedings of The National Academy of Sciences of The United States of America, 79 (23):7127-7131 [Details]
(1980)'The forms of tRNATrp found in avian sarcoma virus and uninfected chicken cells have structural identity but functional distinctions'
Cordell B, DeNoto FM, Atkins JF, Gesteland RF, Bishop JM, Goodman HM; (1980) 'The forms of tRNATrp found in avian sarcoma virus and uninfected chicken cells have structural identity but functional distinctions'. The Journal of Biological Chemistry, 255 (19):9358-9368 [Details]
(1980)'Non-triplet tRNA mRNA interactions in transfer RNA'
J.F. Atkins. (1980) 'Non-triplet tRNA mRNA interactions in transfer RNA'. Cold Spring Harbor Symposium on Quantatitive Biology, 09B :439-449 [Details]
(1979)'Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function'
Atkins JF, Steitz JA, Anderson CW, Model P; (1979) 'Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function'. Cell, 18 (2):247-256 [Details]
(1979)'Normal tRNAs promote ribosomal frameshifting'
Atkins JF, Gesteland RF, Reid BR, Anderson CW; (1979) 'Normal tRNAs promote ribosomal frameshifting'. Cell, 18 (4):1119-1131 [Details]
(1979)'Identification and mapping of the transcriptional and translational products of the yeast plasmid, 2mu circle'
Broach JR, Atkins JF, McGill C, Chow L; (1979) 'Identification and mapping of the transcriptional and translational products of the yeast plasmid, 2mu circle'. Cell, 16 (4):827-839 [Details]
(1979)'Is UAA or UGA part of the recognition signal for ribosomal initiation?'
Atkins JF; (1979) 'Is UAA or UGA part of the recognition signal for ribosomal initiation?'. Nucleic Acids Research, 7 (4):1035-1041 [Details]
(1977)'Further mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments'
Lewis JB, Anderson CW, Atkins JF; (1977) 'Further mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments'. Cell, 12 (1):37-44 [Details]
(1976)'Location of identification of the genes for adenovirus type 2 polypeptides'
Atkins JF, Lewis JB, Anderson CW, Gesteland RF; (1976) 'Location of identification of the genes for adenovirus type 2 polypeptides'. Biochemical Society Transactions, 4 (5) [Details]
(1976)'A map of the restriction targets in yeast 2 micron plasmid DNA cloned on bacteriophage lambda'
Beggs JD, Guerineau M, Atkins JF; (1976) 'A map of the restriction targets in yeast 2 micron plasmid DNA cloned on bacteriophage lambda'. Molecular & General Genetics, 148 (3):287-294 [Details]
(1976)'Bacteriophage T3 and T7 early RNAs are translated by eukaryotic 80S ribosomes: active phage T3 coded S-adenosylmethionine cleaving enzyme is synthesized'
Anderson CW, Atkins JF, Dunn JJ; (1976) 'Bacteriophage T3 and T7 early RNAs are translated by eukaryotic 80S ribosomes: active phage T3 coded S-adenosylmethionine cleaving enzyme is synthesized'. Proceedings of The National Academy of Sciences of The United States of America, 73 (8):2752-2756 [Details]
(1976)'Bacteriophages T7 and T3 as model systems for RNA synthesis and processing'
Dunn JJ, Anderson CW, Atkins JF, Bartelt DC, Crockett WC; (1976) 'Bacteriophages T7 and T3 as model systems for RNA synthesis and processing'. Progress In Nucleic Acid Research and Molecular Biology, Vol 81, 19 :263-273 [Details]
(1976)'Expression of a eukaryotic gene in Escherichia coli'
J.F. Atkins (1976) 'Expression of a eukaryotic gene in Escherichia coli'. Nature, 262 :256-257 [Details]
(1976)'Location and identification of the genes for adenovirus type 2 early polypeptides'
Lewis JB, Atkins JF, Baum PR, Solem R, Gesteland RF, Anderson CW; (1976) 'Location and identification of the genes for adenovirus type 2 early polypeptides'. Cell, 7 (1):141-151 [Details]
(1975)'Enhanced differential synthesis of proteins in a mammalian cell-free system by addition of polyamines'
Atkins JF, Lewis JB, Anderson CW, Gesteland RF; (1975) 'Enhanced differential synthesis of proteins in a mammalian cell-free system by addition of polyamines'. The Journal of Biological Chemistry, 250 (14):5688-5695 [Details]
(1975)'Mapping of adenovirus 2 genes by trans¬lation of RNA selected by hybridization'
J.F. Atkins, J.B. Lewis, C.W. Anderson, P.R. Baum and R.F. Geste¬land. (1975) 'Mapping of adenovirus 2 genes by trans¬lation of RNA selected by hybridization'. Inserm, 47 :293-298 [Details]
(1975)'Mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments'
Lewis JB, Atkins JF, Anderson CW, Baum PR, Gesteland RF; (1975) 'Mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments'. Proceedings of The National Academy of Sciences of The United States of America, 72 (4):1344-1348 [Details]
(1975)'The origin and destiny of adenovirus proteins'
Lewis JB, Anderson CW, Atkins JF, Gesteland RF; (1975) 'The origin and destiny of adenovirus proteins'. Cold Spring Harbor Symposia On Quantitative Biology, 39 Pt 1 :581-590 [Details]
(1975)'The synthetase gene of the RNA phages R17, MS2 and f2 has a single UAG terminator codon'
Atkins JF, Gesteland RF; (1975) 'The synthetase gene of the RNA phages R17, MS2 and f2 has a single UAG terminator codon'. Molecular & General Genetics, 139 (1):19-31 [Details]
(1974)'UGA and non-triplet suppressor reading of the genetic code'
Atkins JF, Ryce S; (1974) 'UGA and non-triplet suppressor reading of the genetic code'. Nature, 249 (457):527-530 [Details]
(1974)'Cell-free synthesis of adenovirus 2 proteins programmed by fractionated messenger RNA: a comparison of polypeptide products and messenger RNA lengths'
Anderson CW, Lewis JB, Atkins JF, Gesteland RF; (1974) 'Cell-free synthesis of adenovirus 2 proteins programmed by fractionated messenger RNA: a comparison of polypeptide products and messenger RNA lengths'. Proceedings of The National Academy of Sciences of The United States of America, 71 (7):2756-2760 [Details]
(1972)'Evolution of DNA base compositions in microorganisms'
Bak AL, Atkins JF, Meyer SA; (1972) 'Evolution of DNA base compositions in microorganisms'. Science, 175 (28):1391-1393 [Details]
(1972)'Low activity of -galactosidase in frameshift mutants of Escherichia coli'
Atkins JF, Elseviers D, Gorini L; (1972) 'Low activity of -galactosidase in frameshift mutants of Escherichia coli'. Proceedings of The National Academy of Sciences of The United States of America, 69 (5):1192-1195 [Details]
(1971)'Histidinol dehydrogenase (his D) mutants of Salmonella typhimurium'
Greeb J, Atkins JF, Loper JC; (1971) 'Histidinol dehydrogenase (his D) mutants of Salmonella typhimurium'. Journal of Bacteriology, 106 (2):421-431 [Details]
(1970)'Transcription initiation in the histidine operon of Salmonella typhimurium'
Atkins JF, Loper JC; (1970) 'Transcription initiation in the histidine operon of Salmonella typhimurium'. Proceedings of The National Academy of Sciences of The United States of America, 65 (4):925-932 [Details]
(1968)'External suppression of a frameshift mutant in salmonella'
Riyasaty S, Atkins JF; (1968) 'External suppression of a frameshift mutant in salmonella'. Journal of Molecular Biology, 34 (3):541-557 [Details]

Book Reviews

YearPublication
(2009)A Gripping Tale of Ribosomal Frameshifting: Extragenic Suppressors of Frameshift Mutations Spotlight P-Site Realignment.
Atkins, JF,Bjork, GR (2009) A Gripping Tale of Ribosomal Frameshifting: Extragenic Suppressors of Frameshift Mutations Spotlight P-Site Realignment. Book Reviews [DOI] [Details]
(2007)Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation.
Ivanov, IP,Atkins, JF (2007) Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Book Reviews [DOI] [Details]
(2006)Recoding in bacteriophages and bacterial IS elements.
Baranov, PV,Fayet, O,Hendrix, RW,Atkins, JF (2006) Recoding in bacteriophages and bacterial IS elements. Book Reviews [DOI] [Details]
(1990)RIBOSOME GYMNASTICS - DEGREE OF DIFFICULTY 9.5, STYLE 10.0.
ATKINS, JF,WEISS, RB,GESTELAND, RF (1990) RIBOSOME GYMNASTICS - DEGREE OF DIFFICULTY 9.5, STYLE 10.0. Book Reviews [Details]

Editorship

YearPublication
(2013)MOLECULAR BIOLOGY Antibiotic re-frames decoding.
Atkins, JF,Baranov, PV (2013) MOLECULAR BIOLOGY Antibiotic re-frames decoding. Editorship [Details]

Other

YearPublication
(2010)The Distinction Between Recoding and Codon Reassignment.
Atkins, JF,Baranov, PV (2010) The Distinction Between Recoding and Codon Reassignment. Other [DOI] [Details]
(2008)Foot and Mouth's Achilles' heel?.
Atkins, JF,Ryan, MD (2008) Foot and Mouth's Achilles' heel?. Other [DOI] [Details]
(2008)Foot and Mouth'S Achilles' Heel?.
Atkins, JF, Ryan, MD; (2008) Foot and Mouth'S Achilles' Heel?. Other [DOI] [Details]
(2007)Translation - Duality In The Genetic Code.
Atkins, JF, Baranov, PV; (2007) Translation - Duality In The Genetic Code. Other [DOI] [Details]
(1990)THE ROLE OF EF-TU AND OTHER TRANSLATION COMPONENTS IN DETERMINING TRANSLOCATION STEP SIZE.
TUOHY, TMF,THOMPSON, S,GESTELAND, RF,HUGHES, D,ATKINS, JF (1990) THE ROLE OF EF-TU AND OTHER TRANSLATION COMPONENTS IN DETERMINING TRANSLOCATION STEP SIZE. Other [Details]
(1990)SEQUENCE OF ESCHERICHIA-COLI K12 VALU OPERON WHICH CONTAINS 3 GENES FOR TRANSFER RNA1VAL AND 1 GENE FOR TRANSFER RNALYS.
OCONNOR, M,GESTELAND, RF,ATKINS, JF (1990) SEQUENCE OF ESCHERICHIA-COLI K12 VALU OPERON WHICH CONTAINS 3 GENES FOR TRANSFER RNA1VAL AND 1 GENE FOR TRANSFER RNALYS. Other [Details]

Honours and Awards

 YearTitleAwarding Body
2007Gold medal from the Royal Irish Academy (inaugural quadrennial medal in the Life Sciences) Royal Irish Academy (inaugural quadrennial medal in the Life Sciences)

Conference Contributions

YearPublication
(2009)NIH Symposium,
Atkins, JF; (2009) Genes to Proteins: Decoding Genetic Information to honor Marshall Nirenberg almost 50 years after deciphering the genetic code. [Invited Oral Presentation], NIH Symposium, Bethesda , 12-NOV-09 - 12-NOV-09. [Details]

Education

 YearInstitutionQualificationSubject
1981Dublin University (TCD) ScD

Teaching Interests

John gave lectures for a few years in a Developmental Biology course for students of UCC's Microbiology and Biochemistry Departments and lectured in molecular biology to Biochemistry Dept. students.

The text of 195 pages with 4 experiments designed for school and college biology classes in association with the Biological Sciences Curriculum Study, in Colorado Springs by J.F. Atkins, A. Ellington, B.E. Friedman, R.F. Gesteland, H.F. Noller, S.M. Pasquale, R.D. Storey, O.C. Uhlenbeck and A.M. Weiner. 2000 entitled "Bringing RNA into view: RNA and its roles in biology" It was later placed on a web piece at the Learn Genetics website where it was downloaded over 26,000 times between 8/2002 -12/2003 (it was the most popular download on the site and 64,506 times between 7/05 and 5/08, but has now been transferred to http://learn.genetics.utah.edu/archive/rna/index.html as an update is being prepared (not involving JFA). The website won several awards including the first Science Prize for Online Resources in Education (SPORE) as described by B. Alberts, Editor-in Chief of Science, Science vol. 327, 504 (2010).


Current Postgraduate Students

 StudentDegree Type
Baclaocos Janinah Doctoral Degree
Coakley Arthur Jerome Doctoral Degree
Yordanova Martina Momchilova Doctoral Degree
Bhatt Pramod Raghupathi Doctoral Degree
Tzani Ioanna Doctoral Degree (Structured)
O Loughlin Sinead Doctoral Degree

Modules Taught

 Term (ID))TitleLinkSubject
2015Research Project GN4002Research Project