2015-present
Joshi K, Cao L, Farabaugh PJ. (2019) The problem of genetic code misreading during protein synthesis. Yeast 36:35-42 (review). Full Text
Joshi K, Bhatt MJ, Farabaugh PJ. (2018) Codon-specific effects of tRNA anticodon loop modifications on translational misreading errors in the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 46(19):10331-10339. Free PMC Article
Manickam N, Joshi K, Bhatt MJ, Farabaugh PJ. Effects of tRNA modification on translational accuracy depend on intrinsic codon-anticodon strength. Nucleic Acids Res. 2016 Feb 29;44(4):1871-81. Free PMC Article
Suresh S, Ahn HW, Joshi K, Dakshinamurthy A, Kananganat A, Garfinkel DJ, Farabaugh PJ. Ribosomal protein and biogenesis factors affect multiple steps during movement of the Saccharomyces cerevisiae Ty1 retrotransposon. Mob DNA. 2015 6:22. doi: 10.1186/s13100-015-0053-5. Free PMC Article
Nord S, Bhatt MJ, Tükenmez H, Farabaugh PJ, Wikström PM. Mutations of ribosomal protein S5 suppress a defect in late-30S ribosomal subunit biogenesis caused by lack of the RbfA biogenesis factor. RNA. 2015 21:1454-68. doi: 10.1261/rna.051383.115. Free PMC Article
2010-2014
Ribas de Pouplana L, Santos MA, Zhu JH, Farabaugh PJ, Javid B. Protein mistranslation: friend or foe? Trends Biochem Sci. 2014 39:355-62. doi: 10.1016/j.tibs.2014.06.002. Full Text
Manickam N, Nag N, Abbasi A, Patel K, Farabaugh PJ. Studies of translational misreading in vivo show that the ribosome very efficiently discriminates against most potential errors. RNA. 2014 20:9-15. doi: 10.1261/rna.039792.113. Free PMC Article
Lamichhane TN, Blewett NH, Crawford AK, Cherkasova VA, Iben JR, Begley TJ, Farabaugh PJ, Maraia RJ. Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast. Mol Cell Biol. 2013 33:2918-29. doi: 10.1128/MCB.00278-13. Free PMC Article
Türkel S, Kaplan G, Farabaugh PJ. Glucose signalling pathway controls the programmed ribosomal frameshift efficiency in retroviral-like element Ty3 in Saccharomyces cerevisiae. Yeast. 2011 28:799-808. doi: 10.1002/yea.1906. Free Article
Kramer EB, Vallabhaneni H, Mayer LM, Farabaugh PJ. A comprehensive analysis of translational missense errors in the yeast Saccharomyces cerevisiae. RNA. 2010 16:1797-808. doi: 10.1261/rna.2201210. Free PMC Article
Dakshinamurthy A, Nyswaner KM, Farabaugh PJ, Garfinkel DJ. BUD22 affects Ty1 retrotransposition and ribosome biogenesis in Saccharomyces cerevisiae. Genetics. 2010 185:1193-205. doi: 10.1534/genetics.110.119115. Free PMC Article
2005-2009
Vallabhaneni H, Farabaugh PJ. Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction. RNA. 2009 15:1100-9. doi: 10.1261/rna.1530509. Free PMC Article
Vallabhaneni H, Fan-Minogue H, Bedwell DM, Farabaugh PJ. Connection between stop codon reassignment and frequent use of shifty stop frameshifting. RNA. 2009 15:889-97. doi: 10.1261/rna.1508109. Free PMC Article
Guarraia C, Norris L, Raman A, Farabaugh PJ. Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon. RNA. 2007 13:1940-7. Free PMC Article
Taliaferro DL, Farabaugh PJ. Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal A site. RNA. 2007 13:1279-86. Free PMC Article
Taliaferro D, Farabaugh PJ. An mRNA sequence derived from the yeast EST3 gene stimulates programmed +1 translational frameshifting. RNA. 2007 13:606-13. Free PMC Article
Kramer EB, Farabaugh PJ. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA. 2007 13:87-96. Free PMC Article
Farabaugh PJ, Kramer E, Vallabhaneni H, Raman A. Evolution of +1 programmed frameshifting signals and frameshift-regulating tRNAs in the order Saccharomycetales. J Mol Evol. 2006 63:545-61.
Raman A, Guarraia C, Taliaferro D, Stahl G, Farabaugh PJ. An mRNA sequence derived from a programmed frameshifting signal decreases codon discrimination during translation initiation. RNA. 2006 12:1154-60. Free PMC Article
Salas-Marco J, Fan-Minogue H, Kallmeyer AK, Klobutcher LA, Farabaugh PJ, Bedwell DM. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol. 2006 26:438-47. Free PMC Article
2000-2004
Stahl G, Salem SN, Chen L, Zhao B, Farabaugh PJ. Translational accuracy during exponential, postdiauxic, and stationary growth phases in Saccharomyces cerevisiae. Eukaryot Cell. 2004 3:331-8. Free PMC Article
Stahl G, Ben Salem S, Li Z, McCarty G, Raman A, Shah M, Farabaugh PJ. Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction. Cold Spring Harb Symp Quant Biol. 2001 66:249-58.
Urbonavicius J, Stahl G, Durand JM, Ben Salem SN, Qian Q, Farabaugh PJ, Björk GR. Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting. RNA. 2003 9:760-8. Free PMC Article
Klobutcher LA, Farabaugh PJ. Shifty ciliates: frequent programmed translational frameshifting in euplotids. Cell. 2002 111:763-6. Free Article
Stahl G, McCarty GP, Farabaugh PJ. Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding. Trends Biochem Sci. 2002 27:178-83.
Schneider R et al. (Farabaugh PJ 13th author) New ways of initiating translation in eukaryotes. Mol Cell Biol. 2001 21:8238-46. Free PMC Article
Li Z, Stahl G, Farabaugh PJ. Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA. RNA. 2001 7:275-84. Free PMC Article
Bidou L, Stahl G, Hatin I, Namy O, Rousset JP, Farabaugh PJ. Nonsense-mediated decay mutants do not affect programmed -1 frameshifting. RNA. 2000 6:952-61. Free PMC Article
Farabaugh PJ. Translational frameshifting: implications for the mechanism of translational frame maintenance. Prog Nucleic Acid Res Mol Biol. 2000 64:131-70.
1995-1999
Sundararajan A, Michaud WA, Qian Q, Stahl G, Farabaugh PJ. Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol Cell. 1999 4:1005-15. Free Article
Burck CL, Chernoff YO, Liu R, Farabaugh PJ, Liebman SW. Translational suppressors and antisuppressors alter the efficiency of the Ty1 programmed translational frameshift. RNA. 1999 5:1451-7. Free PMC Article
Farabaugh PJ, Björk GR. How translational accuracy influences reading frame maintenance. EMBO J. 1999 18:1427-34. Free PMC Article
Vimaladithan A, Farabaugh PJ. Identification and analysis of frameshift sites. Methods Mol Biol. 1998 77:399-411.
Qian Q, Li JN, Zhao H, Hagervall TG, Farabaugh PJ, Björk GR. A new model for phenotypic suppression of frameshift mutations by mutant tRNAs. Mol Cell. 1998 1:471-82. Free Article
Farabaugh PJ, Vimaladithan A. Effect of frameshift-inducing mutants of elongation factor 1alpha on programmed +1 frameshifting in yeast. RNA. 1998 4:38-46. Free PMC Article
Türkel S, Liao XB, Farabaugh PJ. GCR1-dependent transcriptional activation of yeast retrotransposon Ty2-917. Yeast. 1997 13:917-30. Free Article
Farabaugh PJ. Programmed translational frameshifting. Microbiol Rev. 1996 60:103-34. Free PMC Article
Farabaugh PJ. Programmed translational frameshifting. Annu Rev Genet. 1996 30:507-28.
Farabaugh PJ. Post-transcriptional regulation of transposition by Ty retrotransposons of Saccharomyces cerevisiae. J Biol Chem. 1995 270:10361-4. Free Article
Pande S, Vimaladithan A, Zhao H, Farabaugh PJ. Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol Cell Biol. 1995 15:298-304. Free PMC Article
1990-1994
Vimaladithan A, Farabaugh PJ. Special peptidyl-tRNA molecules can promote translational frameshifting without slippage. Mol Cell Biol. 1994 14:8107-16. Free PMC Article
Kawakami K, Pande S, Faiola B, Moore DP, Boeke JD, Farabaugh PJ, Strathern JN, Nakamura Y, Garfinkel DJ. A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics. 1993 135:309-20. Free PMC Article
Farabaugh PJ. Alternative readings of the genetic code. Cell. 1993 74:591-6. Review.
Farabaugh PJ, Zhao H, Vimaladithan A. A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell. 1993 74:93-103.
Türkel S, Farabaugh PJ. Interspersion of an unusual GCN4 activation site with a complex transcriptional repression site in Ty2 elements of Saccharomyces cerevisiae. Mol Cell Biol. 1993 13:2091-103. Free PMC Article
Farabaugh PJ, Vimaladithan A, Türkel S, Johnson R, Zhao H. Three downstream sites repress transcription of a Ty2 retrotransposon in Saccharomyces cerevisiae. Mol Cell Biol. 1993 13:2081-90. Free PMC Article
Belcourt MF, Farabaugh PJ. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell. 1990 62:339-52.
Axelrod NJ, Carmichael GG, Farabaugh PJ. Enhancer and promoter elements from simian virus 40 and polyomavirus can substitute for an upstream activation sequence in Saccharomyces cerevisiae. Mol Cell Biol. 1990 10:947-57. Free PMC Article
Pre-1990
Clare JJ, Belcourt M, Farabaugh PJ. Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon. Proc Natl Acad Sci U S A. 1988 85:6816-20. Free PMC Article
Liao XB, Clare JJ, Farabaugh PJ. The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element. Proc Natl Acad Sci U S A. 1987 84:8520-4. Free PMC Article
Donahue TF, Farabaugh PJ, Fink GR. The nucleotide sequence of the HIS4 region of yeast. Gene. 1982 18:47-59.
Donahue TF, Farabaugh PJ, Fink GR. Suppressible four-base glycine and proline codons in yeast. Science. 1981 212:455-7.
Roeder GS, Farabaugh PJ, Chaleff DT, Fink GR. The origins of gene instability in yeast. Science. 1980 209:1375-80.
Farabaugh PJ, Fink GR. Insertion of the eukaryotic transposable element Ty1 creates a 5-base pair duplication. Nature. 1980 286:352-6.
Farabaugh PJ, Schmeissner U, Hofer M, Miller JH. Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. J Mol Biol. 1978 126:847-57.
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature. 1978 274:775-80.
Miller JH, Coulondre C, Farabaugh PJ. Correlation of nonsense sites in the lacI gene with specific codons in the nucleotide sequence. Nature. 1978 274:770-5.
Farabaugh PJ. Sequence of the lacI gene. Nature. 1978 274:765-9.