Publications

• 1. De Zoysa T
  2. Hauke AC
  3. Iyer NR
  4. Marcus E
  5. Ostrowski SM
  6. Stegemann F
  7. Ermolenko DN
  8. Fay JC
  9. Phizicky EM
  A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; PLoS genetics; Vol 20(1), pp. e1011146. 2024 Jan 31.
• 1. De Zoysa T
  2. Hauke AC
  3. Iyer NR
  4. Marcus E
  5. Ostrowski SM
  6. Fay JC
  7. Phizicky EM
  A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; bioRxiv : the preprint server for biology. 2023 Sep 18.
• 1. Phizicky EM
  2. Hopper AK
  The Life and Times of a tRNA.; RNA (New York, N.Y.). 2023 Apr 13.
• 1. Tasak M
  2. Phizicky EM
  Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay path way in evolutionarily distant yeast species.; PLoS genetics; Vol 18(7), pp. e1010215. 2022 Jul 28.
• 1. Funk HM
  2. DiVita DJ
  3. Sizemore HE
  4. Wehrle K
  5. Miller CLW
  6. Fraley ME
  7. Mullins AK
  8. Guy AR
  9. Phizicky EM
  10. Guy MP
  Identification of a Trm732 Motif Required for 2'-O-methylation of the tRNA Anticodon Loop by Trm7.; ACS omega; Vol 7(16). 2022 Apr 26.
• 1. Han L
  2. Marcus E
  3. Phizicky EM
  A semi-quantitative pull-down assay to study tRNA substrate specificity of modification enzymes.; Methods in enzymology; Vol 658. 2021.
• 1. De Zoysa T
  2. Phizicky EM
  Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences.; PLoS genetics; Vol 16(8). 2020 Aug 25.
• 1. Payea MJ
  2. Hauke AC
  3. De Zoysa T
  4. Phizicky EM
  Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast.; RNA (New York, N.Y.). 2019 Oct 16.
• 1. Ramos J
  2. Han L
  3. Li Y
  4. Hagelskamp F
  5. Kellner SM
  6. Alkuraya FS
  7. Phizicky EM
  8. Fu D
  Formation of tRNA wobble inosine in humans is disrupted by a millennia-old mutation causing intellectual disability.; Molecular and cellular biology. 2019 Jul 01.
• 1. Shaheen R
  2. Tasak M
  3. Maddirevula S
  4. Abdel-Salam GMH
  5. Sayed ISM
  6. Alazami AM
  7. Al-Sheddi T
  8. Alobeid E
  9. Phizicky EM
  10. Alkuraya FS
  PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly.; Human genetics. 2019 Feb 18.
• 1. Han L
  2. Phizicky EM
  A rationale for tRNA modification circuits in the anticodon loop.; RNA (New York, N.Y.). 2018 Jul 19.
• 1. Zimmerman SM
  2. Kon Y
  3. Hauke AC
  4. Ruiz BY
  5. Fields S
  6. Phizicky EM
  Conditional accumulation of toxic tRNAs to cause amino acid misincorporation.; Nucleic acids research. 2018 Jul 11.
• 1. Han L
  2. Guy MP
  3. Kon Y
  4. Phizicky EM
  Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway.; PLoS genetics; Vol 14(3). 2018 Mar 29.
• 1. Payea MJ
  2. Sloma MF
  3. Kon Y
  4. Young DL
  5. Guy MP
  6. Zhang X
  7. De Zoysa T
  8. Fields S
  9. Mathews DH
  10. Phizicky EM
  Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.; RNA (New York, N.Y.). 2017 Dec 19.
• 1. Patra B
  2. Kon Y
  3. Yadav G
  4. Sevold AW
  5. Frumkin JP
  6. Vallabhajosyula RR
  7. Hintze A
  8. Østman B
  9. Schossau J
  10. Bhan A
  11. Marzolf B
  12. Tamashiro JK
  13. Kaur A
  14. Baliga NS
  15. Grayhack EJ
  16. Adami C
  17. Galas DJ
  18. Raval A
  19. Phizicky EM
  20. Ray A
  A genome wide dosage suppressor network reveals genomic robustness.; Nucleic acids research; Vol 45(1). 2017 Jan 09.
• 1. Hrabeta-Robinson E
  2. Marcus E
  3. Cozen AE
  4. Phizicky EM
  5. Lowe TM
  High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq).; Methods in molecular biology (Clifton, N.J.); Vol 1562. 2017.
• 1. Han L
  2. Marcus E
  3. D'Silva S
  4. Phizicky EM
  S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates.; RNA (New York, N.Y.). 2016 Dec 21.
• 1. Shaheen R
  2. Han L
  3. Faqeih E
  4. Ewida N
  5. Alobeid E
  6. Phizicky EM
  7. Alkuraya FS
  A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition.; Human genetics. 2016 Apr 7.
• 1. Guy MP
  2. Shaw M
  3. Weiner CL
  4. Hobson L
  5. Stark Z
  6. Rose K
  7. Kalscheuer VM
  8. Gecz J
  9. Phizicky EM
  Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1.; Human mutation; Vol 36(12). 2015 Dec.
• 1. Cozen AE
  2. Quartley E
  3. Holmes AD
  4. Hrabeta-Robinson E
  5. Phizicky EM
  6. Lowe TM
  ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments.; Nature methods; Vol 12(9). 2015 Sep.
• 1. Phizicky EM
  2. Hopper AK
  tRNA processing, modification, and subcellular dynamics: past, present, and future.; RNA (New York, N.Y.); Vol 21(4). 2015 Apr.
• 1. Han L
  2. Kon Y
  3. Phizicky EM
  Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast.; RNA (New York, N.Y.); Vol 21(2). 2015 Feb.
• 1. Payea MJ
  2. Guy MP
  3. Phizicky EM
  Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway.; Methods in enzymology; Vol 560. 2015.
• 1. Shaheen R
  2. Abdel-Salam GM
  3. Guy MP
  4. Alomar R
  5. Abdel-Hamid MS
  6. Afifi HH
  7. Ismail SI
  8. Emam BA
  9. Phizicky EM
  10. Alkuraya FS
  Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism.; Genome biology; Vol 16. 2015.
• 1. Guy MP
  2. Phizicky EM
  Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes.; RNA (New York, N.Y.); Vol 21(1). 2015 Jan.
• 1. Zhang X
  2. Walker RC
  3. Phizicky EM
  4. Mathews DH
  Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.; Journal of chemical theory and computation; Vol 10(8). 2014 Aug 12.
• 1. Guy MP
  2. Young DL
  3. Payea MJ
  4. Zhang X
  5. Kon Y
  6. Dean KM
  7. Grayhack EJ
  8. Mathews DH
  9. Fields S
  10. Phizicky EM
  Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis.; Genes & development; Vol 28(15). 2014 Aug 1.
• 1. Pop C
  2. Rouskin S
  3. Ingolia NT
  4. Han L
  5. Phizicky EM
  6. Weissman JS
  7. Koller D
  Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.; Molecular systems biology; Vol 10. 2014.
• 1. Guy MP
  2. Phizicky EM
  Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification.; RNA biology; Vol 11(12). 2014.
• 1. Preston MA
  2. D'Silva S
  3. Kon Y
  4. Phizicky EM
  tRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae.; RNA (New York, N.Y.); Vol 19(2). 2013 Feb.
• 1. Guy MP
  2. Podyma BM
  3. Preston MA
  4. Shaheen HH
  5. Krivos KL
  6. Limbach PA
  7. Hopper AK
  8. Phizicky EM
  Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop.; RNA (New York, N.Y.); Vol 18(10). 2012 Oct.
• 1. Dewe JM
  2. Whipple JM
  3. Chernyakov I
  4. Jaramillo LN
  5. Phizicky EM
  The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications.; RNA (New York, N.Y.); Vol 18(10). 2012 Oct.
• 1. Grant TD
  2. Snell EH
  3. Luft JR
  4. Quartley E
  5. Corretore S
  6. Wolfley JR
  7. Snell ME
  8. Hadd A
  9. Perona JJ
  10. Phizicky EM
  11. Grayhack EJ
  Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase.; Nucleic acids research; Vol 40(8). 2012 Apr.
• 1. Whipple JM
  2. Lane EA
  3. Chernyakov I
  4. D'Silva S
  5. Phizicky EM
  The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA.; Genes & development; Vol 25(11). 2011 Jun 01.
• 1. D'Silva S
  2. Haider SJ
  3. Phizicky EM
  A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop.; RNA (New York, N.Y.); Vol 17(6). 2011 Jun.
• 1. Phizicky EM
  2. Hopper AK
  tRNA biology charges to the front.; Genes & development; Vol 24(17). 2010 Sep 1.
• 1. Preston MA
  2. Phizicky EM
  The requirement for the highly conserved G-1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase.; RNA (New York, N.Y.); Vol 16(5). 2010 May.
• 1. Murthi A
  2. Shaheen HH
  3. Huang HY
  4. Preston MA
  5. Lai TP
  6. Phizicky EM
  7. Hopper AK
  Regulation of tRNA bidirectional nuclear-cytoplasmic trafficking in Saccharomyces cerevisiae.; Molecular biology of the cell; Vol 21(4). 2010 Feb 15.
• 1. Phizicky EM
  2. Alfonzo JD
  Do all modifications benefit all tRNAs?; FEBS letters; Vol 584(2). 2010 Jan 21.
• 1. Quartley E
  2. Alexandrov A
  3. Mikucki M
  4. Buckner FS
  5. Hol WG
  6. DeTitta GT
  7. Phizicky EM
  8. Grayhack EJ
  Heterologous expression of L. major proteins in S. cerevisiae: a test of solubility, purity, and gene recoding.; Journal of structural and functional genomics; Vol 10(3). 2009 Sep.
• 1. Phizicky EM
  Waste not, want not: a case for tRNA repair.; Nature structural & molecular biology; Vol 15(8). 2008 Aug.
• 1. Merritt EA
  2. Holmes M
  3. Buckner FS
  4. Van Voorhis WC
  5. Quartly E
  6. Phizicky EM
  7. Lauricella A
  8. Luft J
  9. DeTitta G
  10. Neely H
  11. Zucker F
  12. Hol WG
  Structure of a Trypanosoma brucei alpha/beta-hydrolase fold protein with unknown function.; Acta crystallographica. Section F, Structural biology and crystallization communications; Vol 64(Pt 6). 2008 Jun 1.
• 1. Chernyakov I
  2. Whipple JM
  3. Kotelawala L
  4. Grayhack EJ
  5. Phizicky EM
  Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1.; Genes & development; Vol 22(10). 2008 May 15.
• 1. Jackman JE
  2. Phizicky EM
  Identification of critical residues for G-1 addition and substrate recognition by tRNA(His) guanylyltransferase.; Biochemistry; Vol 47(16). 2008 Apr 22.
• 1. Kotelawala L
  2. Grayhack EJ
  3. Phizicky EM
  Identification of yeast tRNA Um(44) 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNA(Ser) species.; RNA (New York, N.Y.); Vol 14(1). 2008 Jan.
• 1. Jackman JE
  2. Grayhack EJ
  3. Phizicky EM
  The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins.; Methods in molecular biology (Clifton, N.J.); Vol 488. 2008.
• 1. Chernyakov I
  2. Baker MA
  3. Grayhack EJ
  4. Phizicky EM
  Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications.; Methods in enzymology; Vol 449. 2008.
• 1. Malkowski MG
  2. Quartley E
  3. Friedman AE
  4. Babulski J
  5. Kon Y
  6. Wolfley J
  7. Said M
  8. Luft JR
  9. Phizicky EM
  10. DeTitta GT
  11. Grayhack EJ
  Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing.; Proceedings of the National Academy of Sciences of the United States of America; Vol 104(16). 2007 Apr 17.
• 1. Wilkinson ML
  2. Crary SM
  3. Jackman JE
  4. Grayhack EJ
  5. Phizicky EM
  The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4.; RNA (New York, N.Y.); Vol 13(3). 2007 Mar.
• 1. Jackman JE
  2. Kotelawala L
  3. Grayhack EJ
  4. Phizicky EM
  Identification and characterization of modification enzymes by biochemical analysis of the proteome.; Methods in enzymology; Vol 425. 2007.