URMC / Labs / Phizicky Lab / Publications Publications Patra BKon YYadav GSevold AWFrumkin JPVallabhajosyula RRHintze AØstman BSchossau JBhan AMarzolf BTamashiro JKKaur ABaliga NSGrayhack EJAdami CGalas DJRaval APhizicky EMRay A (2017 Jan 09). A genome wide dosage suppressor network reveals genomic robustness. Nucleic acids research. Hrabeta-Robinson EMarcus ECozen AEPhizicky EMLowe TM (2017). High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq). Methods in molecular biology (Clifton, N.J.). Han LMarcus ED'Silva SPhizicky EM (2016 Dec 21). S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates. RNA (New York, N.Y.). Shaheen RHan LFaqeih EEwida NAlobeid EPhizicky EMAlkuraya FS (2016 Apr 7). A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Human genetics. Guy MPShaw MWeiner CLHobson LStark ZRose KKalscheuer VMGecz JPhizicky EM (2015 Dec). Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. Human mutation. Cozen AEQuartley EHolmes ADHrabeta-Robinson EPhizicky EMLowe TM (2015 Sep). ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nature methods. Phizicky EMHopper AK (2015 Apr). tRNA processing, modification, and subcellular dynamics: past, present, and future. RNA (New York, N.Y.). Han LKon YPhizicky EM (2015 Feb). 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.). Payea MJGuy MPPhizicky EM (2015). Methodology for the High-Throughput Identification and Characterization of tRNA Variants That Are Substrates for a tRNA Decay Pathway. Methods in enzymology. Guy MPPhizicky EM (2015 Jan). Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA (New York, N.Y.). Shaheen RAbdel-Salam GMGuy MPAlomar RAbdel-Hamid MSAfifi HHIsmail SIEmam BAPhizicky EMAlkuraya FS (2015). Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome biology. Zhang XWalker RCPhizicky EMMathews DH (2014 Aug 12). Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. Journal of chemical theory and computation. Guy MPYoung DLPayea MJZhang XKon YDean KMGrayhack EJMathews DHFields SPhizicky EM (2014 Aug 1). Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis. Genes & development. Pop CRouskin SIngolia NTHan LPhizicky EMWeissman JSKoller D (2014). Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Molecular systems biology. Guy MPPhizicky EM (2014). Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification. RNA biology. Preston MAD'Silva SKon YPhizicky EM (2013 Feb). tRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae. RNA (New York, N.Y.). Dewe JMWhipple JMChernyakov IJaramillo LNPhizicky EM (2012 Oct). 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.). Guy MPPodyma BMPreston MAShaheen HHKrivos KLLimbach PAHopper AKPhizicky EM (2012 Oct). Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA (New York, N.Y.). Grant TDSnell EHLuft JRQuartley ECorretore SWolfley JRSnell MEHadd APerona JJPhizicky EMGrayhack EJ (2012 Apr). Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase. Nucleic acids research. D'Silva SHaider SJPhizicky EM (2011 Jun). 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.). Whipple JMLane EAChernyakov ID'Silva SPhizicky EM (2011 Jun 1). The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA. Genes & development. Phizicky EMHopper AK (2010 Sep 1). tRNA biology charges to the front. Genes & development. Preston MAPhizicky EM (2010 May). 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.). Murthi AShaheen HHHuang HYPreston MALai TPPhizicky EMHopper AK (2010 Feb 15). Regulation of tRNA bidirectional nuclear-cytoplasmic trafficking in Saccharomyces cerevisiae. Molecular biology of the cell. Phizicky EMAlfonzo JD (2010 Jan 21). Do all modifications benefit all tRNAs? FEBS letters. Quartley EAlexandrov AMikucki MBuckner FSHol WGDeTitta GTPhizicky EMGrayhack EJ (2009 Sep). Heterologous expression of L. major proteins in S. cerevisiae: a test of solubility, purity, and gene recoding. Journal of structural and functional genomics. Phizicky EM (2008 Aug). Waste not, want not: a case for tRNA repair. Nature structural & molecular biology. Merritt EAHolmes MBuckner FSVan Voorhis WCQuartly EPhizicky EMLauricella ALuft JDeTitta GNeely HZucker FHol WG (2008 Jun 1). Structure of a Trypanosoma brucei alpha/beta-hydrolase fold protein with unknown function. Acta crystallographica. Section F, Structural biology and crystallization communications. Chernyakov IWhipple JMKotelawala LGrayhack EJPhizicky EM (2008 May 15). Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5'-3' exonucleases Rat1 and Xrn1. Genes & development. Jackman JEPhizicky EM (2008 Apr 22). Identification of critical residues for G-1 addition and substrate recognition by tRNA(His) guanylyltransferase. Biochemistry. Kotelawala LGrayhack EJPhizicky EM (2008 Jan). 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.). Jackman JEGrayhack EJPhizicky EM (2008). The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins. Methods in molecular biology (Clifton, N.J.). Chernyakov IBaker MAGrayhack EJPhizicky EM (2008). Chapter 11. Identification and analysis of tRNAs that are degraded in Saccharomyces cerevisiae due to lack of modifications. Methods in enzymology. Malkowski MGQuartley EFriedman AEBabulski JKon YWolfley JSaid MLuft JRPhizicky EMDeTitta GTGrayhack EJ (2007 Apr 17). 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. Wilkinson MLCrary SMJackman JEGrayhack EJPhizicky EM (2007 Mar). The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. RNA (New York, N.Y.). Jackman JEKotelawala LGrayhack EJPhizicky EM (2007). Identification and characterization of modification enzymes by biochemical analysis of the proteome. Methods in enzymology. Phizicky EMGrayhack EJ (2006 Sep). Proteome-scale analysis of biochemical activity. Critical reviews in biochemistry and molecular biology. Jackman JEPhizicky EM (2006 Jun 6). tRNAHis guanylyltransferase catalyzes a 3'-5' polymerization reaction that is distinct from G-1 addition. Proceedings of the National Academy of Sciences of the United States of America. Jackman JEPhizicky EM (2006 Jun). tRNAHis guanylyltransferase adds G-1 to the 5' end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases. RNA (New York, N.Y.). Alexandrov AChernyakov IGu WHiley SLHughes TRGrayhack EJPhizicky EM (2006 Jan 6). Rapid tRNA decay can result from lack of nonessential modifications. Molecular cell. Arakaki TTrong IPhizicky EMQuartley EDeTitta GLuft JLauricella AAnderson LKalyuzhniy OWorthey EMyler PJKim DBaker DHol WGMerritt EA (2006 Jan 01). Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major Acta Crystallograph Sect F Struct Biol Cryst Commun. Gelperin DMWhite MAWilkinson MLKon YKung LAWise KJLopez-Hoyo NJiang LPiccirillo SYu HGerstein MDumont MEPhizicky EMSnyder MGrayhack EJ (2005 Dec 1). Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes & development. Gu WHurto RLHopper AKGrayhack EJPhizicky EM (2005 Sep). Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C. Molecular and cellular biology. Phizicky EM (2005 Aug 9). Have tRNA, will travel. Proceedings of the National Academy of Sciences of the United States of America. Cartlidge RAKnebel APeggie MAlexandrov APhizicky EMCohen P (2005 May 4). The tRNA methylase METTL1 is phosphorylated and inactivated by PKB and RSK in vitro and in cells. The EMBO journal. Alexandrov AGrayhack EJPhizicky EM (2005 May). tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. RNA (New York, N.Y.). Steiger MAJackman JEPhizicky EM (2005 Jan). Analysis of 2'-phosphotransferase (Tpt1p) from Saccharomyces cerevisiae: evidence for a conserved two-step reaction mechanism. RNA (New York, N.Y.). Shull NPSpinelli SLPhizicky EM (2005). A highly specific phosphatase that acts on ADP-ribose 1''-phosphate, a metabolite of tRNA splicing in Saccharomyces cerevisiae. Nucleic acids research. Alexandrov AVignali MLaCount DJQuartley Ede Vries CDe Rosa DBabulski JMitchell SFSchoenfeld LWFields SHol WGDumont MEPhizicky EMGrayhack EJ (2004 Sep). A facile method for high-throughput co-expression of protein pairs. Molecular & cellular proteomics : MCP. Xing FHiley SLHughes TRPhizicky EM (2004 Apr 23). The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. The Journal of biological chemistry.