157) Lin C-J, Smibert P, Zhao X, Hu J, Ramroop J, Kellner S, Benton M, Saint R, Govind S, Dedon P, Sternglanz R, Lai EC (2015) An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis. RNA, 2015 Oct 29. [Epub ahead of print].

156) Cao B, Zheng X, Cheng Q, Yao F, Zheng T, Ramesh Babu I, Zhou H, Dedon P, You D (2015) In vitro analysis of phosphorothioate modification of DNA reveals substrate recognition by a multiprotein complex. Sci Rep 5: 12513. PMCID: PMC4515589.

155) Endres L, Begley U, Clark R, Gu C, Dziergowska A, Małkiewicz A, Melendez JA, Dedon PC, Begley TJ (2015) Alkbh8 regulates selenocysteine-protein expression to protect against reactive oxygen species damage. PLoS One 10: e0131335. PMCID: PMC4492958.

154) Chionh YH, Babu IR, Hia F, Ng, SW, Dziergowska A, Malkiewicz A, Begley TJ, Alonso S, Dedon PC (2015) Reprogrammed tRNAs read a code of codons to regulate mycobacterial persistence. Submitted for publication.

153) Cai WLM, Chionh YH, Hia F, Gu G, Kellner S, McBee ME, Ng CS, Pang YJL, Prestwich EG, Lim KS, Babu IR, Begley TJ, Dedon PC (2015) A platform for discovery and quantification of modified ribonucleosides in RNA: Application to stress-induced reprogramming of tRNA modifications. Meth Enz, 560: 29-71. PMCID – in process.

152) McBee MS, Chionh YH, Hia F, Ma D, Lin WW, Sharaf ML, Cai WLM, Jumpathong W, Levine S, Alonso S, Dedon PC (2015) Starvation induces a diabetes-like state in persistent mycobacteria. Submitted for publication.

151) Lin W, De Sessions PF, Ang MLT, Dedon PC, Hibberd ML, Alonso S (2015) A lysosomal in vitro exposure (LivE) model to identify pathways critical for Mycobacterium tuberculosis intracellular persistence. Submitted for publication.

150) Deng W, Babu IR, Su D, Yin S, Begley TJ, Dedon PC (2015) Trm9-catalyzed tRNA modifications regulate global protein expression by codon-biased translation. PLoS Genetics, in revision

149) Nguyen KNT, Nguyen GKT, Nguyen PQT, Dedon PC, Tam JP (2015) Sequence and functional diversity of cyclotides from the medicinal plant Clitoria ternatea. Submitted for publication.

148) Jumpathong W, Chan W, Taghizadeh K, Babu IR, Dedon PC (2015) Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation. Proc Natl Acad Sci USA, 112: E4845-53. PMCID: PMC4568270.

147) Endres L, Dedon PC, Begley TJ (2015) Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses. RNA Biol 12: 603-14. PMCID: PMC4615639

146) Chan CT, Deng W, Li F, DeMott MS, Babu IR, Begley TJ, Dedon PC (2015) Highly predictive reprogramming of tRNA modifications is linked to selective expression of codon-biased genes. Chem Res Toxicol 28: 978-88. PMCID: PMC4438938.

145) Hia F, Chionh YH, Pang YL, DeMott MS, McBee ME, Dedon PC (2015) Mycobacterial RNA isolation optimized for non-coding RNA: High fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides. Nucleic Acids Res 43: e32. PMCID: PMC4357692

144) Ribas de Pouplana L, Dedon PC (2014) More than an adaptor molecule: The emerging role of tRNA in cell signaling and disease. FEBS Lett, 588, 4267. PMCID: PMC4418787.

143) Witkin KL, Hanlon SE, Strasburger JA, Coffin JM, Jaffrey SR, Kevin Howcroft T, Dedon PC, Steitz JA, Daschner PJ, Read-Connole E (2015) RNA editing, epitranscriptomics, and Processing in cancer progression. Cancer Biol Ther, 16: 21-7. PMCID: PMC4622672.

142) Gu C., Begley T.J., Dedon P.C. (2014) tRNA modifications regulate translation during cellular stress. FEBS Lett, 588: 4287-4296. PMCID: PMC4403629.

141) Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, Wernig M, Mullen AC, Xing Y, Giallourakis CC, Chang HY (2014) m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15: 707-719. PMCID: PMC4278749

140) Pang Y.L.J., R. Abo, S.S. Levine, P.C. Dedon (2014) Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. Nucleic Acids Res, 42: e170. PMCID: PMC4267671

139) Cao B., Cheng Q., Gu C., Yao F., DeMott M.S., Zheng X., Deng Z., Dedon P.C., You D. (2014) Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella. Mol Microbiol. 93: 776-785. PMCID: PMC4414249.

138) Cao, B., C. Chen, M.S. DeMott, Q. Cheng, T.A. Clark, X. Xiong, X. Zheng, V. Butty, S.S. Levine, G. Yuan, M. Boitano, K. Luong, Y. Song, X. Zhou, Z. Deng, S.W. Turner, J. Korlach, D. You, L. Wang, S. Chen, P.C. Dedon (2014) Mapping phosphorothioate modifications across bacterial genomes: Partial modification in the presence of restriction and sequence-specificity without apparent consensus. Nat Commun, 5: 3951. PMCID: PMC4322921.

137) Zeiger, E., B. Gollapudi, M. Aardema, S. Auerbach, D. Boverhof, L. Custer, P. Dedon, M. Honma, S. Ishida, A. Kasinski, J.H. Kim, M. Manjanatha, J. Marlowe, S. Pfuhler, I. Pogribny, W. Slikker, L.F. Stankowski, J.Y. Tanir, R. Tice, J. van Benthem, P. White, K.L. Witt, V. Thybaud (2015) Opportunities to Integrate New Approaches in Genetic Toxicology: An ILSI-HESI Workshop Report. Envir Mol Mut, 56: 277-85. PMCID: PMC4615680.

136) Courtes, F.C., C. Gu, N.S.C. Wong, P.C. Dedon, M.G.S. Yap, D.-Y. Lee (2014) 28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures. J. Biotechnol. 174: 16-21. PMCID: PMC4310699.

135) Dedon, P.C., T.J. Begley (2014) A system of RNA modifications and biased codon use control cellular stress response at the level of translation. Chem. Res. Toxicol. 27: 330-337. PMCID: PMC3997223

134) Mandal D., Köhrer C., Su D., Babu I.R., Chan C.T., Liu Y., Söll D., Blum P., Kuwahara M., Dedon P.C., Rajbhandary U.L. (2014) Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs. RNA 20: 177-188. PMCID: PMC3895270

133) Su, D., C.T.Y. Chan, C. Gu, K.S. Lim, Y.H. Chionh, M.E. McBee, B.S. Russell, I. R. Babu, T.J. Begley, P.C. Dedon (2014) Quantitative analysis of tRNA modifications by HPLC-coupled mass spectrometry. Nat Protocols, 9: 828-841. PMCID: PMC4313537

132) Mangerich, A., P.C. Dedon, J.G. Fox, S.R. Tannenbaum, G.N. Wogan (2013) Chemistry meets biology in colitis-associated carcinogenesis. Free Radic. Res. 47: 958-986. PMCID: PMC4316682.

131) Li, Y., Chen, Q., Zheng, D., Yin, L., Chionh, Y.H., Wong, L.H., Tan, S.Q., Tan, T.C., Chan, J.K., Alonso, S., Dedon, P.C., Lim, B., Chen, J. (2013) Induction of functional human macrophages from bone marrow promonocytes by M-CSF in humanized mice. J Immunol. 191: 3192-3199. PMID: 23935193, PMCID: in process. Free full text: http://www.jimmunol.org/content/191/6/3192.long

130) Edrissi, B., Taghizadeh, K., Moeller, B.C., Kracko, D., Doyle-Eisele, M., Swenberg, J.A., Dedon, P.C. (2013) Dosimetry of N6-formyllysine adducts following [13C2H2]-formaldehyde exposures in rats. Chem. Res. Toxicol., 26: 1421-1423. PMCID: PMC3805309

129) Chionh, Y.H., C.-H. Ho, D. Pruksakorn, R. I. Babu, C.S. Ng, F. Hia, M.E. McBee, C. Gu, H. Dong, E. Prestwich, P.-Y. Shi, P. Preiser, S. Alonso, and P.C. Dedon (2013) A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res., 41: e168. PMID: 23907385; PMCID: PMC3783195.

128) Müller, N., Moreno-Villanueva, M., Fischbach, A., Kienhöfer, J., Martello, R., Dedon, P.C., Ullrich, V., Bürkle, A., Mangerich, A. (2013) An automated Fpg-based FADU method for the detection of oxidative DNA lesions and screening of antioxidants. Toxicology, 310C: 15-21. PMID: 23707620, PMCID: PMC3822336.

127) Knutson, C.G., Mangerich, A., Zeng, Y., Raczynski, A.R., Liberman, R.G., Kang, P., Ye, W., Prestwich, E., Lu, K., Wishnok, J.S., Korzenik, J.R., Wogan, G.N., Fox, J.G., Dedon, P.C., Tannenbaum, S.R. (2013) Features of innate immunity dominate serum and tissue protein and cytokine profiles in both mouse and human inflammatory bowel disease. Proc. Natl. Acad. Sci. USA, 110: E2332-41. PMID: 23754421, PMCID: PMC3696795

126) Martello, R., Mangerich, A., Sass, S., Dedon, P.C., Bürkle, A. (2013) Quantification of cellular poly(ADP-ribosyl)ation by stable isotope dilution mass spectrometry reveals tissue- and drug-dependent stress response dynamics. Chem Biol, 8:1567-1575. PMID: 23631432, PMCID: PMC3795969

125) Shell, S., Prestwich, E., Baek, S.-H., Shah, R., Sassetti, C., Dedon, P.C., Fortune, S. (2013) DNA methylation regulates gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. PLoS Pathogens, 9: e1003419.  PMID: 23853579; PMCID: PMC3701705; available at http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003419

124) Edrissi B., Taghizadeh K., Dedon P.C. (2013) Quantitative analysis of histone modifications: formaldehyde is a source of pathological N6-formyllysine that is refractory to histone deacetylases. PLoS Genet. 9(2): e1003328. PMID: 23468656; PMCID: PMC3585032; available at http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003328

123) Prestwich E., Mangerich A., Pang B., McFaline J.L., Lonkar P., Sullivan M.R., Trudel L.J., Taghizadeh K., Dedon P.C. (2013) Increased levels of inosine in a mouse model of inflammation. Chem. Res. Toxicol., 26: 538-546. PMID: 23506120; PMCID: PMC3726579

122) Begley, U., M.S. Sosa, A. Avivar-Valderas, A. Patil, L. Endres, Y. Estrada, C.T.Y. Chan, D. Su, P.C. Dedon, J.A. Aguirre-Ghiso, T.J. Begley (2013) Human tRNA methyltransferase 9 prevents tumor growth by regulating LIN9 and HIF1α.  EMBO Mol. Med., 5: 366-383. PMID: 23381944; PMCID: PMC3598078

121) Cui L., Ye W., Prestwich E., Wishnok J.S., Taghizadeh K., Dedon P.C., Tannenbaum S.R. (2012) Comparative analysis of four oxidized guanine lesions from reactions of DNA with peroxynitrite, singlet oxygen and γ-radiation. Chem. Res. Toxicol. 26: 195-202. PMID: 23140136; PMCID: PMC3578445

120) Lim, K.-S., C. Liang, K. Taghizadeh, J.S. Wishnok, W. Chan, M.S. DeMott, I.R. Babu, S.R. Tannenbaum, P.C. Dedon (2012) In situ analysis of 8-oxo-7,8-dihydro-2’-deoxyguanosine oxidation reveals sequence- and agent-specific damage spectra. J. Am. Chem. Soc. 134: 18053-18064. PMID: 23057664; PMCID: PMC3503518

119) Wogan G.N., P.C. Dedon, S.R. Tannenbaum, J. Fox (2012) Infection, inflammation and colon carcinogenesis. Oncotarget 3: 737-738.  Article available at http://www.impactjournals.com/oncotarget/

      index.php?journal=oncotarget&page=article&op=view&path[]=624

118) Patil, A., M. Dyavaiah, F. Joseph, J.P. Rooney, C.T.Y. Chan, P.C. Dedon, T.J. Begley (2012) Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response. Cell Cycle 11: 3656-3665. PMID: 22935709; PMCID: PMC3478316.

117) Patil, A., C.T.Y. Chan, M. Dyavaiah, J. Rooney, P.C. Dedon, T.J. Begley (2012) Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA Biol., 9: 990-1001. PMID: 22832247; PMCID: PMC3495739

116) Dendroulakis, V., B.S. Russell, C.E. Elmquist, L.J. Trudel, G.N. Wogan, W.M. Deen, P.C. Dedon (2012) A system for exposing molecules and cells to biologically relevant and accurately controlled steady-state concentrations of nitric oxide and oxygen. Nitric Oxide 27: 161-168. PMID: 22728703; PMCID: PMC3424365

115) Mangerich, A., C.G. Knutson, N.M.A. Parry, S. Muthupalani, W. Ye, E.G. Prestwich, L. Cui, J.L. McFaline, M.W. Mobley, Z. Ge, K. Taghizadeh, J.S. Wishnok, G.N. Wogan, J.G. Fox, S.R. Tannenbaum, P.C. Dedon (2012) Infection-induced colitis in mice causes dynamic and tissue-specific changes in stress response and DNA damage leading to colon cancer. Proc. Natl. Acad. Sci. USA 109: E1820-9. PMCID: 3390855

114) Cadet, J., S. Loft, R. Olinski, M.D. Evan, K. Bialkowski, J.R. Wagner, P.C. Dedon, P. Möller, M.M. Greenberg, M.S. Cooke (2012) Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids. Free Rad. Res. 46: 367-81. PMID: 22263561; PMCID: in process.

113) Mutamba, J.T., D. Svilarb, S. Prasongtanakija, X.-H. Wang, Y.-C. Lin, P.C. Dedon, R.W. Sobol and B.P. Engelward (2011) XRCC1 and base excision repair balance in response to nitric oxide. DNA Repair, 10: 1282-93.  PMID: 22041025; PMCID: PMC3593656

112) Dong H, Chang DC, Hua MH, Lim SP, Chionh YH, Hia F, Lee YH, Kukkaro P, Lok SM, Dedon PC, Shi PY (2012) 2’-O Methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS Pathogens, 8: e1002642. PMID: 22496660; PMCID: PMC3320599; available at http://www.plospathogens.org/article/info%3Adoi%2F10. 1371%2Fjournal.ppat.1002642

111) Chan, T.Y.C., Y.L.J. Pang, I.R. Babu, M. Dyavaiah, T.J. Begley and P.C. Dedon (2012) Reprogramming of tRNA modifications controls the oxidative stress response by selective translation of ribosomal protein paralogs. Nat. Comm. 3: 937. PMID: 22760636; PMCID - PMC3535174.

110) Pang, B., J.L. McFaline, N.E. Burgis, M. Dong, K. Taghizadeh, M.R. Sullivan, C.E. Elmquist, R.P. Cunningham and P.C. Dedon (2012) Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA. Proc. Natl. Acad. Sci. USA 109: 2319-24. PMID: 22308425; PMCID: PMC3289290

109) Olipitz, W., D. Wiktor-Brown, J. Shuga, B. Pang, J.L. McFaline, P. Lonkar, A. Thomas, J.T. Mutamba, J.S. Greenberger, L.D. Samson, P.C. Dedon, J.C. Yanch, and B.P. Engelward (2012) Integrated molecular analysis indicates undetectable DNA Damage in mice after continuous irradiation at ~400-fold natural background radiation.  Env. Health. Perspec. 120: 1130-1136. PMID: 22538203; PMCID: PMC3440074.

108) Lim, K.S., K. Taghizadeh, J.S. Wishnok, I.R. Babu, V. Shafirovich, N.E. Geacintov and P.C. Dedon (2011) Sequence-dependent variation in the reactivity of 8-oxo-7,8-dihydro-2’-deoxyguanosine toward oxidation. Chem Res. Toxicol. 25: 366-73.  PMID: 22103813; PMCID: PMC3288455.

107) Lee, Y.A., Z. Liu, P.C. Dedon, N.E. Geacintov, V. Shafirovich (2011) Solvent exposure associated with single abasic sites alters the base sequence dependence of oxidation of guanine in DNA in GG sequence contexts. Chembiochem 12: 1731-1739. PMID: 21656632; PMCID: PMC3517150.

106) Chan, C.T.Y., Y.H. Chionh, C.-H. Ho, K.S. Lim, I.R. Babu, E. Ang, W. Lin, S. Alonso, P.C. Dedon (2011)

Identification of N6,N6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin. Molecules 16: 5168-81.  PMID: 21694680; PMCID: in process

105) Wang, L. S. Chen, K.L. Vergin, S.J. Giovannoni, S.W. Chan, M.S. DeMott, K. Taghizadeh, O.X. Cordero, M. Cutler, S. Timberlake, E.J. Alma, M.F. Polz, J. Pinhassig, Z. Deng, and P.C. Dedon (2011) DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc. Natl. Acad. Sci. USA 108: 2963-2968. PMID: 21285367; PMCID: PMC3041111

104) Hanada, Y., P.C. Dedon, M.S. DeMott (2010) The chemical biology of phosphorothioate modifications of DNA in prokaryotes: Development of affinity purification methods. MIT UROP J. Volume 19.

103) Chan, C.T.Y., M. Dyavaiah, M.S. DeMott, K. Taghizadeh, P.C. Dedon and T.J. Begley (2010) A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genetics 6: e1001247.  PMID 21187895; PMCID: 21187895

102) Chan, S.W.C., and P.C. Dedon (2010) The biological and metabolic fates of endogenous DNA damage products. J. Nucleic Acids 2010: 929047. PMID 21209721; PMCID: PMC3002981

101) Lonkar, P., and P.C. Dedon (2011) Reactive species and DNA damage in chronic inflammation: Reconciling chemical mechanisms and biological fates.  Int. J. Cancer 128: 1999-2009. PMID: 21128231; PMCID: PMC3334345

100) Yun B.H., P.C. Dedon, N.E. Geacintov, V. Shafirovich (2010) One-electron oxidation of a pyrenyl photosensitizer covalently attached to DNA and competition between its further oxidation and DNA hole injection.  Photochem. Photobiol. 86: 563-570.  PMID: 20408978; PMCID: in process

99) Fu, D., J.A.N. Brophy, C.T.Y. Chan, K.A. Atmore, U. Begley, R.S. Paules, P.C. Dedon, T.J. Begley and L.D. Samson (2010) Human AlkB homolog ABH8 is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol. Cell Biol. 30: 2449-2459.  PMID: 20308323; PMCID: PMC2863699

98) Cooke, M., S. Loft, R. Olinski, M. Evans, K. Bialkowski, J. Wagner, P. Dedon, P. Moller, M. Greenberg, and J. Cadet (2010) Recommendations for standardised description of, and nomenclature concerning, oxidatively damaged nucleobases in DNA. Chem. Res. Toxicol. 23: 705-707.  PMID: 20235554; PMCID: in process

97) Dedon, P.C. (2010) Oxidation and deamination of DNA by endogenous sources, in Chemical Carcinogenesis, ed. T. Penning.  Springer, New York.

96) Chan, W., L. Wang, B. Chen, K. Taghizadeh, M.S. Demott, P.C. Dedon (2010) Quantification of the 2-deoxyribonolactone and nucleoside 5’-aldehyde products of 2-deoxyribose oxidation in DNA and cells by isotope-dilution gas chromatography mass spectrometry: Differential effects of γ-radiation and Fe+2-EDTA.  J. Am. Chem. Soc. 132: 6145-6153.  PMID: 20377226; PMCID: PMC2861150

95) Margolin, Y., and P.C. Dedon (2010) A general method for quantifying sequence effects on nucleobase oxidation in DNA. Meth. Molec. Biol. 610: 325-340. PMID: 20013187; PMCID: PMC2859239

94) Fox, J.G., Y. Feng, E.J. Theve, R.C. Fry, J.L.A. Fiala, A.L. Doernte, M. Williams, A.R. Raczynski, J.L. McFaline, J.M. Essigmann, D.B. Schauer, S.R. Tannenbaum, P.C. Dedon, S.A. Weinman, S.M. Lemon, A.B. Rogers (2010) Gut microbes define liver cancer risk in mice exposed to chemical and viral transgenic hepatocarcinogens.  Gut 59: 88-97. PMID: 19850960; PMCID – in process