163) Kellner S, DeMott, MS, Cheng CP, Russell B, Cao B, Dedon PC (2016) Oxidation of labile phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol, accepted for publication.

162) Chionh YH, Babu IR, Hia F, Ng, SW, Dziergowska A, Malkiewicz A, Begley TJ, Alonso S, Dedon PC (2016) Reprogrammed tRNAs read a code of codons to regulate mycobacterial persistence. Nat Commun, 7: 13302. PMCID: in process.

161) Jaroensuk J, Atichartpongkul S, Chionh YH, Wong YH, Liew C, McBee M, Thongdee N, Prestwich E, DeMott M, Mongkolsuk S, Dedon P, Lescar J, Fuangthong M (2016) Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa. Nucleic Acids Res, Sep 28. pii: gkw870. [Epub ahead of print]; DOI: 10.1093/nar/gkw870.

160) Shen L, Liang Z, Gu X, Chen Y, Teo ZWN, Hou X, Cai WM, Dedon PC, Liu L, Yu H (2016) N6-methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Dev Cell. 38: 186-200. PMCID: in process

159) Doyle F, Leonardi A, Endres L, Tenenbaum SA, Dedon PC, Begley TJ (2016) Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT codon utilization tool. Methods. 2016 May 28. [Epub ahead of print]

158) Wang J, Dong H, Chionh YH, McBee ME, Sasilada S, Cunningham RP, Shi PY, Dedon PC (2016) The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA. Nucleic Acids Res. 2016 Jun 30. pii: gkw572. [Epub ahead of print]

157) Molinie B, Wang J, Lu Z-X, Lim KS, Van Wittenberghe N, Howard BD, Daneshvar K, Hillebrand R, Dedon P, Mullen A, Xing Y, Giallourakis CG (2016) m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveals the census and complexity of the m6A epitranscriptome. Nat Methods. 13: 692-698. PMCID: in process.

156) Thiaville JJ, Kellner SM, Yuan Y, Hutineta G, Thiaville PC, Jumpathong W, Mohapatra S, Brochier-Armanet C, Letarov AV, Hillebrand R, Malik CK, Rizzo C, Dedon PC, de Crécy-Lagard V (2016) Novel genomic island modifies DNA with 7-deazaguanine derivatives. Proc Natl Acad Sci USA 113: E1452–E1459. PMCID: PMC4801273.

155) 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, 21: 2103-2118. PMCID: PMC4647464.

154) 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.

153) Endres L, Begley U, Clark R, Gu C, Dziergowska A, MaƂkiewicz 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.

152) 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: PMC4774897.

151) Lin W, De Sessions PF, Teoh G, Mohamed A, Zhu Y, Koh V, Ang MLT, Dedon PC, Hibberd ML, Alonso S (2016) Transcriptional profiling of Mycobacterium tuberculosis exposed to in vitro lysosomal stress. Infect Immun. 2016 Jun 20. pii: IAI.00072-16. [Epub ahead of print].

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, 11: e1005706. PMCID: PMC4689569

149) Nguyen KNT, Nguyen GKT, Nguyen PQT, Dedon PC, Tam JP (2016) Immunostimulating and Gram-negative-specific antibacterial cyclotides from the Butterfly Pea Clitoria ternatea. FEBS J. 283: 2067-2090. PMCID: in process.

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