174) Zhong W, Cui L, Goh BC, Cai Q, Ho P, Chionh YH, Yuan M, El Sahili A, Fothergill-Gilmore LA, Walkinshaw MD, Lescar J, Dedon PC (2017) Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis. Nat Commun, in press.

173) Edrissi B, Taghizadeh K, Moeller B, Yu R, Kracko D, Doyle-Eisele M, Swenberg J, Dedon PC (2017) N6-Formyllysine as a biomarker of formaldehyde exposure: Formation and loss of N6-formyllysine in nasal epithelium in long-term, low-dose inhalation studies in rats. Chem Res Toxicol, Jul 27. doi: 10.1021/acs.chemrestox.7b00075. [Epub ahead of print]

172) Bacsumo JM, Orsini SS, Hu J, DeMott M, Thiaville PM, Elfarash A, Paulines MJ, Rojas-Benítez D, Meineke B, Deutsch C, Iwata-Reuyl D, Limbach PA, Dedon PC, Rice KC, Shuman S, de Crécy-Lagard V (2017) The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. RNA Biol, Jul 20:0. doi: 10.1080/15476286.2017.1353861. [Epub ahead of print]

171) Braun DA, Rao J, Mollet G, Schapiro D, Daugeron M-C, Tan W, Gribouval O, Boyer O, Revy P, Jobst-Schwan T, Schmidt JM, Lawson JA, Schanze D, Ashraf S, Ullmann JFP, Hoogstraten CA, Boddaert N, Collinet B, Martin G, Liger D, Lovric S, Furlano M, Guerrera IC, Sanchez-Ferras O, Hu J, Boschat A-C, Sanquer S, Menten B, Vergult S, De Rocker N, Airik M, Hermle T, Shril S, Widmeier E, Gee HY, Choi WI, Sadowski CE, Pabst WL, Warejko J, Daga A, Basta-Leberre T, Matejas V, Scharmann K, Kienast SD, Behnam B, Beeson B, Begtrup A, Bruce M, Ch'ng G-S, Lin S-P, Chang J-H, Chen C-H, Cho MT, Gaffney PM, Gipson PE, Hsu C-H, Kari JA, Ke Y-Y, Kiraly-Borri C, Lai W-M, Lemyre E, Littlejohn RO, Masri A, Moghtaderi M, Nakamura K, Ozaltin F, Praet M, Prasad C, Prytula A, Roeder E, Rump P, Schnur RE, Shiihara T, Sinha M, Soliman NA, Soulami K, Sweetser DA, Tsai W-H, Tsai J-D, Topaloglu R, Vester U, Viskochil DH, Vatanavicharn N, Waxler JL, Wierenga KJ, Wolf MTF, Wong S-N, Leidel SA, Truglio G, Dedon PC, Poduri A, Mane S, Lifton RP, Bouchard M, Kannu P, Chitayat D, Magen D, Calleweart B, van Tilbeurgh H, Zenker M, Antignac C, Hildebrandt F (2017) Mutations in the KEOPS complex genes cause nephrotic syndrome with primary microcephaly. Nat Genetics, in press.

170) Wong YH, Goh BC, Lim SY, Teo EW, Lim A, Dedon PC, Hanson B, MacAry P, Lescar J (2017) Structural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex. J. Virol., Jun 21. pii: JVI.00406-17. doi: 10.1128/JVI.00406-17. [Epub ahead of print]

169) Kan L, Grozhik AV, Vedanayagam J, Patil DP, Pang N, Lim, Huang YC, Joseph B, Lin CJ, Guo J, Yan D, Kondo S, Deng WM, Dedon PC, Jaffrey SR, Lai EC (2017) The m6A pathway facilitates sex determination in Drosophila. Nat Commun, in press.

168) McBee ME, Chionh YH, Sharaf ML, Ho P, Cai WLM, Dedon PC (2017) Production of superoxide in bacteria is stress- and cell state-dependent: A gating-optimized flow cytometry method that minimizes ROS measurement artifacts with fluorescent dyes. Frontiers Micro, 8: 459. PMCID: PMC5359317

167) Chen C, Wang L. Chen S, Wu X, Gu M, Chen X, Deng Z, Dedon PC, Chen S (2017) Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes. Proc Natl Acad Sci, 114: 4501-4506. PMCID: PMC5410841

166) Edvardson S, Prunetti L, Arraf A, Haas D, Bacusmo JM, Hu JF, Ta-Shma A, Dedon PC, de Crécy-Lagard V, Elpeleg O. (2017) tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy. Eur J Hum Genet. 25: 545-551.

165) Kellner S, DeMott, MS, Cheng CP, Russell B, Cao B, Dedon PC (2017) Oxidation of labile phosphorothioate DNA modifications leads to lethal genomic instability. Nat Chem Biol, 13(8): 888-894. PMCID: PMC5577368.

164) 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: PMC5114619.

163) 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, 44(22):10834-10848. PMCID: PMC5159551.

162) Xu L, Liu X, Sheng N, Oo KS, Liang J, Chionh YH, Xu J, Ye F, Gao Y-G, Dedon P, Fu X-Y (2017) Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans. J Biol Chem, 292(35): 14695-14703. PMCID: PMC5582859

161) 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

160) 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. 107:98-109

159) 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 44(18): 8962-8975. PMCID: PMC5062971.

158) 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.

157) 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.

156) 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.

155) 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.

154) Endres L, Begley U, Clark R, Gu C, Dziergowska A, Malkiewicz 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.

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: PMC4774897.

152) McBee MS, Chionh YH, Hia F, Ma D, Lin WW, Sharaf ML, Cai WLM, Jumpathong W, Levine S, Alonso S, Dedon PC (2016) Starvation induces a diabetes-like state in persistent mycobacteria. In revision.

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. 84(9): 2505-2523. PMCID: PMC4995911.

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