Dedon, P.C., T.J. Begley (2014) Perspective: A system of RNA modifications and biased codon use control cellular stress response at the level of translation. Chem. Res. Toxicol., in press.

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. (2013) 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. 2013 Dec 16. [Epub ahead of print]. PMID: 24344322

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 (2013) Quantitative analysis of tRNA modifications by HPLC-coupled mass spectrometry. Nat Protocols, in press.

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. PMID: 23926919; PMCID: in process.

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.

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. PMID: 24087891; PMCID: PMC3805309

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.

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: in process.

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

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, 2013 Apr 30. [Epub ahead of print].

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

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. PMCID: PMC3585032; available at http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003328

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. Mar 18. [Epub ahead of print]

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

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

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

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.

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 (2012) Human tRNA methyltransferase 9 prevents tumor growth by regulating LIN9 and HIF1α. EMBO Mol. Med., 5: 366-383. PMID: 23381944; PMCID: PMC3598078

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

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.

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.

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., Jan 23. [Epub ahead of print].

Dong, H., D.C. Chang, M.H.C. Hua, S.P. Lim, P.C. Dedon, and P.-Y. Shi (2012) 2’-O Methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS Pathogens, 8: e1002642. Available at http://www.plospathogens.org/article/info%3Adoi%2F10. 1371%2Fjournal.ppat.1002642

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.

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.

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.

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

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 (2011) Integrated molecular analysis indicates undetectable DNA Damage in mice after continuous irradiation at ~400-fold natural background radiation. Env. Health. Perspec., in press.

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.

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.

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. Dengb, and P.C. Dedon (2011) DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc. Natl. Acad. Sci. USA, 108: 2963-2968.

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.

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

Lonkar, P., and P.C. Dedon (2010) Reactive species and DNA damage in chronic inflammation: Reconciling chemical mechanisms and biological fates.  Int. J. Cancer 128: 1999-2009.

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.

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.

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.

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

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.

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.

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

Rai, P., T.T. Onder, J.J. Young, J.L. McFaline, B. Pang, P.C. Dedon and R.A. Weinberg (2009) Continuous elimination of oxidized nucleotides is necessary to prevent rapid onset of cellular senescence. Proc. Nat. Acad. Sci.USA, 106: 169-74.

DeMott, M.S., and P.C. Dedon (2009) The chemistry of inflammation and DNA damage: biological impact of reactive nitrogen species, in The Chemical Biology of DNA Damage, ed. N. Geacintov, S. Broyde. Wiley-VCH, Weinheim, in press.

Prestwich, E.G., and P.C. Dedon (2009) Endogenous DNA damage, in Endogenous Toxins: Diet, Genetics, Disease and Treatment, ed. P.J. O’Brien, R.W. Bruce. Wiley-VCH, Wienheim, in press.

Barth, M.C., D.A. Dederich and P.C. Dedon (2009) Using ionic strength to control supercoiling in large-scale preparations of positively and negatively supercoiled plasmid DNA. Biotechniques 47: 633-635.

Lee, Y.A., A. Durandin, P.C. Dedon, N.E. Geacintov, and V. Shafirovich (2008) Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: Relationship between kinetics and distribution of alkali-labile lesions. J. Phys. Chem. B, 112: 1834-1844.

Son, J., B. Pang, J. McFaline, K. Taghizadeh, P.C. Dedon (2008) Surveying the damage: The challenges of developing nucleic acid biomarkers of inflammation. Molecular Biosys., 4: 902-908.

Ringvoll, J., M.P. Nabong, L.M. Nordstrand, L.B. Meira, B. Pang, A. Bekkelund, P.C. Dedon, S. Bjelland, L.D. Samson, P.Ø. Falnes, and A. Klungland (2008) AlkB homolog 2 (ABH2) is the principle dioxygenase for repair of ethenoadenine lesions in mammalian DNA. Cancer Res., 68: 4142-4149.

Meira, L.B., J.M. Bugni, S.L. Green, C.-W. Lee, B. Pang, D. Borenshtein, B.H. Rickman, A.B. Rogers, C.A. Moroski, J.L. McFaline, D.B. Schauer, P.C. Dedon, J.G. Fox and L.D. Samson (2008) DNA damage induced by chronic inflammation contributes to colon carcinogenesis. J. Clin. Invest., 118: 2516-2525.

Taghizadeh, K., J.L. McFaline, B. Pang, M. Sullivan, M. Dong, E. Plummer, and P.C. Dedon (2008) Quantification of DNA damage products resulting from deamination, oxidation and reaction with products of lipid peroxidation by liquid chromatography isotope dilution tandem mass spectrometry. Nat. Protocols, 3: 1287-1298.

Lim, C.-H., P.C. Dedon and W.M. Deen (2008) Kinetic analysis of intracellular concentrations of reactive nitrogen species. Chem. Res. Toxicol., 21: 2134-47.

Margolin, Y., V. Shafirovich, N.E. Geacintov, M.S. DeMott and P.C. Dedon (2008) DNA sequence context as a determinant of the quantity and chemistry of guanine oxidation produced by hydroxyl radicals and one-electron oxidants. J. Biol. Chem., 283: 35569-35578.

Pang, B., X. Zhou, H. Yu, M. Dong, K. Taghizadeh, J.S. Wishnok, S.R. Tannenbaum and P.C. Dedon (2007) Lipid peroxidation dominates the chemistry of DNA adduct formation in a mouse model of inflammation. Carcinogenesis 8: 1807-1813.

Yun BH, Lee YA, Kim SK, Kuzmin V, Kolbanovskiy A, Dedon PC, Geacintov NE, Shafirovich V. (2007) Photosensitized oxidative DNA damage: from hole injection to chemical product formation and strand cleavage. J. Am. Chem. Soc. 129: 9321-9332

Lee, Y.A., B.H. Yun, S.K. Kim, Y. Margolin, P.C. Dedon, N.E. Geacintov and V. Shafirovich (2007) Mechanisms of guanine oxidation in DNA by carbonate radical anion, a decomposition product of nitrosoperoxycarbonate. Chemistry 3: 4571-81.

Kim MY, Zhou X, Delaney JC, Taghizadeh K, Dedon PC, Essigmann JM, Wogan GN (2007) AlkB Influences the Chloroacetaldehyde-Induced Mutation Spectra and Toxicity in the pSP189 supF Shuttle Vector. Chem Res Toxicol. 20: 1075-1083.

Dedon, P.C., M. DeMott, E. Elmquist, E. Prestwich, B. Pang, J. McFaline (2007) The challenges of developing DNA and RNA biomarkers of inflammation. Biomarkers Med., 1: 293-312.

Chen, B., Z. Xinfeng Zhou, K. Taghizadeh, J. Chen, J. Stubbe and P.C. Dedon (2007) GC-MS methods to quantify the 2-deoxypentos-4-ulose and 3'-phosphoglycolate pathways of 4'-oxidation of deoxyribose: Application to DNA damage produced by γ-radiation and bleomycin. Chem. Res. Toxicol., 20: 1701-1708.

Dedon, P.C. (2007) The chemical toxicology of 2-deoxyribose oxidation in DNA. Chem. Res. Toxicol., 21: 206-219 (invited review for 20th Anniversary Edition).

Wang, L., Chen, S., Xu, T., Taghizadeh, K., Wishnok, J., Zhou, X., You, D., Deng, Z., Dedon, P.C. (2007) Phosphorothioation of DNA in bacteria by dnd genes. Nat. Chem. Biol., 3: 709-710.

Dong, M. and P.C. Dedon (2006) Relatively small increases in the steady-state levels of nucleobase deamination products in DNA from human TK6 cells exposed to toxic levels of nitric oxide. Chem. Res. Toxicol. 19: 50-57.

Zipes, D., M. Pfeffer, N. Zvaifler, R. Glassock, S. Gilman, A. Muñoz, V. Gogolak, L. Gordis, P. Dedon, F. Guengerich, S. Wasserman, J. Witztum, and G. Wogan (2006) Rosuvastatin: An independent analysis of risks and benefits. MedGenMed, 8: 73; available at: http://medgenmed.medscape.com/viewarticle/533930.

Li, C.-Q., B. Pang, T. Kiziltepe, L.J. Trudel, B.P. Engelward,P.C. Dedon, and G.N. Wogan (2006) Threshold effects of nitric oxide-induced toxicity and cellular responses in wild-type and p53-null human lymphoblastoid cells. Chem. Res. Toxicol., 19: 399-406.

Margolin, Y., J.-F. Cloutier, V. Shafirovich, N. Geacintov and P.C. Dedon (2006) Paradoxical hotspots for guanine oxidation by a chemical mediator of inflammation. Nature Chem. Biol. 2: 365-366.

Chen, B., C. Vou, M. Byrns, P. Dedon, and L. Peterson (2006) Formation of 1,4-dioxo-2-butene-derived adducts of 2'-deoxyadenosine and 2'-deoxycytosine in oxidized DNA. Chem. Res. Toxicol., 19: 982-5.

Reiter, T.A., B. Pang, P.C. Dedon, and B. Demple (2006) Resistance to nitric oxide-induced necrosis in heme oxygenase-1 over-expressing pulmonary epithelial cells associated with decreased lipid peroxidation. J. Biol. Chem. 281: 36603-36612

Dedon, P.C. and M.C. Barth (2006) Oxidatively damaged DNA and inflammation, in Oxidative Damage to Nucleic Acids, ed. M. Evans and M. Cooke, Landes Bioscience/Eurekah.com, Austin, TX.

Fry, R., M. DeMott, J. Cosgrove, T. Begley, L. Samson and P. Dedon (2006) The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA. BMC Genomics 7: 313.

Jiang, T., X. Zhou, K. Taghizadeh, M. Dong, P. Dedon (2006) N-Formylation of lysines in histone proteins: A novel secondary modification arising from oxidative DNA damage. Proc. Natl. Acad. Sci. USA 104: 60-65.