Published papers    |   Conference Posters    |  

Past two years; full list at

Xiong X, Wu G, Wei Y, Liu L, Zhang Y, Su R, Jiang X, Li M, Gao H, Tian X, Zhang Y, Hu L, Chen S, Tang Y, Jiang S, Huang R, Li Z, Wang Y, Deng Z, Wang J, Dedon PC, Chen S, Wang L (2020) SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Nat Micro, Apr 6. doi: 10.1038/s41564-020-0700-6.

Leonardi A, Kovalchuk N, Yin L, Endres L, Evke S, Nevins S, Martin S, Dedon PC, Melendez JA, Van Winkle L, Zhang QY, Ding X, Begley TJ (2020) The epitranscriptomic writer ALKBH8 drives tolerance and protects mouse lungs from the environmental pollutant naphthalene. Epigenetics, Apr 17:1-18. doi: 10.1080/15592294.2020.1750213.

Wu X, Cao B, Aquino P, Chiu T-S, Chen C, Jiang S, Deng Z, Chen S, Rohs R, Wang L, Galagan J, Dedon PC (2019) Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate DNA modifications in bacterial genomes. Proc Natl Acad Sci USA, accepted.

Cao B, Wu, X, Zhou J, Wu H, DeMott MS, Gu C, Wang L, You D, Dedon PC (2019) Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage. bioRxiv 845768; doi:

 Kimura S, Dedon PC, Waldor, M (2019) Surveying the landscape of tRNA modifications by combining tRNA sequencing and RNA mass spectrometry. Nat Chem Biol, in press.

DeMott MS, Dedon PC (2019) The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea. Synth Syst Biotechnol, 4:132-133. PMCID: PMC6606745

Yuan Y, Zallot R, Grove, Payan D, Martin-Verstrate I, Sepic S, Balamkundu S, Neelakandane R, Gadi VK, Liu C-F, Swairjo MA, Dedon PC, Almo SC, Gerlt JA, de Crécy-Lagad V (2019) Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. Proc Natl Acad Sci USA, 16:19126-19135. PMCID: PMC6754566

Yam LY, Hsu LY, Yap PH, Yeo TW, Lee V, Schlundt J, Lwin MO, Limmathurotsakul D, Jit M, Dedon P, Turner P, Wilder-Smith A (2019) Antimicrobial Resistance in the Asia Pacific Region: A meeting report. Antimicrob Resist Infect Control 8: 202. PMCID: PMC6921568

Hammam E, Ananda G, Sinha A, Scheidig-Benatar C, Bohec M, Preiser P, Dedon PC, Scherf A, Vembar SS (2019) Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites. Nucleic Acids Res, 48(1):184-199. PMCID: PMC6943133

Hu JF, Yim D, Huber SM, Bacusmo JM, Ma D, DeMott MS, Levine SS, de Crécy-Lagard V, Dedon PC, Cao B (2019) Sequencing-based quantitative mapping of the RNA landscape in a cellular sample. bioRxiv 841130; doi:

Santos MCFD, Anderson CP, Neschen S, Zumbrennen-Bullough KB, Romney SJ, Kahle-Stephan M, Rathkolb B, Gailus-Durner V, Fuchs H, Wolf E, Rozman J, de Angelis MH, Cai WM, Rajan M, Hu J, Dedon PC, Leibold E (2020) Irp2 Regulates Insulin Production Through Iron-Mediated Cdkal1-Catalyzed tRNA Modification. Nat Commun, 11(1):296. PMCID: PMC6962211

Pollo-Oliveira L, Klassen R, Davis NK, Ciftci A, Bacusmo JM, Anderson M, DeMott MS, Dedon PD, Schaffrath R, de Crécy-Lagard V (2020) Loss of Elongator- and KEOPS-dependent tRNA modifications leads to severe growth phenotypes and protein aggregation in yeast. Biopolymers, 10(2): E322. PMCID: PMC7072221.

Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Neelakandan R, Carstens AB, Liu CF, Sassanfar M, Weigele P, Moineau S, Hatfull GF, Dedon PC, Hansen LH, de Crécy-Lagard V (2019) 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun, 10(1):5442. PMCID: PMC6884629.

Huber SM, Leonardi A, Dedon PC, Begley TJ (2019) The versatile roles of the tRNA epitranscriptome during cellular responses to toxic exposures and environmental stress. Toxics, 7(1): E17. PMCID: PMC6468425

Zhong W, Pasunooti KK, Balamkundu S, Wong YH, Nah Q, Chionh YH, McBee ME, Gopal P, Lim SH, Olivier N, Buurman ET, Dick T, Liu CF, Lescar J, Dedon PC (2019) Thienopyrimidinone derivatives that inhibit bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) by restructuring the active site with a tyrosine-flipping mechanism. J Med Chem, 62:7788-7805. PMCID: PMC6748665

Zhong W, Guo J, Cui L, Chionh YH, Li K, El Sahili A, Cai Q, Yuan M, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD, MuY, Lescar J, Dedon PC (2019) Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in Mycobacterium tuberculosis. J Mol Biol, 2019 Aug 2. pii: S0022-2836(19)30484-X. doi: 10.1016/j.jmb.2019.07.033

Baumgarten S, Bryant JM, Sinha A, Reyser T, Preiser PR, Dedon PC, Scherf A (2019) Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development. Nature Micro, 2019 Aug 5. doi: 10.1038/s41564-019-0521-7.

Candiracci J, Migeot V, Chionh YH, Bauer F, Brochier T, Russell B, Shiozaki K, Dedon PC, Hermand D (2019) Reciprocal regulation of TORC signaling and tRNA modifications by Elongator enforces nutrient-dependent cell fate. Science Adv, 5(6):eaav0184. PMCID: PMC6584457.

Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C (2019) Backbone resonance assignment for the full length tRNA-(N1G37) methyltransferase of Pseudomonas aeruginosa. Biomol NMR Assign,

Wang J, Chew BLA, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu X-Y, Lin Z, Shi P-Y, Lu TK, Luo D, Jaffrey SR, Dedon PC (2019) Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids Res, in press. doi: 10.1093/nar/gkz751

Li W, Chan CK, Liu Y, Yao J, Mitic B, Kostic EN, Milosavljevic B, Davinic I, Orem WH, Tatu CA, Dedon PC, Pavlović NM, Chan W (2018) Aristolochic Acids as Persistent Soil Pollutants: Determination of Risk for Human Exposure and Nephropathy from Plant Uptake. J Agric Food Chem, 66: 11468-11476. PMID: 30286603 doi: 10.1021/acs.jafc.8b04770.

Ng CS, Sinha A, Aniweh Y, Nah Q, Babu IR, Gu C, Chionh YH, Dedon PC, Preiser PR (2018) tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. Mol Sys Biol, 14: e8009. PMCID: PMC6171970

Wang L, Jiang S, Deng Z, Dedon P, Chen S (2018) DNA phosphorothioate modification — a new multi-functional epigenetic system in bacteria. FEMS Micro Rev, 43:109-122. PMCID: PMC6435447

Bi X, Yin J, Rao R, Banerjeem B, Balamkundu S, Zhang D, Zhang D, Dedon P, Liu C-F (2018) Thiazolidin-5-imine Formation as a Catalyst-Free Bioorthogonal Reaction for Protein and Live Cell Labeling. Org Lett. 20:7790-7793. DOI: 10.1021/acs.orglett.8b03195

Li Y, Zhong W, Koay AZ, Ng HQ, Ngo A, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Keller TH, Lescar J, Hill J, Dedon PC, Kang C (2018) Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N1G37) methyltransferase. Biomol NMR Assign, 13(1):49-53. doi: 10.1007/s12104-018-9849-9. PMID: 30298375

Yuan Y, Hutinet G, Gamboa Valera J, Hu J, Hillebrand R, Gustafson A, Iwata-Reuyl D, Dedon PC, and de Crécy-Lagard V (2018) Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery. Mol Micro, 110: 469-483. PMCID: PMC6207457, DOI: 10.1111/mmi.14113

Jaroensuk J, Wong YH, Zhong W, Liew C, Maenpuen S, Atichartpongkul S, Chionh YH, Nah JQH, Thongdee N, McBee M, Prestwich E, DeMott M, Chaiyen P, Mongkolsuk S, Dedon P, Lescar J, Fuangthong M (2018) Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa. RNA, in press.

Zhong W, Koay AZ, Ngo A, Nah Q, Wong YH, Chionh YH, Li Y, Ng HQ, Stenta CK, Poulsen A, Kang C, Keller TH, Lescar J, Hill J, Dedon PC (2019) Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors. ACS Infect Dis. 5: 326-335. PMCID: in process.

Rothenberg DA, Taliaferro JM, Huber SM, Begley TJ, Dedon PC, Burge CB, White FM (2018) A proteomics approach to profiling the temporal translational response to stress and growth. iScience. 9: 367-381. DOI: 10.1016/j.isci.2018.11.004. PMCID: PMC6249402

Keegan C, Krutzik S, Schenk M, Scumpia PO, Lu J, Pang YLJ, Russell BS, Lim KS, Shell S, Prestwich E, Su D, Elashoff D, Hershberg RM, Bloom BR, Belisle JT, Fortune S, Dedon PC, Pellegrini M, Modlin RL (2018) Mycobacterium tuberculosis transfer RNA induces IL-12p70 via synergistic activation of pattern recognition receptors within a cell network. J Immunol, 200: 3244-3258. PMCID: PMC5916334

Chan C, Pham P, Dedon PC, Begley TJ (2018) Lifestyle modifications: Coordinating the tRNA epitranscriptome and an alternative genetic code to adapt translation during stress responses. Genome Biol, 19: 228.

Gu C, Ramos J, Begley U, Dedon PC, Fu D, Begley TJ (2018) Phosphorylation of human TRM9L is a critical regulator of oxidative stress survival and tumor growth suppression. Sci Adv, 4: eaas9184. PMCID: PMC6040840