Peter C. Dedon

Publications

• Queuosine Salvage in Houston 1: A Unique Evolutionary Path
  BioRxiv : the Preprint Server for Biology. Dec, 2023  |   Pubmed ID: 38106016
• The Greatwall-Endosulfine-PP2A/B55 Pathway Controls Entry into Quiescence by Promoting Translation of Elongator-tuneable Transcripts
  Research Square. Dec, 2023  |   Pubmed ID: 38105947
• Molecular Coping Mechanisms: Reprogramming TRNAs To Regulate Codon-Biased Translation of Stress Response Proteins
  Accounts of Chemical Research. Dec, 2023  |   Pubmed ID: 37992267
• Dengue Virus Exploits the Host TRNA Epitranscriptome to Promote Viral Replication
  BioRxiv : the Preprint Server for Biology. Nov, 2023  |   Pubmed ID: 37986976
• Discovery Adductomics Provides a Comprehensive Portrait of Tissue-, Age- and Sex-specific DNA Modifications in Rodents and Humans
  Nucleic Acids Research. Nov, 2023  |   Pubmed ID: 37843128
• Nanopore-based Direct Sequencing of RNA Transcripts with 10 Different Modified Nucleotides Reveals Gaps in Existing Technology
  G3 (Bethesda, Md.). Nov, 2023  |   Pubmed ID: 37655917
• Cohesin Contributes to Transcriptional Repression of Stage-specific Genes in the Human Malaria Parasite
  EMBO Reports. Oct, 2023  |   Pubmed ID: 37592911
• Four Additional Natural 7-deazaguanine Derivatives in Phages and How to Make Them
  Nucleic Acids Research. Sep, 2023  |   Pubmed ID: 37572349
• A Systems-level Mass Spectrometry-based Technique for Accurate and Sensitive Quantification of the RNA Cap Epitranscriptome
  Nature Protocols. Sep, 2023  |   Pubmed ID: 37567932
• An RNA Modification Enzyme Directly Senses Reactive Oxygen Species for Translational Regulation in Enterococcus Faecalis
  Nature Communications. Jul, 2023  |   Pubmed ID: 37433804
• Accumulation of MA Exhibits Stronger Correlation with MAPT Than β-amyloid Pathology in an APP /MAPT Mouse Model of Alzheimer's Disease
  Research Square. May, 2023  |   Pubmed ID: 37292629
• Rifaximin Potentiates Clarithromycin Against and in Zebrafish
  JAC-antimicrobial Resistance. Jun, 2023  |   Pubmed ID: 37168836
• Accumulation of MA Exhibits Stronger Correlation with MAPT Than β-amyloid Pathology in an APP /MAPT Mouse Model of Alzheimer's Disease
  BioRxiv : the Preprint Server for Biology. Mar, 2023  |   Pubmed ID: 37034774
• DNA Modifications Enabling Proximity Biotinylation
  Bioconjugate Chemistry. Mar, 2023  |   Pubmed ID: 36888923
• Dysfunctional TRNA Reprogramming and Codon-biased Translation in Cancer
  Trends in Molecular Medicine. Nov, 2022  |   Pubmed ID: 36241532
• Arsenite Toxicity is Regulated by Queuine Availability and Oxidation-induced Reprogramming of the Human TRNA Epitranscriptome
  Proceedings of the National Academy of Sciences of the United States of America. Sep, 2022  |   Pubmed ID: 36095201
• The Absence of the Queuosine TRNA Modification Leads to Pleiotropic Phenotypes Revealing Perturbations of Metal and Oxidative Stress Homeostasis in Escherichia Coli K12
  Metallomics : Integrated Biometal Science. Sep, 2022  |   Pubmed ID: 36066904
• Queuine Salvaging in the Human Parasite
  Cells. Aug, 2022  |   Pubmed ID: 36010587
• Nanopore Sequencing for Detection and Characterization of Phosphorothioate Modifications in Native DNA Sequences
  Frontiers in Microbiology. 2022  |   Pubmed ID: 35531280
• Crystal Structure and Functional Analysis of Mycobacterial Erythromycin Resistance Methyltransferase Erm38 Reveals Its RNA-binding Site
  The Journal of Biological Chemistry. Feb, 2022  |   Pubmed ID: 35007529
• Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses
  Angewandte Chemie (International Ed. in English). Oct, 2021  |   Pubmed ID: 34339593
• Bacteriophage VB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA
  International Journal of Molecular Sciences. Jul, 2021  |   Pubmed ID: 34298953
• Detecting the Epitranscriptome
  Wiley Interdisciplinary Reviews. RNA. Nov, 2021  |   Pubmed ID: 33987958
• Functional Characterization of the MA-Dependent Translational Modulator PfYTH.2 in the Human Malaria Parasite
  MBio. Apr, 2021  |   Pubmed ID: 33906926
• Quantitative Mapping of the Cellular Small RNA Landscape with AQRNA-seq
  Nature Biotechnology. Aug, 2021  |   Pubmed ID: 33859402
• Queuine Is a Nutritional Regulator of Entamoeba Histolytica Response to Oxidative Stress and a Virulence Attenuator
  MBio. Mar, 2021  |   Pubmed ID: 33688012
• TRNA-modifying Enzyme Mutations Induce Codon-specific Mistranslation and Protein Aggregation in Yeast
  RNA Biology. Apr, 2021  |   Pubmed ID: 32893724
• Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications
  Biomolecules. Oct, 2020  |   Pubmed ID: 33126637
• Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens
  Cell Systems. Sep, 2020  |   Pubmed ID: 32970993
• Detection of PreQ0 Deazaguanine Modifications in Bacteriophage CAjan DNA Using Nanopore Sequencing Reveals Same Hypermodification at Two Distinct DNA Motifs
  Nucleic Acids Research. Oct, 2020  |   Pubmed ID: 32941607
• Crystal Structure of the Periplasmic Sensor Domain of Histidine Kinase VbrK Suggests Indirect Sensing of β-lactam Antibiotics
  Journal of Structural Biology. Nov, 2020  |   Pubmed ID: 32890780
• Pyruvate Kinase from Plasmodium Falciparum: Structural and Kinetic Insights into the Allosteric Mechanism
  Biochemical and Biophysical Research Communications. Nov, 2020  |   Pubmed ID: 32878705
• Exploring the Virulence Gene Interactome with CRISPR/dCas9 in the Human Malaria Parasite
  Molecular Systems Biology. Aug, 2020  |   Pubmed ID: 32816370
• DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome
  Biomolecules. Aug, 2020  |   Pubmed ID: 32806589
• Epigenetic Competition Reveals Density-dependent Regulation and Target Site Plasticity of Phosphorothioate Epigenetics in Bacteria
  Proceedings of the National Academy of Sciences of the United States of America. Jun, 2020  |   Pubmed ID: 32518115
• Nick-seq for Single-nucleotide Resolution Genomic Maps of DNA Modifications and Damage
  Nucleic Acids Research. Jul, 2020  |   Pubmed ID: 32484547
• The Epitranscriptomic Writer ALKBH8 Drives Tolerance and Protects Mouse Lungs from the Environmental Pollutant Naphthalene
  Epigenetics. Oct, 2020  |   Pubmed ID: 32303148
• SspABCD-SspE is a Phosphorothioation-sensing Bacterial Defence System with Broad Anti-phage Activities
  Nature Microbiology. Jul, 2020  |   Pubmed ID: 32251370
• Loss of Elongator- and KEOPS-Dependent TRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast
  Biomolecules. Feb, 2020  |   Pubmed ID: 32085421
• Irp2 Regulates Insulin Production Through Iron-mediated Cdkal1-catalyzed TRNA Modification
  Nature Communications. Jan, 2020  |   Pubmed ID: 31941883
• Discovery of a New Predominant Cytosine DNA Modification That is Linked to Gene Expression in Malaria Parasites
  Nucleic Acids Research. Jan, 2020  |   Pubmed ID: 31777939
• 7-Deazaguanine Modifications Protect Phage DNA from Host Restriction Systems
  Nature Communications. Nov, 2019  |   Pubmed ID: 31784519
• Quantifying the RNA Cap Epitranscriptome Reveals Novel Caps in Cellular and Viral RNA
  Nucleic Acids Research. Nov, 2019  |   Pubmed ID: 31504804
• Discovery of Novel Bacterial Queuine Salvage Enzymes and Pathways in Human Pathogens
  Proceedings of the National Academy of Sciences of the United States of America. Sep, 2019  |   Pubmed ID: 31481610
• Thienopyrimidinone Derivatives That Inhibit Bacterial TRNA (Guanine37-)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism
  Journal of Medicinal Chemistry. Sep, 2019  |   Pubmed ID: 31442049
• Crystal Structure and Catalytic Mechanism of the Essential MG37 TRNA Methyltransferase TrmD from
  RNA (New York, N.Y.). Nov, 2019  |   Pubmed ID: 31399541
• Transcriptome-wide Dynamics of Extensive MA MRNA Methylation During Plasmodium Falciparum Blood-stage Development
  Nature Microbiology. Dec, 2019  |   Pubmed ID: 31384004
• Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium Tuberculosis
  Journal of Molecular Biology. Sep, 2019  |   Pubmed ID: 31381898
• The Road Less Traveled: A New Phosphorothioate Antiviral Defense Mechanism Discovered in Archaea
  Synthetic and Systems Biotechnology. Sep, 2019  |   Pubmed ID: 31312729
• Backbone Resonance Assignment for the Full Length TRNA-(NG37) Methyltransferase of Pseudomonas Aeruginosa
  Biomolecular NMR Assignments. Oct, 2019  |   Pubmed ID: 31175551
• The Versatile Roles of the TRNA Epitranscriptome During Cellular Responses to Toxic Exposures and Environmental Stress
  Toxics. Mar, 2019  |   Pubmed ID: 30934574
• Backbone Resonance Assignment for the N-terminal Region of Bacterial TRNA-(NG37) Methyltransferase
  Biomolecular NMR Assignments. Apr, 2019  |   Pubmed ID: 30298375
• DNA Phosphorothioate Modification-a New Multi-functional Epigenetic System in Bacteria
  FEMS Microbiology Reviews. Mar, 2019  |   Pubmed ID: 30289455
• Lifestyle Modifications: Coordinating the TRNA Epitranscriptome with Codon Bias to Adapt Translation During Stress Responses
  Genome Biology. Dec, 2018  |   Pubmed ID: 30587213
• A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth
  IScience. Nov, 2018  |   Pubmed ID: 30466063
• TRNA Epitranscriptomics and Biased Codon Are linked to Proteome Expression in
  Molecular Systems Biology. Oct, 2018  |   Pubmed ID: 30287681
• Aristolochic Acids As Persistent Soil Pollutants: Determination of Risk for Human Exposure and Nephropathy from Plant Uptake
  Journal of Agricultural and Food Chemistry. Oct, 2018  |   Pubmed ID: 30286603
• Identification of the Minimal Bacterial 2'-deoxy-7-amido-7-deazaguanine Synthesis Machinery
  Molecular Microbiology. Nov, 2018  |   Pubmed ID: 30159947
• Phosphorylation of Human TRM9L Integrates Multiple Stress-signaling Pathways for Tumor Growth Suppression
  Science Advances. Jul, 2018  |   Pubmed ID: 30009260
• Transfer RNA Induces IL-12p70 Via Synergistic Activation of Pattern Recognition Receptors Within a Cell Network
  Journal of Immunology (Baltimore, Md. : 1950). May, 2018  |   Pubmed ID: 29610140
• The TA Modification Acts As a Positive Determinant for the Anticodon Nuclease PrrC, and is Distinctively Nonessential in Streptococcus Mutans
  RNA Biology. 2018  |   Pubmed ID: 28726545
• Allosteric Pyruvate Kinase-based "logic Gate" Synergistically Senses Energy and Sugar Levels in Mycobacterium Tuberculosis
  Nature Communications. Dec, 2017  |   Pubmed ID: 29215013
• Mutations in KEOPS-complex Genes Cause Nephrotic Syndrome with Primary Microcephaly
  Nature Genetics. Oct, 2017  |   Pubmed ID: 28805828
• N-Formyllysine As a Biomarker of Formaldehyde Exposure: Formation and Loss of N-Formyllysine in Nasal Epithelium in Long-Term, Low-Dose Inhalation Studies in Rats
  Chemical Research in Toxicology. Aug, 2017  |   Pubmed ID: 28692800
• The MA Pathway Facilitates Sex Determination in Drosophila
  Nature Communications. Jul, 2017  |   Pubmed ID: 28675155
• Three Distinct 3-methylcytidine (mC) Methyltransferases Modify TRNA and MRNA in Mice and Humans
  The Journal of Biological Chemistry. 09, 2017  |   Pubmed ID: 28655767
• Oxidation of Phosphorothioate DNA Modifications Leads to Lethal Genomic Instability
  Nature Chemical Biology. Aug, 2017  |   Pubmed ID: 28604692
• Convergence of DNA Methylation and Phosphorothioation Epigenetics in Bacterial Genomes
  Proceedings of the National Academy of Sciences of the United States of America. Apr, 2017  |   Pubmed ID: 28400512
• 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 in Microbiology. 2017  |   Pubmed ID: 28377755
• TRNA N6-adenosine Threonylcarbamoyltransferase Defect Due to KAE1/TCS3 (OSGEP) Mutation Manifest by Neurodegeneration and Renal Tubulopathy
  European Journal of Human Genetics : EJHG. May, 2017  |   Pubmed ID: 28272532
• TRNA-mediated Codon-biased Translation in Mycobacterial Hypoxic Persistence
  Nature Communications. Nov, 2016  |   Pubmed ID: 27834374
• Methylation at Position 32 of TRNA Catalyzed by TrmJ Alters Oxidative Stress Response in Pseudomonas Aeruginosa
  Nucleic Acids Research. Dec, 2016  |   Pubmed ID: 27683218
• The Role of Sequence Context, Nucleotide Pool Balance and Stress in 2'-deoxynucleotide Misincorporation in Viral, Bacterial and Mammalian RNA
  Nucleic Acids Research. Oct, 2016  |   Pubmed ID: 27365049
• Gene- and Genome-based Analysis of Significant Codon Patterns in Yeast, Rat and Mice Genomes with the CUT Codon UTilization Tool
  Methods (San Diego, Calif.). Sep, 2016  |   Pubmed ID: 27245397
• Immunostimulating and Gram-negative-specific Antibacterial Cyclotides from the Butterfly Pea (Clitoria Ternatea)
  The FEBS Journal. Jun, 2016  |   Pubmed ID: 27007913
• Novel Genomic Island Modifies DNA with 7-deazaguanine Derivatives
  Proceedings of the National Academy of Sciences of the United States of America. Mar, 2016  |   Pubmed ID: 26929322
• Trm9-Catalyzed TRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation
  PLoS Genetics. Dec, 2015  |   Pubmed ID: 26670883
• An Extensive Allelic Series of Drosophila Kae1 Mutants Reveals Diverse and Tissue-specific Requirements for T6A Biogenesis
  RNA (New York, N.Y.). Dec, 2015  |   Pubmed ID: 26516084
• Metabolic Fate of Endogenous Molecular Damage: Urinary Glutathione Conjugates of DNA-derived Base Propenals As Markers of Inflammation
  Proceedings of the National Academy of Sciences of the United States of America. Sep, 2015  |   Pubmed ID: 26283391
• A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of TRNA Modifications
  Methods in Enzymology. 2015  |   Pubmed ID: 26253965
• Alkbh8 Regulates Selenocysteine-Protein Expression to Protect Against Reactive Oxygen Species Damage
  PloS One. 2015  |   Pubmed ID: 26147969
• Codon-biased Translation Can Be Regulated by Wobble-base TRNA Modification Systems During Cellular Stress Responses
  RNA Biology. 2015  |   Pubmed ID: 25892531
• Highly Predictive Reprogramming of TRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes
  Chemical Research in Toxicology. May, 2015  |   Pubmed ID: 25772370
• 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 Research. Mar, 2015  |   Pubmed ID: 25539917
• Diverse Cell Stresses Induce Unique Patterns of TRNA Up- and Down-regulation: TRNA-seq for Quantifying Changes in TRNA Copy Number
  Nucleic Acids Research. Dec, 2014  |   Pubmed ID: 25348403
• TRNA Modifications Regulate Translation During Cellular Stress
  FEBS Letters. Nov, 2014  |   Pubmed ID: 25304425
• Pathological Phenotypes and in Vivo DNA Cleavage by Unrestrained Activity of a Phosphorothioate-based Restriction System in Salmonella
  Molecular Microbiology. Aug, 2014  |   Pubmed ID: 25040300
• Genomic Mapping of Phosphorothioates Reveals Partial Modification of Short Consensus Sequences
  Nature Communications. Jun, 2014  |   Pubmed ID: 24899568
• Quantitative Analysis of Ribonucleoside Modifications in TRNA by HPLC-coupled Mass Spectrometry
  Nature Protocols. Apr, 2014  |   Pubmed ID: 24625781
• 28S RRNA is Inducibly Pseudouridylated by the MTOR Pathway Translational Control in CHO Cell Cultures
  Journal of Biotechnology. Mar, 2014  |   Pubmed ID: 24480570
• A System of RNA Modifications and Biased Codon Use Controls Cellular Stress Response at the Level of Translation
  Chemical Research in Toxicology. Mar, 2014  |   Pubmed ID: 24422464
• 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 (New York, N.Y.). Feb, 2014  |   Pubmed ID: 24344322
• Dosimetry of N⁶-formyllysine Adducts Following [¹³C²H₂]-formaldehyde Exposures in Rats
  Chemical Research in Toxicology. Oct, 2013  |   Pubmed ID: 24087891
• Induction of Functional Human Macrophages from Bone Marrow Promonocytes by M-CSF in Humanized Mice
  Journal of Immunology (Baltimore, Md. : 1950). Sep, 2013  |   Pubmed ID: 23935193
• Chemistry Meets Biology in Colitis-associated Carcinogenesis
  Free Radical Research. Nov, 2013  |   Pubmed ID: 23926919
• A Multidimensional Platform for the Purification of Non-coding RNA Species
  Nucleic Acids Research. Sep, 2013  |   Pubmed ID: 23907385
• DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium Tuberculosis
  PLoS Pathogens. 2013  |   Pubmed ID: 23853579
• Chemical and Cytokine Features of Innate Immunity Characterize Serum and Tissue Profiles in Inflammatory Bowel Disease
  Proceedings of the National Academy of Sciences of the United States of America. Jun, 2013  |   Pubmed ID: 23754421
• An Automated Fpg-based FADU Method for the Detection of Oxidative DNA Lesions and Screening of Antioxidants
  Toxicology. Aug, 2013  |   Pubmed ID: 23707620
• Quantification of Cellular Poly(ADP-ribosyl)ation by Stable Isotope Dilution Mass Spectrometry Reveals Tissue- and Drug-dependent Stress Response Dynamics
  ACS Chemical Biology. Jul, 2013  |   Pubmed ID: 23631432
• Increased Levels of Inosine in a Mouse Model of Inflammation
  Chemical Research in Toxicology. Apr, 2013  |   Pubmed ID: 23506120
• Quantitative Analysis of Histone Modifications: Formaldehyde is a Source of Pathological N(6)-formyllysine That is Refractory to Histone Deacetylases
  PLoS Genetics. 2013  |   Pubmed ID: 23468656
• Comparative Analysis of Four Oxidized Guanine Lesions from Reactions of DNA with Peroxynitrite, Singlet Oxygen, and γ-radiation
  Chemical Research in Toxicology. Feb, 2013  |   Pubmed ID: 23140136
• In Situ Analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine Oxidation Reveals Sequence- and Agent-specific Damage Spectra
  Journal of the American Chemical Society. Oct, 2012  |   Pubmed ID: 23057664
• Increased TRNA Modification and Gene-specific Codon Usage Regulate Cell Cycle Progression During the DNA Damage Response
  Cell Cycle (Georgetown, Tex.). Oct, 2012  |   Pubmed ID: 22935709
• Translational Infidelity-induced Protein Stress Results from a Deficiency in Trm9-catalyzed TRNA Modifications
  RNA Biology. Jul, 2012  |   Pubmed ID: 22832247
• Reprogramming of TRNA Modifications Controls the Oxidative Stress Response by Codon-biased Translation of Proteins
  Nature Communications. Jul, 2012  |   Pubmed ID: 22760636
• A System for Exposing Molecules and Cells to Biologically Relevant and Accurately Controlled Steady-state Concentrations of Nitric Oxide and Oxygen
  Nitric Oxide : Biology and Chemistry. Oct, 2012  |   Pubmed ID: 22728703
• Infection-induced Colitis in Mice Causes Dynamic and Tissue-specific Changes in Stress Response and DNA Damage Leading to Colon Cancer
  Proceedings of the National Academy of Sciences of the United States of America. Jul, 2012  |   Pubmed ID: 22689960
• Integrated Molecular Analysis Indicates Undetectable Change in DNA Damage in Mice After Continuous Irradiation at ~ 400-fold Natural Background Radiation
  Environmental Health Perspectives. Aug, 2012  |   Pubmed ID: 22538203
• 2'-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase
  PLoS Pathogens. 2012  |   Pubmed ID: 22496660
• Defects in Purine Nucleotide Metabolism Lead to Substantial Incorporation of Xanthine and Hypoxanthine into DNA and RNA
  Proceedings of the National Academy of Sciences of the United States of America. Feb, 2012  |   Pubmed ID: 22308425
• Biologically Relevant Oxidants and Terminology, Classification and Nomenclature of Oxidatively Generated Damage to Nucleobases and 2-deoxyribose in Nucleic Acids
  Free Radical Research. Apr, 2012  |   Pubmed ID: 22263561
• Sequence-dependent Variation in the Reactivity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Toward Oxidation
  Chemical Research in Toxicology. Feb, 2012  |   Pubmed ID: 22103813
• XRCC1 and Base Excision Repair Balance in Response to Nitric Oxide
  DNA Repair. Dec, 2011  |   Pubmed ID: 22041025
• Identification of N6,N6-dimethyladenosine in Transfer RNA from Mycobacterium Bovis Bacille Calmette-Guérin
  Molecules (Basel, Switzerland). Jun, 2011  |   Pubmed ID: 21694680
• Solvent Exposure Associated with Single Abasic Sites Alters the Base Sequence Dependence of Oxidation of Guanine in DNA in GG Sequence Contexts
  Chembiochem : a European Journal of Chemical Biology. Jul, 2011  |   Pubmed ID: 21656632
• Reactive Species and DNA Damage in Chronic Inflammation: Reconciling Chemical Mechanisms and Biological Fates
  International Journal of Cancer. May, 2011  |   Pubmed ID: 21387284
• DNA Phosphorothioation is Widespread and Quantized in Bacterial Genomes
  Proceedings of the National Academy of Sciences of the United States of America. Feb, 2011  |   Pubmed ID: 21285367
• The Biological and Metabolic Fates of Endogenous DNA Damage Products
  Journal of Nucleic Acids. Dec, 2010  |   Pubmed ID: 21209721
• A Quantitative Systems Approach Reveals Dynamic Control of TRNA Modifications During Cellular Stress
  PLoS Genetics. Dec, 2010  |   Pubmed ID: 21187895
• One-electron Oxidation of a Pyrenyl Photosensitizer Covalently Attached to DNA and Competition Between Its Further Oxidation and DNA Hole Injection
  Photochemistry and Photobiology. 2010  |   Pubmed ID: 20408978
• 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 Gamma-radiation and Fe2+-EDTA
  Journal of the American Chemical Society. May, 2010  |   Pubmed ID: 20377226
• Human AlkB Homolog ABH8 Is a TRNA Methyltransferase Required for Wobble Uridine Modification and DNA Damage Survival
  Molecular and Cellular Biology. May, 2010  |   Pubmed ID: 20308323
• Recommendations for Standardized Description of and Nomenclature Concerning Oxidatively Damaged Nucleobases in DNA
  Chemical Research in Toxicology. Apr, 2010  |   Pubmed ID: 20235554
• A General Method for Quantifying Sequence Effects on Nucleobase Oxidation in DNA
  Methods in Molecular Biology (Clifton, N.J.). 2010  |   Pubmed ID: 20013187
• An Improved Method for Large-scale Preparation of Negatively and Positively Supercoiled Plasmid DNA
  BioTechniques. Jul, 2009  |   Pubmed ID: 19594448
• Continuous Elimination of Oxidized Nucleotides is Necessary to Prevent Rapid Onset of Cellular Senescence
  Proceedings of the National Academy of Sciences of the United States of America. Jan, 2009  |   Pubmed ID: 19118192
• DNA Sequence Context As a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-electron Oxidants
  The Journal of Biological Chemistry. Dec, 2008  |   Pubmed ID: 18948263
• Kinetic Analysis of Intracellular Concentrations of Reactive Nitrogen Species
  Chemical Research in Toxicology. Nov, 2008  |   Pubmed ID: 18828639
• Quantification of DNA Damage Products Resulting from Deamination, Oxidation and Reaction with Products of Lipid Peroxidation by Liquid Chromatography Isotope Dilution Tandem Mass Spectrometry
  Nature Protocols. 2008  |   Pubmed ID: 18714297
• Surveying the Damage: the Challenges of Developing Nucleic Acid Biomarkers of Inflammation
  Molecular BioSystems. Sep, 2008  |   Pubmed ID: 18704228
• DNA Damage Induced by Chronic Inflammation Contributes to Colon Carcinogenesis in Mice
  The Journal of Clinical Investigation. Jul, 2008  |   Pubmed ID: 18521188
• AlkB Homologue 2-mediated Repair of Ethenoadenine Lesions in Mammalian DNA
  Cancer Research. Jun, 2008  |   Pubmed ID: 18519673
• 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
  The Journal of Physical Chemistry. B. Feb, 2008  |   Pubmed ID: 18211057
• The Chemical Toxicology of 2-deoxyribose Oxidation in DNA
  Chemical Research in Toxicology. Jan, 2008  |   Pubmed ID: 18052112
• Challenges in Developing DNA and RNA Biomarkers of Inflammation
  Biomarkers in Medicine. Aug, 2007  |   Pubmed ID: 20477404
• GC/MS Methods to Quantify the 2-deoxypentos-4-ulose and 3'-phosphoglycolate Pathways of 4' Oxidation of 2-deoxyribose in DNA: Application to DNA Damage Produced by Gamma Radiation and Bleomycin
  Chemical Research in Toxicology. Nov, 2007  |   Pubmed ID: 17944541
• AlkB Influences the Chloroacetaldehyde-induced Mutation Spectra and Toxicity in the PSP189 SupF Shuttle Vector
  Chemical Research in Toxicology. Aug, 2007  |   Pubmed ID: 17658757
• Lipid Peroxidation Dominates the Chemistry of DNA Adduct Formation in a Mouse Model of Inflammation
  Carcinogenesis. Aug, 2007  |   Pubmed ID: 17347141
• N-formylation of Lysine in Histone Proteins As a Secondary Modification Arising from Oxidative DNA Damage
  Proceedings of the National Academy of Sciences of the United States of America. Jan, 2007  |   Pubmed ID: 17190813
• The DNA-damage Signature in Saccharomyces Cerevisiae is Associated with Single-strand Breaks in DNA
  BMC Genomics. Dec, 2006  |   Pubmed ID: 17163986
• Rosuvastatin: an Independent Analysis of Risks and Benefits
  MedGenMed : Medscape General Medicine. Jun, 2006  |   Pubmed ID: 16926812
• Formation of 1,4-dioxo-2-butene-derived Adducts of 2'-deoxyadenosine and 2'-deoxycytidine in Oxidized DNA
  Chemical Research in Toxicology. Aug, 2006  |   Pubmed ID: 16918236
• Paradoxical Hotspots for Guanine Oxidation by a Chemical Mediator of Inflammation
  Nature Chemical Biology. Jul, 2006  |   Pubmed ID: 16751762
• Threshold Effects of Nitric Oxide-induced Toxicity and Cellular Responses in Wild-type and P53-null Human Lymphoblastoid Cells
  Chemical Research in Toxicology. Mar, 2006  |   Pubmed ID: 16544944
• 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
  Chemical Research in Toxicology. Jan, 2006  |   Pubmed ID: 16411656
• Development of Enzymatic Probes of Oxidative and Nitrosative DNA Damage Caused by Reactive Nitrogen Species
  Mutation Research. Feb, 2006  |   Pubmed ID: 16274707
• Biological Role of Glutathione in Nitric Oxide-induced Toxicity in Cell Culture and Animal Models
  Free Radical Biology & Medicine. Dec, 2005  |   Pubmed ID: 16274884
• Quantification of DNA Strand Breaks and Abasic Sites by Oxime Derivatization and Accelerator Mass Spectrometry: Application to Gamma-radiation and Peroxynitrite
  Analytical Biochemistry. Aug, 2005  |   Pubmed ID: 15964542
• Differential Oxidation of Deoxyribose in DNA by Gamma and Alpha-particle Radiation
  Radiation Research. Jun, 2005  |   Pubmed ID: 15913397
• Chemical and Biological Evidence for Base Propenals As the Major Source of the Endogenous M1dG Adduct in Cellular DNA
  The Journal of Biological Chemistry. Jul, 2005  |   Pubmed ID: 15878883
• Delineation of the Chemical Pathways Underlying Nitric Oxide-induced Homologous Recombination in Mammalian Cells
  Chemistry & Biology. Mar, 2005  |   Pubmed ID: 15797220
• Effects of Peroxynitrite Dose and Dose Rate on DNA Damage and Mutation in the SupF Shuttle Vector
  Chemical Research in Toxicology. Jan, 2005  |   Pubmed ID: 15651852
• 5'-(2-phosphoryl-1,4-dioxobutane) As a Product of 5'-oxidation of Deoxyribose in DNA: Elimination As Trans-1,4-dioxo-2-butene and Approaches to Analysis
  Chemical Research in Toxicology. Nov, 2004  |   Pubmed ID: 15540938
• Reaction of 2'-deoxyribonucleosides with Cis- and Trans-1,4-dioxo-2-butene
  Biochemical and Biophysical Research Communications. Oct, 2004  |   Pubmed ID: 15381076
• Reactive Nitrogen Species in the Chemical Biology of Inflammation
  Archives of Biochemistry and Biophysics. Mar, 2004  |   Pubmed ID: 14989259
• Analysis of 3'-phosphoglycolaldehyde Residues in Oxidized DNA by Gas Chromatography/negative Chemical Ionization/mass Spectrometry
  Chemical Research in Toxicology. Dec, 2003  |   Pubmed ID: 14680370
• Absence of 2'-deoxyoxanosine and Presence of Abasic Sites in DNA Exposed to Nitric Oxide at Controlled Physiological Concentrations
  Chemical Research in Toxicology. Sep, 2003  |   Pubmed ID: 12971791
• Indirect Mutagenesis by Oxidative DNA Damage: Formation of the Pyrimidopurinone Adduct of Deoxyguanosine by Base Propenal
  Proceedings of the National Academy of Sciences of the United States of America. Sep, 1998  |   Pubmed ID: 9736698