Peter C Dedon

Peter C Dedon

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Peter C Dedon

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Backbone resonance assignment for the full length tRNA-(NG37) methyltransferase of Pseudomonas aeruginosa.

Biomol NMR Assign 2019 10 7;13(2):327-332. Epub 2019 Jun 7.

Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.

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http://dx.doi.org/10.1007/s12104-019-09900-2DOI Listing
October 2019

The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea.

Synth Syst Biotechnol 2019 Sep 22;4(3):132-133. Epub 2019 Jun 22.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.synbio.2019.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606745PMC
September 2019

Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium tuberculosis.

J Mol Biol 2019 Sep 2;431(19):3690-3705. Epub 2019 Aug 2.

Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.07.033DOI Listing
September 2019

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA.

Nucleic Acids Res 2019 Sep 2. Epub 2019 Sep 2.

Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore.

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http://dx.doi.org/10.1093/nar/gkz751DOI Listing
September 2019

Transcriptome-wide dynamics of extensive mA mRNA methylation during Plasmodium falciparum blood-stage development.

Nat Microbiol 2019 Aug 5. Epub 2019 Aug 5.

Biology of Host-Parasite Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.

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http://dx.doi.org/10.1038/s41564-019-0521-7DOI Listing
August 2019

Backbone resonance assignment for the N-terminal region of bacterial tRNA-(NG37) methyltransferase.

Biomol NMR Assign 2019 04 8;13(1):49-53. Epub 2018 Oct 8.

Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.

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http://dx.doi.org/10.1007/s12104-018-9849-9DOI Listing
April 2019

Thiazolidin-5-imine Formation as a Catalyst-Free Bioorthogonal Reaction for Protein and Live Cell Labeling.

Org Lett 2018 12 5;20(24):7790-7793. Epub 2018 Dec 5.

School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551 , Singapore.

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http://pubs.acs.org/doi/10.1021/acs.orglett.8b03195
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http://dx.doi.org/10.1021/acs.orglett.8b03195DOI Listing
December 2018

Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses.

Genome Biol 2018 12 27;19(1):228. Epub 2018 Dec 27.

The RNA Institute, College of Arts and Science, University at Albany, SUNY, Albany, NY, 12222, USA.

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http://dx.doi.org/10.1186/s13059-018-1611-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307160PMC
December 2018

Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery.

Mol Microbiol 2018 11 12;110(3):469-483. Epub 2018 Oct 12.

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.

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http://dx.doi.org/10.1111/mmi.14113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207457PMC
November 2018

A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth.

iScience 2018 Nov 5;9:367-381. Epub 2018 Nov 5.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2018.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249402PMC
November 2018

tRNA epitranscriptomics and biased codon are linked to proteome expression in .

Mol Syst Biol 2018 10 4;14(10):e8009. Epub 2018 Oct 4.

Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171970PMC
http://dx.doi.org/10.15252/msb.20178009DOI Listing
October 2018

Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression.

Sci Adv 2018 07 11;4(7):eaas9184. Epub 2018 Jul 11.

The RNA Institute and Department of Biological Sciences, University at Albany, State University of New York, NY 12222, USA.

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http://dx.doi.org/10.1126/sciadv.aas9184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6040840PMC
July 2018

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.

Authors:
Daniela A Braun Jia Rao Geraldine Mollet David Schapiro Marie-Claire Daugeron Weizhen Tan Olivier Gribouval Olivia Boyer Patrick Revy Tilman Jobst-Schwan Johanna Magdalena Schmidt Jennifer A Lawson Denny Schanze Shazia Ashraf Jeremy F P Ullmann Charlotte A Hoogstraten Nathalie Boddaert Bruno Collinet Gaëlle Martin Dominique Liger Svjetlana Lovric Monica Furlano I Chiara Guerrera Oraly Sanchez-Ferras Jennifer F Hu Anne-Claire Boschat Sylvia Sanquer Björn Menten Sarah Vergult Nina De Rocker Merlin Airik Tobias Hermle Shirlee Shril Eugen Widmeier Heon Yung Gee Won-Il Choi Carolin E Sadowski Werner L Pabst Jillian K Warejko Ankana Daga Tamara Basta Verena Matejas Karin Scharmann Sandra D Kienast Babak Behnam Brendan Beeson Amber Begtrup Malcolm Bruce Gaik-Siew Ch'ng Shuan-Pei Lin Jui-Hsing Chang Chao-Huei Chen Megan T Cho Patrick M Gaffney Patrick E Gipson Chyong-Hsin Hsu Jameela A Kari Yu-Yuan Ke Cathy Kiraly-Borri Wai-Ming Lai Emmanuelle Lemyre Rebecca Okashah Littlejohn Amira Masri Mastaneh Moghtaderi Kazuyuki Nakamura Fatih Ozaltin Marleen Praet Chitra Prasad Agnieszka Prytula Elizabeth R Roeder Patrick Rump Rhonda E Schnur Takashi Shiihara Manish D Sinha Neveen A Soliman Kenza Soulami David A Sweetser Wen-Hui Tsai Jeng-Daw Tsai Rezan Topaloglu Udo Vester David H Viskochil Nithiwat Vatanavicharn Jessica L Waxler Klaas J Wierenga Matthias T F Wolf Sik-Nin Wong Sebastian A Leidel Gessica Truglio Peter C Dedon Annapurna Poduri Shrikant Mane Richard P Lifton Maxime Bouchard Peter Kannu David Chitayat Daniella Magen Bert Callewaert Herman van Tilbeurgh Martin Zenker Corinne Antignac Friedhelm Hildebrandt

Nat Genet 2017 Oct 14;49(10):1529-1538. Epub 2017 Aug 14.

Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

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http://www.nature.com/doifinder/10.1038/ng.3933
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http://dx.doi.org/10.1038/ng.3933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819591PMC
October 2017

Three distinct 3-methylcytidine (mC) methyltransferases modify tRNA and mRNA in mice and humans.

J Biol Chem 2017 09 27;292(35):14695-14703. Epub 2017 Jun 27.

From the Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599 Singapore,

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http://dx.doi.org/10.1074/jbc.M117.798298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582859PMC
September 2017

Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability.

Nat Chem Biol 2017 Aug 12;13(8):888-894. Epub 2017 Jun 12.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nchembio.2407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577368PMC
August 2017

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.

Chem Res Toxicol 2017 08 27;30(8):1572-1576. Epub 2017 Jul 27.

Department of Environmental Sciences and Engineering, University of North Carolina , Chapel Hill, North Carolina 27514, United States.

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http://dx.doi.org/10.1021/acs.chemrestox.7b00075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807069PMC
August 2017

The mA pathway facilitates sex determination in Drosophila.

Nat Commun 2017 07 4;8:15737. Epub 2017 Jul 4.

Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA.

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http://dx.doi.org/10.1038/ncomms15737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500889PMC
July 2017

tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy.

Eur J Hum Genet 2017 05 8;25(5):545-551. Epub 2017 Mar 8.

Monique and Jacques Roboh Department of Genetic Research, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel.

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http://dx.doi.org/10.1038/ejhg.2017.30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437908PMC
May 2017

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.

Proc Natl Acad Sci U S A 2017 04 11;114(17):4501-4506. Epub 2017 Apr 11.

Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China;

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http://dx.doi.org/10.1073/pnas.1702450114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410841PMC
April 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.

Front Microbiol 2017 21;8:459. Epub 2017 Mar 21.

Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and TechnologySingapore, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, CambridgeMA, USA.

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http://dx.doi.org/10.3389/fmicb.2017.00459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359317PMC
March 2017

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence.

Nat Commun 2016 11 11;7:13302. Epub 2016 Nov 11.

Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #03-14 Enterprise Wing, Singapore 138602, Singapore.

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http://www.nature.com/articles/ncomms13302
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http://dx.doi.org/10.1038/ncomms13302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114619PMC
November 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 Oct 30;44(18):8962-8975. Epub 2016 Jun 30.

Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Biological Engineering & Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA

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http://dx.doi.org/10.1093/nar/gkw572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062971PMC
October 2016

Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool.

Methods 2016 09 28;107:98-109. Epub 2016 May 28.

State University of New York - SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY.

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http://dx.doi.org/10.1016/j.ymeth.2016.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014648PMC
September 2016

Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress.

Infect Immun 2016 Sep 19;84(9):2505-23. Epub 2016 Aug 19.

Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore

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http://dx.doi.org/10.1128/IAI.00072-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995911PMC
September 2016

N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis.

Dev Cell 2016 07 7;38(2):186-200. Epub 2016 Jul 7.

Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2016.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364302PMC
July 2016

Immunostimulating and Gram-negative-specific antibacterial cyclotides from the butterfly pea (Clitoria ternatea).

FEBS J 2016 06 20;283(11):2067-90. Epub 2016 Apr 20.

School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore.

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http://dx.doi.org/10.1111/febs.13720DOI Listing
June 2016

A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.

Methods Enzymol 2015 17;560:29-71. Epub 2015 Jul 17.

Singapore-MIT Alliance for Research and Technology, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2015.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4774897PMC
May 2016

Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage.

PLoS One 2015 6;10(7):e0131335. Epub 2015 Jul 6.

Colleges of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York 12203, United States of America; RNA Institute and Cancer Research Center, University at Albany, State University of New York, Albany, New York 12222, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131335PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492958PMC
March 2016

Novel genomic island modifies DNA with 7-deazaguanine derivatives.

Proc Natl Acad Sci U S A 2016 Mar 29;113(11):E1452-9. Epub 2016 Feb 29.

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700; University of Florida Genetics Institute, Gainesville, FL 32610

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http://dx.doi.org/10.1073/pnas.1518570113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801273PMC
March 2016

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.

PLoS Genet 2015 Dec 15;11(12):e1005706. Epub 2015 Dec 15.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689569PMC
December 2015

Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation.

Proc Natl Acad Sci U S A 2015 Sep 17;112(35):E4845-53. Epub 2015 Aug 17.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139

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http://dx.doi.org/10.1073/pnas.1503945112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568270PMC
September 2015

Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes.

Chem Res Toxicol 2015 May 13;28(5):978-88. Epub 2015 Apr 13.

∥College of Nanoscale Science, State University of New York, Albany, New York 12203, United States.

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http://dx.doi.org/10.1021/acs.chemrestox.5b00004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438938PMC
May 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 2015 Mar 24;43(5):e32. Epub 2014 Dec 24.

Singapore MIT Alliance for Research and Technology, 1 CREATE Way, 138602, Singapore Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

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http://dx.doi.org/10.1093/nar/gku1317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357692PMC
March 2015

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number.

Nucleic Acids Res 2014 Dec 27;42(22):e170. Epub 2014 Oct 27.

Department of Biological Engineering and Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

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http://dx.doi.org/10.1093/nar/gku945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267671PMC
December 2014

tRNA modifications regulate translation during cellular stress.

FEBS Lett 2014 Nov 7;588(23):4287-96. Epub 2014 Oct 7.

Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2014.09.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403629PMC
November 2014

Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella.

Mol Microbiol 2014 Aug 23;93(4):776-85. Epub 2014 Jul 23.

State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1111/mmi.12692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414249PMC
August 2014

Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry.

Nat Protoc 2014 Apr 13;9(4):828-41. Epub 2014 Mar 13.

1] Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA. [2] Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore. [3] Center for Environmental Health Science, MIT, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nprot.2014.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313537PMC
April 2014

A system of RNA modifications and biased codon use controls cellular stress response at the level of translation.

Chem Res Toxicol 2014 Mar 27;27(3):330-7. Epub 2014 Jan 27.

Department of Biological Engineering, Center for Environmental Health Science, Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

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http://dx.doi.org/10.1021/tx400438dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997223PMC
March 2014

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures.

J Biotechnol 2014 Mar 27;174:16-21. Epub 2014 Jan 27.

Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.jbiotec.2014.01.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310699PMC
March 2014

DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis.

PLoS Pathog 2013 4;9(7):e1003419. Epub 2013 Jul 4.

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1003419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701705PMC
February 2014

Dosimetry of N⁶-formyllysine adducts following [¹³C²H₂]-formaldehyde exposures in rats.

Chem Res Toxicol 2013 Oct 10;26(10):1421-3. Epub 2013 Oct 10.

Department of Biological Engineering, ‡Center for Environmental Health Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts, 02139, United States.

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http://dx.doi.org/10.1021/tx400320uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3805309PMC
October 2013

A multidimensional platform for the purification of non-coding RNA species.

Nucleic Acids Res 2013 Sep 1;41(17):e168. Epub 2013 Aug 1.

Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Applied Biological Science Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand, Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Immunology Programme, Life Science Institute, Centre for Life Science, Singapore 117456 and Novartis Institute for Tropical Disease, Singapore 138670.

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http://dx.doi.org/10.1093/nar/gkt668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783195PMC
September 2013

Induction of functional human macrophages from bone marrow promonocytes by M-CSF in humanized mice.

J Immunol 2013 Sep 9;191(6):3192-9. Epub 2013 Aug 9.

Interdisciplinary Research Group in Infectious Diseases, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology, Singapore 138602.

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http://dx.doi.org/10.4049/jimmunol.1300742DOI Listing
September 2013

Quantification of cellular poly(ADP-ribosyl)ation by stable isotope dilution mass spectrometry reveals tissue- and drug-dependent stress response dynamics.

ACS Chem Biol 2013 Jul 13;8(7):1567-75. Epub 2013 May 13.

Molecular Toxicology Group and ‡Konstanz Research School Chemical Biology, University of Konstanz , Konstanz 78464, Germany.

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http://dx.doi.org/10.1021/cb400170bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795969PMC
July 2013

Quantitative analysis of histone modifications: formaldehyde is a source of pathological n(6)-formyllysine that is refractory to histone deacetylases.

PLoS Genet 2013 28;9(2):e1003328. Epub 2013 Feb 28.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.plos.org/10.1371/journal.pgen.1003328
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http://dx.doi.org/10.1371/journal.pgen.1003328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3585032PMC
June 2013

Increased levels of inosine in a mouse model of inflammation.

Chem Res Toxicol 2013 Apr 4;26(4):538-46. Epub 2013 Apr 4.

Department of Biological Engineering and ‡Center for Environmental Health Science, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02193, United States.

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http://dx.doi.org/10.1021/tx300473nDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3726579PMC
April 2013

A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α.

EMBO Mol Med 2013 Mar 4;5(3):366-83. Epub 2013 Feb 4.

College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA.

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http://dx.doi.org/10.1002/emmm.201201161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598078PMC
March 2013

Comparative analysis of four oxidized guanine lesions from reactions of DNA with peroxynitrite, singlet oxygen, and γ-radiation.

Chem Res Toxicol 2013 Feb 24;26(2):195-202. Epub 2013 Jan 24.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1021/tx300294dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578445PMC
February 2013

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response.

Cell Cycle 2012 Oct 30;11(19):3656-65. Epub 2012 Aug 30.

College of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA.

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http://dx.doi.org/10.4161/cc.21919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478316PMC
October 2012

In situ analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine oxidation reveals sequence- and agent-specific damage spectra.

J Am Chem Soc 2012 Oct 22;134(43):18053-64. Epub 2012 Oct 22.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503518PMC
October 2012

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins.

Nat Commun 2012 Jul 3;3:937. Epub 2012 Jul 3.

Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1038/ncomms1938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535174PMC
July 2012

Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications.

RNA Biol 2012 Jul 1;9(7):990-1001. Epub 2012 Jul 1.

Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495739PMC
July 2012

Sequence-dependent variation in the reactivity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine toward oxidation.

Chem Res Toxicol 2012 Feb 2;25(2):366-73. Epub 2011 Dec 2.

Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

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http://dx.doi.org/10.1021/tx200422gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288455PMC
February 2012

XRCC1 and base excision repair balance in response to nitric oxide.

DNA Repair (Amst) 2011 Dec 29;10(12):1282-93. Epub 2011 Oct 29.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.

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http://dx.doi.org/10.1016/j.dnarep.2011.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593656PMC
December 2011

Identification of N6,N6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin.

Molecules 2011 Jun 21;16(6):5168-81. Epub 2011 Jun 21.

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.3390/molecules16065168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264175PMC
June 2011

Reactive species and DNA damage in chronic inflammation: reconciling chemical mechanisms and biological fates.

Int J Cancer 2011 May;128(9):1999-2009

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://doi.wiley.com/10.1002/ijc.25815
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334345PMC
May 2011

DNA phosphorothioation is widespread and quantized in bacterial genomes.

Proc Natl Acad Sci U S A 2011 Feb 1;108(7):2963-8. Epub 2011 Feb 1.

Department of Biological Engineering, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1073/pnas.1017261108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041111PMC
February 2011

A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress.

PLoS Genet 2010 Dec 16;6(12):e1001247. Epub 2010 Dec 16.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002981PMC
December 2010

The biological and metabolic fates of endogenous DNA damage products.

J Nucleic Acids 2010 Dec 16;2010:929047. Epub 2010 Dec 16.

Department of Biological Engineering, Massachusetts Institute of Technology, NE47-277, Cambridge, MA 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010698PMC
December 2010

One-electron oxidation of a pyrenyl photosensitizer covalently attached to DNA and competition between its further oxidation and DNA hole injection.

Photochem Photobiol 2010 May-Jun;86(3):563-70. Epub 2010 Apr 7.

Chemistry Department and Radiation and Solid State Laboratory, New York University, New York City, NY, USA.

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http://dx.doi.org/10.1111/j.1751-1097.2010.00719.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705723PMC
September 2010

A general method for quantifying sequence effects on nucleobase oxidation in DNA.

Methods Mol Biol 2010 ;610:325-40

Biological Engineering Division and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859239PMC
February 2010

Continuous elimination of oxidized nucleotides is necessary to prevent rapid onset of cellular senescence.

Proc Natl Acad Sci U S A 2009 Jan 31;106(1):169-74. Epub 2008 Dec 31.

Whitehead Institute for Biomedical Research and Ludwig Center for Molecular Oncology, 9 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1073/pnas.0809834106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629241PMC
January 2009

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 2008 Dec 23;283(51):35569-78. Epub 2008 Oct 23.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M806809200
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602890PMC
December 2008

Kinetic analysis of intracellular concentrations of reactive nitrogen species.

Chem Res Toxicol 2008 Nov;21(11):2134-47

Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722615PMC
November 2008

Surveying the damage: the challenges of developing nucleic acid biomarkers of inflammation.

Mol Biosyst 2008 Sep 9;4(9):902-8. Epub 2008 Jul 9.

Department of Biological Engineering, Massachusetts Institute of Technology, NE47-277, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1039/b719411kDOI Listing
September 2008

DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice.

J Clin Invest 2008 Jul;118(7):2516-25

Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://www.jci.org/articles/view/35073
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423313PMC
July 2008

AlkB homologue 2-mediated repair of ethenoadenine lesions in mammalian DNA.

Cancer Res 2008 Jun;68(11):4142-9

Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet HF and University of Oslo, Blindern, Oslo, Norway.

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http://dx.doi.org/10.1158/0008-5472.CAN-08-0796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725713PMC
June 2008

The chemical toxicology of 2-deoxyribose oxidation in DNA.

Authors:
Peter C Dedon

Chem Res Toxicol 2008 Jan 4;21(1):206-19. Epub 2007 Dec 4.

Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachussetts 02139, USA.

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January 2008