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Author Details

Thomas J Begley
University at Albany
1998
80
35
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37433804An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis.Nat Commun2023
37992267Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins.Acc Chem Res2023
37986976Dengue virus exploits the host tRNA epitranscriptome to promote viral replication.bioRxiv2023
35327975Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen.Genes (Basel)2022
36241532Dysfunctional tRNA reprogramming and codon-biased translation in cancer.Trends Mol Med2022
36066904The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12.Metallomics2022
36036467Selenoproteins and the senescence-associated epitranscriptome.Exp Biol Med (Maywood)2022
36095201Arsenite toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome.Proc Natl Acad Sci U S A2022
35987429Codon Usage and mRNA Stability are Translational Determinants of Cellular Response to Canonical Ferroptosis Inducers.Neuroscience2022
35979951Disease-associated inosine misincorporation into RNA hinders translation.Nucleic Acids Res2022
33332971Base Pairing and Functional Insights into <i>N</i><sup>3</sup>-Methylcytidine (m<sup>3</sup>C) in RNA.ACS Chem Biol2021
33859402Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.Nat Biotechnol2021
33688012Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator.mBio2021
34458821Sulfur modification in natural RNA and therapeutic oligonucleotides.RSC Chem Biol2021
33987958Detecting the epitranscriptome.Wiley Interdiscip Rev RNA2021
32994210Genome Profiling for Aflatoxin B<sub>1</sub> Resistance in <i>Saccharomyces cerevisiae</i> Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B<sub>1</sub>-Associated DNA Damage.G3 (Bethesda)2020
32085421Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast.Biomolecules2020
31765888Loss of epitranscriptomic control of selenocysteine utilization engages senescence and mitochondrial reprogramming<sup>â¿¿</sup>.Redox Biol2020
30934574The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress.Toxics2019
31476365Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins.Free Radic Biol Med2019
30466063A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth.iScience2018
30009260Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression.Sci Adv2018
30587213Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses.Genome Biol2018
28445781Mitochondrial ROS control of cancer.Semin Cancer Biol2017
32962315tRNA Modification Detection Using Graphene Nanopores: A Simulation Study.Biomolecules2017
28458064Towards precision prevention: Technologies for identifying healthy individuals with high risk of disease.Mutat Res2017
26799652Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).Autophagy2016
27834374tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence.Nat Commun2016
27245397Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool.Methods2016
24713076Oral ingestion of silver nanoparticles induces genomic instability and DNA damage in multiple tissues.Nanotoxicology2015
26670883Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.PLoS Genet2015
26444223Comparative analysis of redox and inflammatory properties of pristine nanomaterials and commonly used semiconductor manufacturing nano-abrasives.Toxicol Lett2015
26253965A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.Methods Enzymol2015
26147969Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage.PLoS One2015
25892531Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses.RNA Biol2015
25755069Gcn5 Modulates the Cellular Response to Oxidative Stress and Histone Deacetylase Inhibition.J Cell Biochem2015
25805774Erratum for Lamichhane et al., lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast.Mol Cell Biol2015
25772370Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes.Chem Res Toxicol2015
24422464A system of RNA modifications and biased codon use controls cellular stress response at the level of translation.Chem Res Toxicol2014
25304425tRNA modifications regulate translation during cellular stress.FEBS Lett2014
24968945High throughput screening identifies modulators of histone deacetylase inhibitors.BMC Genomics2014
25127496Mitochondria, energetics, epigenetics, and cellular responses to stress.Environ Health Perspect2014
24625781Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry.Nat Protoc2014
23381944A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α.EMBO Mol Med2013
23716598Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast.Mol Cell Biol2013
22191691Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: activities, predications, and potential roles in human health.DNA Cell Biol2012
22966490Guidelines for the use and interpretation of assays for monitoring autophagy.Autophagy2012
22935709Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response.Cell Cycle2012
23038810Alkylation sensitivity screens reveal a conserved cross-species functionome.Mol Cancer Res2012
22760636Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins.Nat Commun2012
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Collaborators

Leona D Samson
Massachusetts Institute of Technology
Co-authored papers 14
Rebecca C Fry
Co-authored papers 4
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 4
Scott J Bultman
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
Co-authored papers 3
Val??rie de Cr??cy-Lagard
University of Florida
Co-authored papers 3
Robert W Sobol
University of South Alabama
Co-authored papers 3
Brian J Haas
Broad Institute of MIT and Harvard
Co-authored papers 3
Lawrence H Boise
Winship Cancer Institute, Emory University
Co-authored papers 2
Maria T Diaz-Meco
Co-authored papers 2
Marie-Jos??e H??bert
Universite de Montreal
Co-authored papers 2
Joel N Meyer
Duke University Nicholas School of the Environment.
Co-authored papers 2
Sovan Sarkar
CRUK MRC Oxford Institute for Radiation Oncology, University of Oxford
Co-authored papers 2
Malene Hansen
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 2
Daniel T Shaughnessy
National Institute of Environmental Health Sciences, National Institutes of Health
Co-authored papers 2
Kun-Liang Guan
University of California San Diego
Co-authored papers 2
Ana Maria Cuervo
Albert Einstein College of Medicine
Co-authored papers 2
Laura Santambrogio
Weill Cornell School of Medicine
Co-authored papers 2
Ioannis P Nezis
University of Warwick
Co-authored papers 2
Masashi Narita
Co-authored papers 2
Karin Przyklenk
Co-authored papers 2
Jason E Gestwicki
Institute for Neurodegenerative Diseases, University of California San Francisco
Co-authored papers 2
Svetlana Dokudovskaya
CNRS UMR9018, Institut Gustave Roussy, Universite Paris-Saclay
Co-authored papers 2
Hirotaka Watada
Co-authored papers 2
Sara Cherry
University of Pennsylvania
Co-authored papers 2
Carlos L??pez-Ot??n
Instituto Universitario de Oncologia, Universidad de Oviedo
Co-authored papers 2
David Sulzer
New York State Psychiatric Institute, Research Foundation for Mental Hygiene
Co-authored papers 2
David M Sabatini
Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology
Co-authored papers 2
J. Wade Harper
Harvard Medical School
Co-authored papers 2
Nikolai V Gorbunov
Armed Forces Radiobiology Research Institute
Co-authored papers 2
Juan Fueyo
The University of Texas M.D. Anderson Cancer Center
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Release 1.2