Publications

 

  • Rooney, J., Patel, A., Begley, U., Conklin, D. S., Cunningham, R. P., and Begley T. J. Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. (accepted at Genomics)
    Genomics
  • Rooney, J., Patel, A., Zappala, M. R., Conklin, D. S., Cunningham, R. P., and Begley T. J. A Molecular Bar-Coded DNA Repair Resource for Pooled Toxicogenomic Screens. (in press at DNA Repair)
    DNA Repair
  • Begley*, U., Dyavaiah*, M., Patel*, A., Rooney*. DiRenzo, D., Young. C, Conklin, D. S. Zitomer, R. S. and, Begley T. J. (2007) Trm9 Catalyzed tRNA Modifications Link Translation to the DNA Damage Response. Molecular Cell 28:860-870 (Highlighted in Faculty of 1000 and News and Views in Nature Chemical Biology)
    Molecular Cell
  • Rusyn I., Fry R.C., Begley T.J., Klapacz J., Svensson J.P., Ambrose M., Samson L.D. 2007. Transcriptional Networks in S. cerevisiae Linked to an Accumulation of Base Excision Repair Intermediates. PLoS ONE. 2(11): 1252-1260
    PLoS ONE
  • Fry, R., DeMott, M., Cosgrove, J. Begley, T. J., Samson, L. D., and Dedon, P. 2006. The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA. BMC Genomics 7: 313-20
    BMC Genomics
  • Workman, C. T., Mak, H. C., McCuine, S., Tagne, J. B., Agarwal, M., Ozier, O., Begley, T. J. , Samson, L. D, and Ideker T. 2006. A systems approach to mapping DNA damage response pathways. Science 312:1054-9
    Science
  • Fry, R. C., Begley, T. J. and Samson L. D. Genome-Wide Responses to DNA Damaging Agents, Annual Review of Microbiology Annual Review of Microbiology (2005) 59: 357-377
    Annual Reviews
  • Begley, T. J. Interactomes as a Base Unit in Systems Biology, BioSystems, (2005) 1: 2-8
    Biosystems
  • Said, M . R.*, Begley, T. J.*, Oppenheim, A. V., Lauffenburger, D. A. and Samson, L. D. Global Network Analysis of Phenotypic Effects: Protein Networks and S. cerevisiae Damage Recovery. PNAS (2004) 101:18006-11
    Proceedings of the National Academy of Sciences
  • Begley, T. J ., Rosenbach, A. S., Ideker, T. and Samson, L. D. Hot Spots for Toxicity Modulation Identified by Genomic Phenotyping and Localization Mapping. Molecular Cell ( 2004) 16:117-25.
    Molecular Cell
  • Begley, T. J. and Samson L. D.
    Reversing DNA damage with a directional bias.
    Nature Structural and Molecular Biology, 2004 Aug;11(8):688-90.
  • Begley, T. J. and Samson L. D.
    Network Responses to Damaging Agents
    DNA Repair, 2004 g-Sep;3(8-9):1123-32
  • Begley, T. J. and Samson L. D.
    A Fix for RNA.
    Nature, (2003) 421: 795-796
  • Begley, T. J. and Samson L. D.
    AlkB mystery solved: Oxidative demethylation of N1-methyladenine and N3-methylcytosine adducts by a direct repair mechanism.
    Trends in Biochemical Sciences (2003) 28: 93-96
  • Begley, T.J., Haas, B. J., Morales JC, Kool, E.T. and Cunningham, R.P.
    Kinetics and binding of the thymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substrates.
    DNA Repair. (2003) 2: 107-120
  • Begley, T. J., Rosenbach, A. S., Ideker, T. and Samson, L. D.
    Recovery Pathways in S. cerevisiae Revealed by Genomic Phenotyping and Interactome Mapping.
    Mol Cancer Res (2002) 1: 103-112.
  • Mol C.D., Arvai A.S., Begley T.J., Cunningham R.P. and Tainer J.A.
    Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.
    J Mol Biol (2002) 315: 373-84.
  • Begley, T.J., Jelinsky, S.A. and Samson, L.D.
    Complex Transcriptional responses to Macromolecular Damaging Agents: Regulatory Responses Specific for Sn2 Alkylation and the MAG1 Gene.
    Cold Spring Harbor Symposia on Quantitative Biology, (2000) 383 - 393.
  • Begley, T.J., Haas, B.J., Noel, J., Shektman, A., Williams, W. A., and Cunningham, R.P.
    A New Member of the Endonuclease III Family of DNA Repair Enzymes Which Removes Methylated Purines from DNA.
    Curr Biol (1999) 9: 653-656.
  • Begley, T.J. and Cunningham, R.P.
    Methanobacterium thermoformicicum Thymine DNA Mismatch Glycosylase: Conversion of an N- glycosylase to an AP Lyase.
    Protein Engineering (1999), 12: 333-340
  • Fetrow, J.S., Spitzer, J.S., Gilden, B.M., Mellender, S.J., Begley, T.J., Haas, B.J., Boose, T.L.
    Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and glycine 77 in omega-loop D of yeast iso-1-cytochrome c.
    Biochemistry (1998) 37: 2477-87
 
Copyright © 2006 Thomas J. Begley, Ph.D. All Rights Reserved.
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