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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
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