At NYU
• Goehring, L., Huang, T.T+. and Smith, D.J+. (2023) Transcription-Replication Conflicts as a source of Genome Instability. Annual Review of Genetics,2023. Link to paper
•Rosas, R., Aguilar, R.R., Arslanovic, N., Seck, A., Smith, D.J., Tyler, J.K., and Churchill, M.E.A. (2023) A novel Single Alpha-Helix-DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function. eLife, 12:e83538. Link to paper
• Coleman, K.E., Yin, Y., Kit Leng Lui, S., Keegan, S., Fenyö, D., Smith, D.J., Rothenberg, E. and Huang, T.T. (2022) USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nature Communications 1;13(1):1740. Link to paper
• Koussa N.C. and Smith D.J. (2021). Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae. G3. In press. Link to paper
• Koussa N.C. and Smith D.J. (2021). Limiting DNA polymerase delta alters replication dynamics and leads to a dependence on checkpoint activation and recombination-mediated DNA repair. PLoS Genetics 17(1):e1009322. Link to paper
• Kit Leng Lui S, Keegan S, Tonzi P, Kahli M, Chen Y.H, Chalhoub N, Coleman K.E, Fenyo D+, Smith D.J+ and Huang TT+. (2021). Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells. (+co-corresponding authors) Nature Protocols 16(2):1193-1218. Link to paper
• Kellner, V. and Smith, D.J. (2020). Hold on Tight: Lagging-Strand DNA Polymerases Synthesize Multiple Okazaki Fragments without Letting Go. Molecular Cell 80(1):6-8.
• Porcella, S.Y., Koussa, N.C., Tang, C.P., Kramer, D.N., Srivastava, P. and Smith, D.J. (2020). Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation. PLOS Genetics 7;16(5):e1008755. Link to paper
• Yeung, R. and Smith, D.J. (2020). Determinants of Replication-Fork Pausing at tRNA Genes in Saccharomyces cerevisiae. Genetics 214(4):825-838 Link to paper
• Chen, Y-H*., Keegan, S*., Kahli, M*., Tonzi, P., Fenyö, D+., Huang, T.T+. and Smith, D.J+. (2019). Transcription Shapes DNA Replication Initiation and Termination in Human Cells. (+co-corresponding authors). Nature Structural and Molecular Biology. Link to paper
• Kahli, M*., Osmundson, J.S*., Yeung, R. and Smith, D.J. (2019). Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo. Nucleic Acids Research. https://doi.org/10.1093/nar/gky1242
•. Fu, I., Smith, D.J.and Broyde, S. (2019). Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome. DNA Repair. https://doi.org/10.1016/j.dnarep.2018.11.012
• Osmundson, J.S., Kumar, J., Yeung, R. and Smith, D.J. (2017). Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes. Nature Structural and Molecular Biology 24, 162-170. Link to paper
• Clausen, A.R., Lujan, S.A., Burkholder, A.B., Orebaugh, C.D., Williams, J.S., Clausen, M.F., Malc, E.P., Mieczkowski, P.A., Fargo, D.C., Smith, D.J. and Kunkel, T.A. (2015). Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nature Structural and Molecular Biology 22, 185–191. Download pdf
Papers from postdoc, PhD and undergraduate work
• McGuffee, S. R.*, Smith, D. J.*, and Whitehouse, I. (2013). Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Molecular Cell 50, 123-135. Download pdf
• Whitehouse, I., and Smith, D. J. (2013). Chromatin dynamics at the replication fork: there's more to life than histones. Current Opinion in Genetics and Development 23(2), 140-6. Download pdf
• Borges, V., Smith, D. J., Whitehouse, I., and Uhlmann, F. (2013). An Eco1-independent sister chromatid cohesion establishment pathway in S. cerevisiae. Chromosoma 122, 121-134. Download pdf
• Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438. Download pdf
• Smith, D. J., Konarska, M. M., and Query, C. C. (2009). Insights into branch nucleophile positioning and activation from an orthogonal pre-mRNA splicing system in yeast. Molecular Cell 34, 333-343. Download pdf
• Smith, D. J., and Konarska, M. M. (2009). Identification and characterization of a short 2'-3' bond-forming ribozyme. RNA 15, 8-13. Download pdf
• Smith, D. J., and Konarska, M. M. (2009). A critical assessment of the utility of protein-free splicing systems. RNA 15, 1-3. Download pdf
• Smith, D. J., and Konarska, M. M. (2008). Mechanistic insights from reversible splicing catalysis. RNA 14, 1975-8. Download pdf
• Smith, D. J., Query, C. C., and Konarska, M. M. (2008). "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. Molecular Cell 30, 657-666. Download pdf
• Smith, D. J., Query, C. C., and Konarska, M. M. (2007). trans-splicing to spliceosomal U2 snRNA suggests disruption of branch site-U2 pairing during pre-mRNA splicing. Molecular Cell 26, 883-890. Download pdf
• Mosedale, D. E., Smith, D. J., Aitken, S., Schofield, P. M., Clarke, S. C., McNab, D., Goddard, H., Gale, C. R., Martyn, C. N., Bethell, H. W., Barnard, C., Hayns, S., Nugent, C., Panicker, A., and Grainger, D. J. (2005). Circulating levels of MCP-1 and eotaxin are not associated with presence of atherosclerosis or previous myocardial infarction. Atherosclerosis 183, 268-274. Download pdf
• Goehring, L., Huang, T.T+. and Smith, D.J+. (2023) Transcription-Replication Conflicts as a source of Genome Instability. Annual Review of Genetics,2023. Link to paper
•Rosas, R., Aguilar, R.R., Arslanovic, N., Seck, A., Smith, D.J., Tyler, J.K., and Churchill, M.E.A. (2023) A novel Single Alpha-Helix-DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function. eLife, 12:e83538. Link to paper
• Coleman, K.E., Yin, Y., Kit Leng Lui, S., Keegan, S., Fenyö, D., Smith, D.J., Rothenberg, E. and Huang, T.T. (2022) USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nature Communications 1;13(1):1740. Link to paper
• Koussa N.C. and Smith D.J. (2021). Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae. G3. In press. Link to paper
• Koussa N.C. and Smith D.J. (2021). Limiting DNA polymerase delta alters replication dynamics and leads to a dependence on checkpoint activation and recombination-mediated DNA repair. PLoS Genetics 17(1):e1009322. Link to paper
• Kit Leng Lui S, Keegan S, Tonzi P, Kahli M, Chen Y.H, Chalhoub N, Coleman K.E, Fenyo D+, Smith D.J+ and Huang TT+. (2021). Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells. (+co-corresponding authors) Nature Protocols 16(2):1193-1218. Link to paper
• Kellner, V. and Smith, D.J. (2020). Hold on Tight: Lagging-Strand DNA Polymerases Synthesize Multiple Okazaki Fragments without Letting Go. Molecular Cell 80(1):6-8.
• Porcella, S.Y., Koussa, N.C., Tang, C.P., Kramer, D.N., Srivastava, P. and Smith, D.J. (2020). Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation. PLOS Genetics 7;16(5):e1008755. Link to paper
• Yeung, R. and Smith, D.J. (2020). Determinants of Replication-Fork Pausing at tRNA Genes in Saccharomyces cerevisiae. Genetics 214(4):825-838 Link to paper
• Chen, Y-H*., Keegan, S*., Kahli, M*., Tonzi, P., Fenyö, D+., Huang, T.T+. and Smith, D.J+. (2019). Transcription Shapes DNA Replication Initiation and Termination in Human Cells. (+co-corresponding authors). Nature Structural and Molecular Biology. Link to paper
• Kahli, M*., Osmundson, J.S*., Yeung, R. and Smith, D.J. (2019). Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo. Nucleic Acids Research. https://doi.org/10.1093/nar/gky1242
•. Fu, I., Smith, D.J.and Broyde, S. (2019). Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome. DNA Repair. https://doi.org/10.1016/j.dnarep.2018.11.012
• Osmundson, J.S., Kumar, J., Yeung, R. and Smith, D.J. (2017). Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes. Nature Structural and Molecular Biology 24, 162-170. Link to paper
• Clausen, A.R., Lujan, S.A., Burkholder, A.B., Orebaugh, C.D., Williams, J.S., Clausen, M.F., Malc, E.P., Mieczkowski, P.A., Fargo, D.C., Smith, D.J. and Kunkel, T.A. (2015). Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nature Structural and Molecular Biology 22, 185–191. Download pdf
Papers from postdoc, PhD and undergraduate work
• McGuffee, S. R.*, Smith, D. J.*, and Whitehouse, I. (2013). Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. Molecular Cell 50, 123-135. Download pdf
• Whitehouse, I., and Smith, D. J. (2013). Chromatin dynamics at the replication fork: there's more to life than histones. Current Opinion in Genetics and Development 23(2), 140-6. Download pdf
• Borges, V., Smith, D. J., Whitehouse, I., and Uhlmann, F. (2013). An Eco1-independent sister chromatid cohesion establishment pathway in S. cerevisiae. Chromosoma 122, 121-134. Download pdf
• Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438. Download pdf
• Smith, D. J., Konarska, M. M., and Query, C. C. (2009). Insights into branch nucleophile positioning and activation from an orthogonal pre-mRNA splicing system in yeast. Molecular Cell 34, 333-343. Download pdf
• Smith, D. J., and Konarska, M. M. (2009). Identification and characterization of a short 2'-3' bond-forming ribozyme. RNA 15, 8-13. Download pdf
• Smith, D. J., and Konarska, M. M. (2009). A critical assessment of the utility of protein-free splicing systems. RNA 15, 1-3. Download pdf
• Smith, D. J., and Konarska, M. M. (2008). Mechanistic insights from reversible splicing catalysis. RNA 14, 1975-8. Download pdf
• Smith, D. J., Query, C. C., and Konarska, M. M. (2008). "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. Molecular Cell 30, 657-666. Download pdf
• Smith, D. J., Query, C. C., and Konarska, M. M. (2007). trans-splicing to spliceosomal U2 snRNA suggests disruption of branch site-U2 pairing during pre-mRNA splicing. Molecular Cell 26, 883-890. Download pdf
• Mosedale, D. E., Smith, D. J., Aitken, S., Schofield, P. M., Clarke, S. C., McNab, D., Goddard, H., Gale, C. R., Martyn, C. N., Bethell, H. W., Barnard, C., Hayns, S., Nugent, C., Panicker, A., and Grainger, D. J. (2005). Circulating levels of MCP-1 and eotaxin are not associated with presence of atherosclerosis or previous myocardial infarction. Atherosclerosis 183, 268-274. Download pdf