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Selected Publications

A complete list can be found on Google Scholar.

  • Shearwin, K.E. and Egan, J.B. (2000) Establishment of lysogeny in bacteriophage 186 - DNA binding and transcriptional activation by the CII protein. Journal of Biological Chemistry  275, 29113-29122.
  • Dodd, I.B., Perkins, A.J., Tsemitsidis, D., and Egan, J.B. (2001) Octamerization of lambda CI repressor is needed for effective repression of PRM and efficient switching from lysogeny. Genes & Development 15, 3013-3022.
  • Shearwin, K.E., Dodd, I.B. and Egan, J.B. (2002) The helix-turn-helix motif of the coliphage 186 immunity repressor binds to two distinct recognition sequences. Journal of Biological Chemistry 277, 3186-3194.
  • Dodd, I.B., Shearwin, K.E., Perkins, A., Burr, T., Hochschild, A. and Egan, J.B. (2004) Cooperativity in long range gene regulation by the l CI repressor. Genes and Development 18, 344-354.
  • Callen, B.P., Shearwin, K.E., and Egan, J.B. (2004) Transcriptional interference between convergent promoters caused by elongation over the promoter. Molecular Cell 14, 647-656.
  • Sneppen, K., Dodd, I.B., Shearwin, K.E., Palmer, A., Schubert, R.A., Callen, B.C. and Egan, J.B. (2005) A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli. Journal of Molecular Biology 346, 399-409.
  • Dodd, I.B., Shearwin, K.E. and Egan, J.B. (2005) Revisited gene regulation in bacteriophage lambda. Current Opinion in Genetics and Development 15, 145-152.
  • Shearwin, K.E., Callen, B.P. and Egan, J.B. (2005) Transcriptional interference – a crash course. Trends in Genetics 21, 339-345.
  • Trusina, A., Sneppen, K., Dodd, I.B., Shearwin, K.E. and Egan, J.B. (2005) Functional alignment of regulatory networks – a study of temperate phages. PLOS Computational Biology 1 (7), e74 599-603.
  • Pinkett, H., Shearwin, K.E., Stayrook, S., Dodd., I.B., Burr, T., Hochschild, A., Egan, J.B. and Lewis, M. (2006) The structural basis of cooperative regulation at an alternative genetic switch. Molecular Cell 21, 605-615.
  • Schubert, R.A. and Shearwin, K.E. (2006) How bacterial genes get turned on. Microbiology Australia 27, 109-111.
  • Dodd, I. B., Micheelsen, M. A., Sneppen, K. & Thon, G. (2007). Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129, 813-22.
  • Dodd, I.B., Shearwin, K.E. and Sneppen, K. (2007) Modelling transcriptional interference and DNA looping in gene regulation. Journal of Molecular Biology 369, 1200-1213.
  • Schubert*, R.A., Dodd*, I.B., Egan, J.B. and Shearwin, K.E. (2007) Cro’s role in the CI–Cro bistable switch is critical for l’s transition from lysogeny to lytic development. Genes and Development 21, 2461-2472. * equal contributions
  • Sneppen, K. Micheelsen, M.A. and Dodd, I.B. (2008) Ultrasensitive gene regulation by positive feedback loops in nucleosome modification. Molecular Systems Biology 4, Article 182.
  • Mitarai, N., Dodd, I.B., Crooks, M.T. and Sneppen, K. (2008) The generation of promoter-mediated transcriptional noise in bacteria. PLOS Computational Biology 4, e1000109.
  • Palmer, A.C., Ahlgren-Berg, A., Egan, J.B., Dodd, I.B. and Shearwin, K.E. (2009) Potent transcriptional interference by pausing of RNA polymerase over a downstream promoter. Molecular Cell 34, 545-555.
  • Avlund M, Dodd IB, Semsey S, Sneppen K, Krishna S. (2009) Why do phage play dice? Journal of
    Virol
    ogy
    83(22), 11416-20.
  • Avlund M, Dodd IB, Sneppen K, Krishna S. (2009) Minimal gene regulatory circuits that
    can count like bacteriophage lambda. Journal of Molecular Biology 394(4), 681-93.
  • Micheelsen MA, Mitarai N, Sneppen K, Dodd IB. (2010) Theory for the stability and
    regulation of epigenetic landscapes. Phys Biol. 7(2), 026010.
  • Avlund M, Krishna S, Semsey S, Dodd IB, Sneppen K. (2010) Minimal gene regulatory
    circuits for a lysis-lysogeny choice in the presence of noise. PLoS One. 5(12), e15037.
  • Hao N, Whitelaw ML, Shearwin KE, Dodd IB, Chapman-Smith A. (2011) Identification of
    residues in the N-terminal PAS domains important for dimerization of Arnt and
    AhR. Nucleic Acids Research 39(9), 3695-709.
  • Dodd IB, Sneppen K. (2011) Barriers and silencers: a theoretical toolkit for control
    and containment of nucleosome-based epigenetic states. Journal of Molecular Biology 414(4), 624-37.
  • Palmer AC, Egan JB, Shearwin KE. (2011) Transcriptional interference by RNA
    polymerase pausing and dislodgement of transcription factors. Transcription
    2(1), 9-14.
  • Dodd, IB, Sneppen, K (2012) A simple histone code opens many paths to epigenetics. PLOS Computational Biology doi: 10.1371/journal.pcbi.1002643
  • Lun*, C., Murchland*, I., Shearwin, K.E. and Dodd, I.B. (2013) Enhancer-like long-range transcriptional activation by lambda CI-mediated DNA looping. Proceeding of the National Academy of Sciences USA (PNAS) 110 (8), 2922-2927. Published ahead of print February 4 2013 doi:10.1073/pnas.1221322110 (impact factor: 9.7) * equal first authors
  • Wang, H., Dunlap, D., Dodd, I.B., Shearwin*, K.E., Finzi*, L. (2013) Single molecule analysis of DNA wrapping and looping by a circular 14-mer wheel of the bacteriophage 186 CI repressor. Nucleic Acids Research (accepted March 29, 2013).* Co-corresponding authors (impact factor: 8.0)
  • Gao N., Shearwin K., Mack J., Finzi L., Dunlap D. (2013) Purification of bacteriophage lambda repressor. Protein Expression and Purification 90 (1) 30-36.
  • St. Pierre*, F., Lun*, C., Priest, D.G., Endy, D., Dodd, I.B., Shearwin, K.E. (2013) One-step cloning and chromosomal integration of DNA. ACS Synthetic Biology 2 (9), 537-541. (featured on cover) * equal first authors
  • Lun C., Murchland, I., Dodd, I.B. and Shearwin, K.E. (2013) Bacteriophage lambda repressor mediates the formation of a complex enhancer-like structure. Transcription 4 (5) 1-5. http://dx.doi.org/10.4161/trns.26101 (featured on cover)
  • Lun C., St. Pierre, F. and Shearwin, K.E. (2013) Repurposing site- specific recombinases for synthetic biology Future Microbiology 8 (11) 1361-1364.
  • Priest, D.G., Lun C., Kumar, S., Dunlap, D., Dodd, I.B. and Shearwin, K.E. (2014) Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors. Proceeding of the National Academy of Sciences USA (PNAS) 111 (1) 349-354.
  • Hao, N., Krishna, S., Ahlgren-Berg, A., Cutts, E.E., Shearwin, K.E. and Dodd, I.B. (2014) Road rules for traffic on DNA--systematic analysis of transcriptional roadblocking in vivo. Nucleic Acids Research doi: 10.1093/nar/gku627.
  • David G Priest , Sandip Kumar , Yan Yan , David Dunlap , Ian B Dodd, Shearwin, K.E. (2014) Quantitation of interactions between two DNA loops demonstrates loop-domain insulation in E. coli cells. PNAS 111(42):E4449-E4457 doi:10.1073/pnas.1410764111
  • Murchland, I., Ahlgren-Berg, A., Priest, D.G., Dodd, I.B. and Shearwin, K.E. (2014) Promoter Activation by CII, a Potent Transcriptional Activator from Bacteriophage 186 Journal of Biological Chemistry  289, 32094-32108. doi:10.1074/jbc.M114.608026

Book Chapters

  • Palmer, A.C. and Shearwin, K.E. (2009) Guidance for Data Collection and Computational Modelling of Regulatory Networks in Methods in Molecular Biology: Computational Systems Biology. Humana Press, Totowa, New Jersey. Volume 541, Chapter 15.
Shearwin Laboratory
Address

North Terrace Campus
Level 3, Molecular Life Sciences
The University of Adelaide
SA 5005
AUSTRALIA

Contact

Keith Shearwin
T: +61 8 8313 5361
F: +61 8 8313 4362
email