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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
    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. (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

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


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