Publications
- 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.
- 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. and Shearwin, K. (2009) Experimental design and data collection for computational modelling of regulatory networks in Methods in Molecular Biology volume 541, 337-354 Computational Systems Biology.
- 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.
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