The evolution of TE families, primarily in mammals has been the defining topic of my evolutionary genetics career. Working with John Brookfield at the University of Nottingham, we have looked at the origin of many TE families in mammals and traced their histories to the present day.
One of the most interesting questions in evolution, the key question in my opinion, is how species evolve. What causes a species to divide in two in a permanent (or at least semi-permanent) manner? Is it just the accumulation of mutations over time? Do these changes need to be large, or can many small changes have this effect? Is it based on genetic or geographic isolation?
Riesch, R., Muschick, M., Lindtke, D., Villoutreix, R., Comeault, A. A., Farkas, T. E., … & de Carvalho, C. F. (2017). Transitions between phases of genomic differentiation during stick-insect speciation. Nature ecology & evolution, 1(4), 0082.
During my Phd I studied transcription factors and transcription factor binding sites (TFBS), primarily looking at prediction algorithms and at whether gene function can be predicted by analysis of the transcription factors regulating it.
Flower K*, Hellen E* et al. (2010) Evaluation of a prediction protocol to identify potential targets of epigenetic reprogramming by the cancer associated Epstein Barr Virus. PLOS One. 5:e9443. *Joint first authors
I have also provided bioinformatics support for a number of other studies – primarily sequence similarity searching, phylogeny and genomic annotation.
Also published as:
Cottage A et al. (2005) Predicting Protein Function and Structure Using Bioinformatics Protocols: A Case Study of the SAND Protein Family. Nato Science Series Sub Series I Life and Behavioural Sciences. 368:162.