Work

Research History

Pre (Research) History

I have a background in mathematics and computing. I spent several years working in London for financial companies as a FORTRAN programmer and system analyst and then a while in Cambridge working for a Parke-Davis/Warner Lambert as Computer System Manager at the Parke-Davis Neuroscence Reserch Unit, responsible for making almost everything with a keyboard and some things without, talk to the network and share data. Getting some of the “wetware” to share data and adopt new procedures proved considerably more challenging than getting the hardware and software to talk to each other. While working for PDNRU I also started an undergradute degree in Science and Mathematical Modelling with the Open University. I left PDRU and worked for a couple of years as a TCP/IP network specialist before spending a couple of years as a database programmer writing front ends for SQL databases using VisualBasic. While working freelance I completed my OU degree and after my degree I moved from Cambridge and came to Dundee to undertake a PhD.

Over the years I have written hundreds of thousands of lines of C, C++ and Objective-C, tens of thousands of lines of Python, FORTRAN and VisualBasic, a few thousand lines of Java and even some PERL. But I now focus almost exclusively on R, you tend to have to write fewer lines to get what you want done..

Publications

Meier, B., Volkova, N., Hong, Y., Schofield, P., Campbell, P. J., Gerstung, M., & Gartner, A. (2017). Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers. bioRxiv, 149153. https://doi.org/10.1101/149153

Burgess, A. E. F., Schofield, P. G., Hubbard, S. F., Chaplain, M. a. J., & Lorenzi, T. (2016). Dynamical Patterns of Coexisting Strategies in a Hybrid Discrete-continuum Spatial Evolutionary Game Model. Mathematical Modelling of Natural Phenomena, 11(5), 49–64. https://doi.org/10.1051/mmnp/201611504

Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., … Barton, G. J. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA. https://doi.org/10.1261/rna.053959.115

Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S., & Owen-Hughes, T. (2016). The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PLoS Genetics, 12(3), e1005940. https://doi.org/10.1371/journal.pgen.1005940

Seifert, A., Schofield, P., Barton, G. J., & Hay, R. T. (2015). Proteotoxic stress reprograms the chromatin landscape of SUMO modification. Science Signalling, 8(384).

Gierliński, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., … Barton, G. J. (2015). Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. Bioinformatics, 31(22), 3625–3630. https://doi.org/10.1093/bioinformatics/btv425

Roberts, D. M., Schofield, P. G., Donn, S., & Daniell, T. J. (2012). Directed terminal restriction analysis tool (DRAT): An aid to enzyme selection for directed terminal-restriction fragment length polymorphisms. Methods in Ecology and Evolution, 3, 24–28.

Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., … Owen-Hughes, T. (2011a). A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization. Science, 333, 1758–1760.

Gkikopoulos, T., Singh, V., Tsui, K., Awad, S., Renshaw, M. J., Scholfield, P., … Owen-Hughes, T. (2011b). The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. Embo Journal, 30, 1919–1927.

van Koningsbruggen, S., Gierlinski, M., Schofield, P., Martin, D., Barton, G. J., Ariyurek, Y., … Lamond, A. I. (2010). High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli. Molecular Biology of the Cell, 21, 3735–3748.

Preedy, K. F., Schofield, P. G., Liu, S., Matzavinos, A., Chaplain, M. A. J., & Hubbard, S. F. (2010). Modelling contact spread of infection in host-parasitoid systems: Vertical transmission of pathogens can cause chaos. Journal of Theoretical Biology, 262, 441–451.

Reed, B., Rhodes, S., Schofield, P., & Wylie, K. (2009). Gender Variance in the UK: Prevalence, incidence growth and geographic distribution. GIRES Technical Report.

Jones, H., & Schofield, P. (2008). Thermal and Other Remote Sensing of Plant Stress. General Applications Plant Physiology.

Pearce, I. G., Chaplain, M. A. J., Schofield, P. G., Anderson, A. R. A., & Hubbard, S. F. (2007). Chemotaxis-induced spatio-temporal heterogeneity in multi-species host-parasitoid systems. Journal of Mathematical Biology, 55, 365–388.

Preedy, K. F., Schofield, P. G., Chaplain, M. A. J., & Hubbard, S. F. (2007). Disease induced dynamics in host-parasitoid systems: Chaos and coexistence. Journal of the Royal Society Interface, 4, 463–471.

Pearce, I. G., Chaplain, M. A. J., Schofield, P. G., Anderson, A. R. A., & Hubbard, S. F. (2006). Modelling the spatio-temporal dynamics of multi-species host-parasitoid interactions: Heterogeneous patterns and ecological implications. J Theor Biol, 241(4), 876–886.

Fytrou, A., Schofield, P. G., Kraaijeveld, A. R., & Hubbard, S. F. (2006). Wolbachia infection suppresses both host defence and parasitoid counter-defence. Proceedings of the Royal Society B: Biological Sciences, 273(1588), 791–796.

Schofield, P. G., Chaplain, M. A. J., & Hubbard, S. F. (2005). Dynamic heterogeneous spatio-temporal pattern formation in host-parasitoid systems with synchronised generations. J Math Biol, 50(5), 559–583.

Schofield, P. G., Chaplain, M. A. J., & Hubbard, S. F. (2002). Mathematical modelling of host-parasitoid systems: Effects of chemically mediated parasitoid foraging strategies on within- and between-generation spatio-temporal dynamics. J. Theor. Biol., 214, 31–47.

Schofield, P. (2002). Spatially Explicit Models of Turelli-Hoffmann Wolbachia Invasive Wave Fronts. Journal of Theoretical Biology, 215(1), 121–131.

Schofield, P. G. (2002). Spatio-temporal Mathematical Models for the Investigation of Host-Parasitoid Systems and Wolbachia-infection Dynamics (Ph.D. Thesis). University of Dundee; University of Dundee, Dundee.

Schofield, P., Chaplain, M., & Hubbard, S. F. (2000). Spatio-temporal mathematical models of host-parasitoid systems. European Communications of Mathematical and Theoretical Biology, 2(12-17).