Peter Cock
I joined the Institute in 2008, where I have been doing comparative genetics and other bioinformatics work, with a particular focus on viruses and nematodes (for example, a project to sequence the potato cyst nematode Globodera pallida, an economically important plant pest here in Scotland).
Current research interests
My applied work on particular plant pathogens requires programming and scripting. My language of choice is Python, and since my PhD I have used and contributed to the Biopython libraries. Biology is becoming increasingly a big-data science, with technologies like microarrays and now high throughput sequencing, and dealing with this kind of data and associated tools and file formats forms a large part of my work. I try to release most of my code as open source, mostly on GitHub but I also use Bitbucket (for example, my contributions to Galaxy). I started writing an (external) blog Blasted Bioinformatics!? on the hands-on computational side of my work in 2011.
Past research
I completed my PhD at the University of Warwick's MOAC Doctoral Training Centre, titled Two-component regulation: modelling, predicting and identifying protein-protein interactions and assessing signalling networks of bacteria.
Bibliography
The following list is manually curated, you can also try the semi-automatic list of my publications on Google Scholar (with citation counts of dubious accuracy), and I have registered ORCID 0000-0001-9513-9993.
- Katayama, T., et al. 2013. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. Journal of Biomedical Semantics 4:6. DOI: 10.1186/2041-1480-4-6
- Kamei, H., Cock, P.J.A. 2013. Computation of balanced equivalence relations and their lattice for a coupled cell network. SIADS 12(1), 352-382.
- Palomares-Rius, J.E., Jones, J.T., Cock, P.J.A., Castillo, P., Blok, V. 2013. Activation of hatching in diapaused and quiescent Globodera pallida. Parasitology 140(4):445-54. DOI: 10.1017/S0031182012001874
- Milne, I., Stephen, G., Bayer, M., Cock, P.J.A., Pritchard, L., Cardle, L., Shaw, P.D., Marshall, D. 2013. Using Tablet for visual exploration of second-generation sequencing data. Briefings in Bioinformatics 14(2), 193-202.
- Palomares-Rius, J.E., Hedley, P.E., Cock, P.J., Morris, J.A., Jones, J.T., Vovlas, N., Blok, V. 2012. Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes. Mol Plant Pathol. 13(9):1120-1134.
- Talevich, E., Invergo, B.M., Cock, P.J.A. and Chapman, B.A. 2012. Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 13:209.
- Swanson, M.M., Reavy, B., Kira, K.S. Cock, P.J.A., Hopkins, D.W., Torrance, L., Koonin, E.V., Taliansky, M. 2012. Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes. PLoS ONE 7(7): e40683.
- Jupe, F., Pritchard, L., Etherington, G.J., MacKenzie, K., Cock, P.J.A., Wright, F., Kumar Sharma, S., Bolser, D., Bryan, G. J., Jones, J.D.G., and Hein, I. 2012. Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13:75.
- McGavin, W.J., Mitchell, C., Cock, P.J.A., Wright, K.M. and MacFarlane, S.A. 2012. Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA. Journal of General Virology 93(2), 430-437.
- Mcnally, R.R., Toth, I.K., Cock, P.J.A., Pritchard, L., Hedley, P.E., Morris, J.A., Zhao, Y., and Sundin, W.G. 2012. Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors. Molecular Plant Pathology 13(2), 160–173.
- Wang, D., Qi, M., Calla, B., Korban, S.S. Clough, S.J., Cock, P.J.A., Sundin, G.W., Toth, I., and Zhao, Y. 2012. Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora. Molecular Plant-Microbe Interactions 25(1), 6-17.
- Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa, K., Kanzaki, N., et al. 2011. Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus. PLoS Pathogens 7(9), e1002219.
- McGavin, W.J., Cock, P.J.A. and MacFarlane, S.A. 2010. Partial sequence and RT-PCR diagnostic test for the plant rhabdovirus Raspberry vein chlorosis virus. Plant Pathology 60(3), 462-467.
- Cock, P.J.A., Fields, C.J., Goto, N., Heuer, M.L., and Rice, P.M. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38(6), 1767-1771.
- Cock, P.J.A. and Whitworth, D.E. 2010. Evolution of relative reading frame bias in unidirectional prokaryotic gene overlaps. Molecular Biology and Evolution 27(4), 753-756.
- Jones, J., et al. 2009. Identification and functional characterisation of effectors in Expressed Sequence Tags from various life cycle stages of the potato cyst nematode Globodera pallida. Molecular Plant Pathology 10(6), 815-828.
- Cock, P.J.A., Antao, T. Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., and de Hoon, M.J.L. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11), 1422-1423.
- Whitworth, D.E. and Cock, P.J.A. 2009. Evolution of prokaryotic two-component systems: insights from comparative genomics. Amino Acids 37(3), 459-466.
- Whitworth, D.E. and Cock, P.J.A. 2008. Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships. Microbiology 154(2), 360-372.
- Whitworth, D.E. and Cock, P.J.A. 2008. Myxobacterial Two-Component Systems. Chapter 10 in Myxobacteria: Multicellularity and Differentiation (2007, D.E. Whitworth, ed), ASM Press, ISBN: 978-1-55581-420-5.
- Cock, P.J.A. and Whitworth, D.E. 2007. Evolution of prokaryotic two-component system signalling pathways: gene fusions and fissions. Molecular Biology and Evolution 24(11), 2355-2357.
- Cock, P.J.A. and Whitworth, D.E. 2007. Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes. Journal Of Molecular Evolution 64(4), 457-462.
Scientific/Conference Posters
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Related websites
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