Research
With high throughput technologies including sequencing and phenotyping, biology has increasingly become a big-data science. This gave rise to the interdisciplinary area of bioinformatics, where the day-to-day work requires programming and scripting skills in addition to biological knowledge. More recently the term Research Software Engineer has come into use, a label which also fits what I do. My programming language of choice is Python, and since my PhD I have used and contributed to Biopython and other widely used libraries.
I am an advocate of open source software in science, and release most of my code as open source, mainly on GitHub but I also use Bitbucket occasionally. I also serve on the board of the Open Bioinformatics Foundation (OBF) as president, and previously secretary then treasurer, and have co-chaired the OBF organised Bioinformatics Open Source Conference (BOSC). I write an (external) blog Blasted Bioinformatics!? on the hands-on computational side of my work. I am a qualified Software Carpentry instructor, and have taught Python programming on multiple Software Carpentry Workshops or guest lectures at local universities.
Much of my earlier genomics work was linked to identification of candidate effector proteins, by which we mean proteins a plant pathogen, such as a nematode or aphid, produces and excretes into the host plant to manipulate it to its benefit – for example suppressing immune responses. Another strand of work covers molecular diagnostics, using a marker gene like a barcode to enable large scale surveys using environmental DNA – including nematodes and bacteria in soil, or oomycetes in plant or water samples.
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. I have now co-supervised multiple PhD students to completion of their own doctorates.
Publications
The following Publications have not yet been migrated to the James Hutton Institute's Pure service and relate to the research outputs from the two legacy organisations: The Macaulay Land Use Research Institute and The Scottish Crop Research Institute.
Journals
- McGavin, W.J.; Cock, P.J.A.; MacFarlane, S.A. (2011) Partial sequence and RT-PCR diagnostic test for the plant rhabdovirus Raspberry vein chlorosis virus., Plant Pathology, 60, 462-467.
- Cock, P.J.A.; Whitworth, D.E. (2010) Evolution of relative reading frame bias in unidirectional prokaryotic gene overlaps., Molecular Biology and Evolution, 27, 753-756.
- Cock, P.J.A.; Fields, C.J.; Goto, N.; Heuer, M.L.; Rice, P.M. (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants., Nucleic Acids Research, 38, 1767-1771.
- Whitworth, D.E.; Cock, P.J.A. (2009) Evolution of prokaryotic two-component systems: insights from comparative genomics., Amino Acids, 37, 459-466.
- 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.; de Hoon M.J.L. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics., Bioinformatics, 25, 1422-1423.
- Whitworth, D.E.; Cock, P.J.A. (2008) Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships., Microbiology, 154, 360-372.
- Cock, P.J.A.; Whitworth, D.E. (2007) Evolution of prokaryotic two-component system signalling pathways: gene fusions and fissions., Molecular Biology and Evolution, 24, 2355-2357.
- Cock, P.J.A.; Whitworth, D.E. (2007) Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes., Journal of Molecular Evolution. 64, 457-462.
Books / chapters
- Whitworth, D.E.; Cock, P.J.A. (2008) Two-component signal transduction systems of the Myxobacteria., In: Whitworth, D.E. (ed.). Myxobacteria: Multicellularity and Differentiation. ASM Press, Washington, D.C., pp169-190.
Conference papers
- McNally, R.R.; Sundin, G.W.; Zhao, Y.F.; Toth, I.K.; Cock, P.J.A.; Hedley, P.E. (2010) Microarray characterisation of the HrpL regulon of the fire blight pathogen Erwinia amylovora., 12th International Workshop on Fire Blight, Warsaw, Poland, 16-20 August 2010.
- Robertson, L.; Radhakrishnan, R.; Cock, P.J.A.; Blok, V.C.; Smith, A.; Grenier, E.; Hunt, M.; Berriman, M.; Jones, J.T. (2010) Functional analysis of pioneer effectors from plant parasitic nematodes., 4th Annual Meeting of COST 872 Nemagenics: Exploiting genomics to understand plant-nematode interactions, Lisbon, Portugal, 24-27 May 2010.
Conference posters / abstracts
- MacFarlane, S.; McGavin, W.; Cock, P.J.A.; Mitchell, C.A. (2011) Raspberry leaf and bud mite spreads a newly discovered virus to raspberry crops., East Malling Research/HDC Soft Fruit Day, East Malling, Kent, 23 November 2011.
- MacFarlane, S.; McGavin, W.; Cock, P.J.A.; Mitchell, C. (2011) Identification of raspberry leaf blotch virus (RLBV), a new virus associated with the raspberry leaf and bud mite (Phyllocoptes gracilis) and leaf blotch disorder., 10th International Rubus and Ribes Meeting, Zlatibor, Serbia, 22-26 June 2011.
- Blok, V.C.; Cock, P.J.A.; Hunt, M.; Hedley, P.E.; Morris, J.; Jones, J.T. (2010) Investigations of the expression of the multipartite mtDNA of Globodera pallida., 4th Annual Meeting of COST 872 Nemagenics: Exploiting genomics to understand plant-nematode interactions, Lisbon, Portugal, 24-27 May 2010 (Poster).
- Blok, V.C.; Cock, P.J.A.; Hunt, M.; Hedley, P.E.; Morris, J.; Jones, J.T. (2010) Investigations of the expression of the multipartite mtDNA of Globodera pallida., Society of Nematologists Annual Meeting, Boise, Idaho, USA, 11-14 July 2010 (Poster).
