Skip to navigation Skip to content

Peter Cock

Staff picture: Peter Cock
Controlling Weeds, Pests and Diseases
Information and Computational Sciences
Bioinformatician / Computational Biologist
peter.cock@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

I joined the Institute in 2008, where I have been doing comparative genetics and other bioinformatics work. The common theme has been plant pathogens, covering multiple kingdowms of life from viruses to nematodes (for example, a project to sequence the potato cyst nematode Globodera pallida, an economically important plant pest here in Scotland).

Current research interests

With high throughput technologies including sequencing and phenotyping, biology is increasingly becoming 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. My 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. I also serve on the board of the Open Bioinformatics Foundation (OBF) as treasurer, and previously secretary, 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 genomics work has been 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 - 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.

Bibliography

  • Cock, P.; Pritchard, L. (2014) Galaxy as a platform for identifying candidate pathogen effectors., In: Birch, P.R.J., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods and Protocols. Methods in Molecular Biology, Volume 1127. Humana Press, New York, 2nd ed. Chapter 1, 3-15.
  • 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.

Printed from /staff/peter-cock on 12/11/19 05:18:47 AM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.