Dr. Peter Cock

Bioinformatician / Research Software Engineer
Information and Computational Sciences
E: peter.cock@hutton.ac.uk
T: +44 (0)344 928 5428 (*)
I worked at the Institute from finishing my PhD in 2008 through to 2024 as a bioinformatician, primarily with plant pathogens. This covered multiple kingdoms of life including viruses, bacteria, and Eukaryotes like nematodes. One of the first major projects I was part of sequenced the potato cyst nematode Globodera pallida, an economically important plant pest here in Scotland. Most recently my work was focused on metabarcoding of environmental DNA for oomycetes with implications for tree health, developing the THAPBI PICT pipeline. I served on the Post-Graduate Student Committee (PGSC), and the Equity, Diversity and Inclusion (EDI) committee.

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

Journals

Books / chapters

  • 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.

Technical / contract reports

  • Pagaling, E.; Buswell, V.; Cooper, A.; Hedley, P.; Cock, P.; Robinson, L.; Morris, J. (2024) Testing the validity of using eDNA for carbon origin analysis from sediment cores, Natural England website
  • Pagaling, E.; Cooper, A.; Cock, P.; Freitag, T.; Avery, L. (2024) Review of biases in metabarcoding primers for DNA analysis, Natural England catalogue
  • Cock, P.; Gurd, J.; Kuhfuss, L.; Piras, S. (2022) Introducing experimental methods for the study of resource and landrelated decisions in rural Scotland Final project report, MDT project report.

Conference papers

  • Cooke, D.; Randall, E; Keillor, B.; Cock, P. (2022) eDNA metabarcoding as a powerful tool to track plant pathogens, Presentation at Underpinning National Capacity DNA technologies, skills and infrastructure workshop, Perth, UK. 5 Dec 2022.
  • Cooke, D.; Brierley, J.; Toth, I.; Randall, E.; Humphris, S.; Jones, J.; Cock, P. (2022) Applications of DNA metabarcoding for plant pathogen tracking and diagnostics, Crop Production in Northern Britain Conference, 1-2 March 2022, Online.
  • Cock, P.; Cooke, D.E.L.; Pritchard, L. (2020) THAPBI PICT – a metabarcoding analysis pipeline developed as a Phytophthora ITS1 classification tool., Presentation at the BOSC track of the Bioinformatics Community Conference (BCC2020), 19 July 2020. (Online)
  • Green, S.; Cooke, D.E.L.; Frederickson-Matika, D.; Clark, B.; Randall, E.; Clark, M.; Pettit, T.; Dunn, M.; Schlenzig, A.; Pritchard, L.; Thorpe, P.; Cock, P.; Barbrook, J. (2019) Phytophthora communities in UK plant nurseries and links to management practice: opportunities for mitigation through accreditation., Presentation at the 9th Meeting of the IUFRO Working Party 7.02.09: Phytophthora in Forests and Natural Ecosystems, Sardinia 17-25 October 2019.
  • Cooke, D.E.L.; Randall, E.; Clark, B.; Thorpe, P.; Cock, P.J.; Pritchard, L.; Pettitt, T.; Frederickson-Matika, D.; Green, K.R. (2019) Phytophthora eDNA barcoding for natural ecosystem surveillance., 20th Oomycete Molecular Genetics Network Annual Meeting, Scottish Association for Marine Science (SAMS), Oban, 10-12 July 2019. Presentation.
  • Orr, J.; Cock, P.; Davies, K.; Blok, V. (2016) Mapping Pasteuria distribution in Scotland., The Dundee Conference: Crop Protection in Northern Britain 2016, Dundee, 23-24 February 2016, pp 283-285.
  • Harris, N.L.; Cock, P.J.A.; Chapman, B.; Goecks, J.; Hotz, H-R.; Lapp, H. (2015) The Bioinformatics Open Source Conference (BOSC) 2013., The 14th Annual Bioinformatics Open Source Conference (BOSC 2013), Berlin, Germany, 19-20 July 2013. Bioinformatics, 31, 299-300.
  • Thorpe, P.; Cock, P.J.A.; Mantelin, S.; Reid, a.; Cotton, J.; Lilley, C.J.; Urwin, P.E.; Blok, V.C.; Jones, J.T. (2012) Identification and functional characterisation of effectors from the potato cyst nematode Globodera pallida., Association of Applied Biologists Conference, Crop Genomics and Crop Improvement, University of East Anglia, Norwich, 5-6 December 2012.
  • Jones, J.T.; Thorpe, P.; Cock, P.J.A.; Mantelin, S.; Urwin, P.E.; Blok, V.C. (2012) Identification and characterisation of effectors of Globodera pallida., Effectome Meeting V, Lauret, France, 24-26 October 2012.
  • Palomares-Rius, J.E.; Jones, J.T.; Hedley, P.; Cock, P.J.A.; Blok, V.C. (2012) Gene expression of Globodera pallida in different potato genetic backgrounds., Proceedings Crop Protection in Northern Britain, Dundee, 28-29 February, 2012, pp285-289.
  • 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

  • Pritchard, P.; Cock, P.J.A.; Thorpe, P.; Randall, E.; Green, S.; Cooke, D.E.L. (2019) Metabarcoding diagnostics of Phytophthora species in environmental samples., XVIII International Congress on Molecular Plant-Microbe Interactions, Glasgow, UK, 14-18 July 2019. Abstract.
  • Green, S.; Cooke, D.E.L.; Frederickson-Matika, D.; Clark, B.; Randall, E.; Thorpe, P.; Pritchard, L.; Cock, P.; Pettitt, T.; Schlenzig, A.; Barbrook, J. (2019) PHYTO-THREATS: An analysis of Phytophthora communities in plant nurseries., Proceedings of XXV IUFRO World Congress 2019: Forest Research and Cooperation for Sustainable Development, Curitiba, Brazil 29 September – 5 October 2019. Pesquisa Forestal Brasileira – Brazilian Journal of Forestry Research, Colombo, v. 39, e201902043. Abstract.
  • Eves-van den Akker, S.; Laetsch, D.R.; Thorpe, P.; Lilley, C.J.; Danchin, E.G.J.; DaRocha, M.; Rancurel, C.; Holroyd, N.E.; Cotton, J.A.; Szitenberg, A.; Grenier, E.; Montarry, J.; Mimee, B.; Duceppe, M.; Boyes, I.; Marvin, J.M.C.; Jones, L.M.; Yusup, H.B.; Lafond-Lapalme, J.; Esquibet, M.; Sabeh, M.; Rott, M.; Overmars, H.; Finkers-Tomczak, A.; Smant, G.; Koutsovoulos, G.; Blok, V.; Mantelin, S.; Cock, P.J.A.; Phillips, W.; Henrissat, B.; Urwin, P.E.; Blaxter, M.; Jones, J.T. (2016) The genome of the yellow potato cyst nematode, globodera rostochiensis, reveals in-sights into the bases of parasitism and virulence., Journal of Nematology, 48, p317. Abstract.
  • Eves-van den Akker, S.; Lilley, C.J.; Danchin, E.G.J.; Rancurel, C.; Cock, P.J.A.; Urwin, P.E.; Jones, J.T. (2016) The transciptome of Nacobbus aberrans reveals insights int o the evolution of sedentary endoparasitism in plant-parasitic nematodes., Journal of Nematology, 48, p317. Abstract.
  • Orr, J.; Cock, P.; Davies, K.G.; Blok, V.C. (2016) A metagenetic tool to study nematode and pasteuria population dynamics., Journal of Nematology, 48, p359. Abstract.
  • Eves-van den Akker, S.; Lilley, C.J.; Danchin, E.G.J.; Rancurel, C.; Cock, P.J.A.; Jones, L.M.; Yusup, H.B.; Jones, J.T.; Urwin, P.E. (2015) Comparative genomics / transciptomics to study effector gene birth in plant-parasitic nematodes., Journal of Nematology, 47, 235. (Abstract)
  • Pritchard, L.; Bayer, M.; Cock, P.; Flores, P.; Jones, S.; Milne, I.; Shaw, P.; Marshall, D. (2014) James Hutton Institute Bioinformatics Grouping., Data Science Research Day, University of Edinburgh, 12 September 2014.
  • Hein, I.; Gilroy, E.; Hornyik, C.; Bryan, G.; Milne, I.; Toth, I.K.; Ducreux, L.; Torrance, L.; Milne, L.; Cock, P.; Pritchard, L.; Sharma, K.; MacFarlane, S.; Zhang, R.; Hedley, P.; Jones, J.; Birch, P.; Taylor, M.; Dale, F.; McNaughton, I.; Wright, J.; Prashar, A.; Blok, V.; Carnegie, P.; Chapman, S. (2013) Utilising the potato genome., Potatoes in Practice 2013, Balruddery Farm, Invergowrie, Dundee, 8 August 2013.
  • Jones, J.T.; Blok, V.C.; Cock, P.J.A.; Mantelin, S.; Smith, A. (2012) Genome sequence of the potato cyst nematode and its exploitation for control., Proceedings Crop Protection in Northern Britain, Dundee, 28-29 February, 2012.
  • Palomares-Rius, J.E.; Jones, J.T.; Hedley, P.E.; Morris, J.A.; Cock, P.J.A.; Blok, V.C. (2012) Gene expression of Globodera pallida in different potato genetic backgrounds., Environmental Management and Crop Protection. CPNB 2012: The Dundee Conference, 28-29 February 2012. (Poster)
  • Guzeeva, E.; Wright, K.M.; Mantelin, S.; Smith, A.; Cock, P.J.; Blok, V,C.; Jones, J,T. (2012) Cell biology of effectors: subcellular localisations of effectors from the potato cyst nematode Globodera pallida., 31st International Symposium of the European Society of Nematologists, Adana Turkey, 23-27 September 2012.
  • 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).