Peter Cock
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
- 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.; 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.
- Vélez, M.L.; La Manna, L.; Tarabini, M.; Gomez, F.; Elliott, M.; Hedley, P.E.; Cock, P.; Greslebin, A. (2020) Phytophthora austrocedri in Argentina and co-inhabiting Phytophthoras: roles of anthropogenic and abiotic factors in species distribution and diversity., Forests, 11, Article No. 1223.
- Varypatakis, K.; Véronneau, P-Y.; Thorpe, P.J.; Cock, P.J.A.; Tze-Yin Lim, J.; Armstrong, M.R.; Janakowski, S.; Sobczak, M.; Hein, I.; Mimee, B.; Jones, J.T.; Blok, V.C. (2020) The genomic impact of selection for virulence against resistance in the potato cyst nematode Globodera pallida., Genes, 11, Article No. 1429.
- Orr, J.N.; Neilson, R.; Freitag, T.E.; Roberts, D.M.; Davies, K.G.; Blok, V.C.; Cock, P.J.A. (2020) Parallel microbial ecology of pasteuira and nematode species in Scottish soils., Frontiers in Plant Science, 10, Article No. 1763.
- 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)
- Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. (2019) Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data., Journal of General Virology, 100, 533-542.
- 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.
- Thorpe, P.; Escudero-Martinez, C.M.; Cock, P.J.A.; Eves-van den Akker, S.; Bos, J.I.B. (2018) Shared transcriptional control and disparate gain and loss of aphid parasitism genes., Genome Biology and Evolution, 10, 2716-2733.
- Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B.A.; Rowe, J.; Tomkins-Tinch, C.H.; Valieris, R.; Caprez, A.; Batut, B.; Haudgaard, M.; Cokelaer, T.; Beauchamp, K.A.; Pedersen, B.S.; Hoogstrate, Y.; Bretaudeau, A.; Ryan, D.; Le Corguillé, G.; Yusuf, D.; Luna-Valero, S.; Kirchner, R.; Brinda, K.; Wollmann, T.; Raden, M.; Pantano, L.; Soranzo, N.; van Heeringen, S.J.; Charlop-Powers, Z.; Unneberg, P.; de Smet, M.; Martin, M.; Von Kuster, G.; Antao, T.; Miladi, M.; Brueffer, C.; Thornton, K.; van den Beek, M.; Maticzka, D.; Blank, C.; Will, S.; Gravouil, K.; Wolff, J.; Holtgrewe, M.; Fallmann, J.; Piro, V.C.; Shlyakhter, I.; Yousif, A.; Mabon, P.; Zhang, X-O.; Cabral, J.; Shen, W.; Thomas, C.; Brown, J.; Enns, E.; de Hollander, M.; Boekel, J.; Kelleher, J.; Bouvier, D.; Turaga, N.; de Ruiter, J.R.; Choudhary, S.; Harding, N.; Kratz, A.; Fang, Z.; Kleinkauf, R.; Timm, H.; Khan, A.; Cock, P.J.A.; Seiler, E.; Nguyen, H.; Brislawn, C.; Stovner, E.B.; Johnson, J.E.; Hägglund, E.; Ewels, P.; Chambers, M.; Pruesse, E.; Guimera, R.V.; Ye, S.; Dunn, W.A.; Parsons, L.; Cornwell, M.; Reynolds, A.; Bargull, M.; Grassi, E.; Koppstein, D.; Patro, R.; Wohlers, I.; Stoler, N.; Blankenberg, D.; He, G.; Freeberg, M.; Farouini, R.; Junge, A.; Bogema, D.R.; Singh, S.; Cumbo, F.; Larson, D.E.; Wang, L.; Workentine, M.L.; Devisetty, U.K.; Laurent, S.; Garnier, X.; Agren, R.; Roger, P.; Eppley, J.M.; Li, W.; Rausch, R.; Chande, A.T.; Taylor, J.; Stöcker, B.K.; Milne, I.; Wright, P.R.; Taranto, A.P.; Chicco, D.; Abdennur, N.; Sennblad, B.; Baaijens, J.A.; Gopez, M.; Enache, O.M.; Pinello, L.; Srivastava, A.; de Bruijn, I.; Kensche, P.R.; Blin, K.; Pirola, Y.; Preussner, J.; Knudsen, M.; Bendall, M.L.; rai, V.; Gonnella, G.; Stahl, C.; Miles, A.; Waters, N.R.; Hiltemann, S.; Boursin, Y.; Perez-Riverol, Y.; Schmeier, S.; Clarke, E.; Arvai, K.; Jung, M.; Stephen, G.; Domenico, T.; seiler, J.; Rasche, E.; Kornobis, E.; Beisser, D.; Rahmann, S.; Mikheyev, A.S.; Tran, C.; Capellades, J.; Moskalenko, O.; Schröder, C.; Dirmeier, S.; Webster, T.H.; Salatino, A.E.; Urgese, G.; Köster, J. (2018) Bioconda: A sustainable and comprehensive software distribution for the life sciences., Nature Methods, 15, 475-476.
- Nascimento, F.; Vicente, C.; Cock, P.; Tavares, M.; Rossi, M.; Hasegawa, K.; Mota, M. (2018) From plants to nematodes: Serratia grimesii BXF1 genome reveals an adaptation to the modulation of multi-species interactions., Microbial Genomics, 4, Article No. 000178.
- Eves-van den Akker, S.; Laetsch, D.R.; Thorpe, P.; Lilley, C.J.; Danchin, E.G.J.; Da Rocha, M.; Rancurel, C.; Holroyd, N.E.; Cotton, J.A.; Szitenberg, A.; Grenier, E.; Montarry, J.; Mimee, B.; Duceppe, M.O.; 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 insights into the basis of parasitism and virulence., Genome Biology, 17, Article No. 124.
- Vicente, C.S.L.; Nascimento, F.X.; Ikuyo, Y.; Cock, P.J.A.; Mota, M.; Hasegawa, K. (2016) The genome and genetics of a high oxidative stress tolerant Serratia sp LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus., BMC Genomics, 17, Article No. 301.
- Vicente, C.S.L.; Nascimento, F.X.; Barbosa, P.; Ke, H.M.; Tsai, I.J.; Hirao, T.; Cock, P.J.A.; Kikuchi, T.; Hasegawa, K.; Mota, M. (2016) Evidence for an opportunistic and endophytic lifestyle of the Bursaphelenchus xylophilus-associated bacteria Serratia marcescens PWN146 isolated from wilting Pinus pinaster., Microbial Ecology, 72, 669-681.
- Thorpe, P.; Cock, P.J.A.; Bos, J. (2016) Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets., BMC Genomics, 17, Article No. 172.
- Espada, M.; Silva, A.C.; Eves-van den Akker, S.; Cock, P.J.A.; Mota, M.; Jones, J.T. (2016) Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy., Molecular Plant Pathology, 17, 286-295.
- Palomares-Rius, J.E.; Hedley, P.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Blok, V.C. (2016) Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate., PeerJ, 4, Article No. e1654.
- Harris, N.L.; Cock, P.J.A.; Lapp, H.; Chapman, B.; Davey, R.; Fields, C.; Hokamp, K.; Munoz-Torres, M. (2016) The 2015 Bioinformatics Open Source Conference (BOSC 2015)., PLoS Computational Biology, 12, Article No. e1004691.
- Bolleman, J.T.; Mungall, C.J.; Strozzi, F.; Baran, J.; Dumontier, M.; Bonnal, R.J.P.; Buels, R.; Hoehndorf, R.; Fujisawa, T.; Katayama, T.; Cock, P.J.A. (2016) FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation., Journal of Biomedical Semantics, 7, Article No. 39.
- 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.
- Eves-van den Akker, S.; Lilley, C.J.; Reid, A.; Pickup, J.; Anderson, E.; Cock, P.J.A.; Blaxter, M.; Urwin, P.E.; Jones, J.T.; Blok, V.C. (2015) A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual., Molecular Ecology, 24, 5842-5851.
- Lu, Y.W.; McGavin, W.; Cock, P.J.A.; Schnettler, E.; Yan, F.; Chen, J.P.; MacFarlane, S.A. (2015) Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins., Journal of General Virology, 96, 3432-3439.
- Cock, P.J.A.; Chilton, J.M.; Gruning, B.; Johnson, J.E.; Soranzo, N. (2015) NCBI BLASTplus integrated into Galaxy. Technical note., GigaScience, 4, Article No. 39.
- Reavy, B.; Swanson, M.M.; Cock, P.J.A.; Dawson, L.A.; Freitag, T.E.; Singh, B.K.; Torrance, L.; Mushegain, A.R.; Taliansky, M. (2015) Distinct circular single-stranded DNA viruses exist in different soil types., Applied and Environmental Microbiology, 81, 3934-3945.
- Cock, P.J.A.; Bonfield, J.; Chevreux, B.; Li, H. (2015) SAM/BAM format v1.5 extensions for de novo assemblies., bioRxiv, 29 May 2015, 3pp.
- 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.
- Eves-van den Akker, S.; Lilley, C.J.; Danchin, E.G.J.; Rancurel, C.; Cock, P.J.A.; Urwin, P.E.; Jones, J.T. (2014) The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes., Genome Biology and Evolution, 6, 2181-2194.
- Thorpe, P.; Mantelin, S.; Cock, P.J.A.; Blok, V.C.; Coke M.C.; van Den Akker, S.E.; Guzeeva, E.; Lilley, C.J.; Smant, G.; Reid, A.J.; Wright, K.M.; Urwin, P.E.; Jones, J.T. (2014) Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida., BMC Genomics, 15, Article No. 923.
- Cotton, J.A.; Lilley, C.J.; Jones, L.M.; Kikuchi, T.; Reid, A.J.; Thorpe, P.; Tsai, I.J.; Beasley, H.; Blok, V.C.; Cock, P.J.A.; Eves-van den Akker, S.; Holroyd, N.; Hunt, M.; Mantelin, S.; Naghra, H.; Pain, A.; Palomares-Rius, J.E.; Zarowiecki, M.; Berriman, M.; Jones, J.T.; Urwin, P.E. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode., Genome Biology, 15, Article No. R43.
- Kikuchi, T.; Cock, P.J.A.; Helder, J.; Jones, J.T. (2014) Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase., Nematology, 16, 99-107.
- Moller, S.; Afgan, E.; Banck, M.; Bonnal, R.J.P.; Booth, T.; Chilton, J.; Cock, P.J.A.; Gumbel, M.; Harris, N.; Holland, R.; Kalas, M.; Kajan, L.; Kibukawa, E.; Powel, D.R.; Prins, P.; Quinn, J.; Sallou, O.; Strozzi, F.; Seemann, T.; Sloggett, C.; Soiland-Reyes, S.; Spooner, W.; Steinbiss, S.; Tille, A.; Travis, A.J.; Guimera, R.V.; Katayama, T.; Chapman, B.A. (2014) Community-driven development for computational biology at Sprints, Hackathons and Codefests., BMC Bioinformatics, 15(Suppl 14), S7.
- Katayama, T.; Wilkinson, M.D.; Aoki-Kinoshita, K.F.; Kawashima, S.; Yamamoto, Y.; Yamaguchi, A.; Okamoto, S.; Kawano, S.; Kim, J.D.; Wang, Y.; Wu, H.Y.; Kano, Y.; Ono, H.; Bono, H.; Kocbek, S.; Aerts, J.; Akune, Y.; Antezana, E.; Arakawa, K.; Aranda, B.; Baran, J.; Bolleman, J.; Bonnal, R.J.P.; Buttigieg, P.L.; Campbell, M.P.; Chen, Y.A.; Chiba, H.; Cock, P.J.A.; Cohen, K.B.; Constantin, A.; Duck, G.; Dumontier, M.; Fujisawa, T.; Fujiwara, T.; Goto, N.; Hoehndorf, R.; Igarashi, Y.; Itaya, H.; Ito, M.; Iwasaki, W.; Kalas, M.; Katoda, T.; Kim, T.; Kokubu, A.; Komiyama, Y.; Kotera, M.; Laibe, C.; Lapp, H.; Lutteke, T.; Marshall, M.S.; Mori, T.; Mori, H.; Morita, M.; Murakami, K.; Nakao, M.; Narimatsu, H.; Nishide, H.; Nishimura, Y.; Nystrom-Persson, J.; Ogishima, S.; Okamura, Y.; Okuda, S.; Oshita, K.; Packer, N.H.; Prins, P.; Ranzinger, R.; Rocca-Serra, P.; Sansone, S.; Sawaki, H.; Shin, S.H.; Splendiani, A.; Strozzi, F.; Tadaka, S.; Toukach, P.; Uchiyama, I.; Umezaki, M.; Vos, R.; Whetzel, P.L.; Yamada, I.; Yamasaki, C.; Yamashita, R.; York, W.S.; Zmasek, C.M.; Kawamoto, S.; Takagi, T. (2014) BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains., Journal of Biomedical Semantics, 5, Article No.5.
- 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.
- Jupe, F.; Witek, K.; Verweij, W.; Sliwka, J.; Pritchard, L.; Etherington, G.J.; Maclean, D.; Cock, P.J.; Leggett, R.M.; Bryan, G.J.; Cardle, L.; Hein, I.; Jones, J.D.G. (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations., Plant Journal, 76, 530-544.
- Kamei, H.; Cock, P.J.A. (2013) Computation of balanced equivalence relations and their lattice for a coupled cell network., Siam Journal on Applied Dynamical Systems, 12, 352-382.
- Palomares-Rius, J.E.; Jones, J.T.; Cock, P.J.; Castillo, P.; Blok, V.C. (2013) Activation of hatching in diapaused and quiescent Globodera pallida., Parasitology, 140, 445-454.
- Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F. (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
- Katayama, T.; Wilkinson, M.D.; Micklem, G.; Kawashima, S.; Yamaguchi, A.; Nakao, M.; Yamamoto, Y.; Okamoto, S.; Oouchida, K.; Hong-Woo ,C.; Aerts, J.; Afzal, H.; Antezana, E.; Arakawa, K.; Aranda, B.; Belleau, F.; Bolleman, J.; Bonnal, R.J.P.; Chapman, B.; Cock, P.J.A.; Eriksson, T.; Gordon, P.M.K.; Goto, N.; Hayashi, K.: Horn, H.; Ishiwata, R.; Kaminuma, E.; Kasprzyk, A.; Kawaji, H.; Kido, N.; Kim, Y-J.; Kinjo, A.R.; Konishi, F.; Kwon, K-H.; Labarga, A.; Lamprecht, A-L.; Lin, Y.; Lindenbaum, P.; McCarthy, L.; Morita, H.; Murakami, K.; Nagao, K.; Nishida, K.; Nishimura, K.; Nishizawa, K.; Ogishima, S.; Ono, K.; Oshita, K.; Park, K-J.; Prins, P.; Saito, T.L.; Samwald, M.; Satagopam, V.P.; Shigemoto, Y.; Smith, R.; Splendiani, A.; Sugawara, H.; Taylor, J.; Vos, R.A.; Withers, D.; Yamasaki, C.; Zmasek, C.M.; Kawamoto, S.; Okubo, K.; Asai K.; Takagi, T. (2013) The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies., Journal of Biomedical Semantics, 4(6).
- Vélez, M.L.; La Manna, L.; Tarabini, M.; Gomez, F.; Elliott, M.; Hedley, P.E.; Cock, P.; Greslebin, A. (2020) Phytophthora austrocedri in Argentina and co-inhabiting Phytophthoras: roles of anthropogenic and abiotic factors in species distribution and diversity., Forests, 11, Article No. 1223.
- Varypatakis, K.; Véronneau, P-Y.; Thorpe, P.J.; Cock, P.J.A.; Tze-Yin Lim, J.; Armstrong, M.R.; Janakowski, S.; Sobczak, M.; Hein, I.; Mimee, B.; Jones, J.T.; Blok, V.C. (2020) The genomic impact of selection for virulence against resistance in the potato cyst nematode Globodera pallida., Genes, 11, Article No. 1429.
- Orr, J.N.; Neilson, R.; Freitag, T.E.; Roberts, D.M.; Davies, K.G.; Blok, V.C.; Cock, P.J.A. (2020) Parallel microbial ecology of pasteuira and nematode species in Scottish soils., Frontiers in Plant Science, 10, Article No. 1763.
- Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. (2019) Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data., Journal of General Virology, 100, 533-542.
- Thorpe, P.; Escudero-Martinez, C.M.; Cock, P.J.A.; Eves-van den Akker, S.; Bos, J.I.B. (2018) Shared transcriptional control and disparate gain and loss of aphid parasitism genes., Genome Biology and Evolution, 10, 2716-2733.
- Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B.A.; Rowe, J.; Tomkins-Tinch, C.H.; Valieris, R.; Caprez, A.; Batut, B.; Haudgaard, M.; Cokelaer, T.; Beauchamp, K.A.; Pedersen, B.S.; Hoogstrate, Y.; Bretaudeau, A.; Ryan, D.; Le Corguillé, G.; Yusuf, D.; Luna-Valero, S.; Kirchner, R.; Brinda, K.; Wollmann, T.; Raden, M.; Pantano, L.; Soranzo, N.; van Heeringen, S.J.; Charlop-Powers, Z.; Unneberg, P.; de Smet, M.; Martin, M.; Von Kuster, G.; Antao, T.; Miladi, M.; Brueffer, C.; Thornton, K.; van den Beek, M.; Maticzka, D.; Blank, C.; Will, S.; Gravouil, K.; Wolff, J.; Holtgrewe, M.; Fallmann, J.; Piro, V.C.; Shlyakhter, I.; Yousif, A.; Mabon, P.; Zhang, X-O.; Cabral, J.; Shen, W.; Thomas, C.; Brown, J.; Enns, E.; de Hollander, M.; Boekel, J.; Kelleher, J.; Bouvier, D.; Turaga, N.; de Ruiter, J.R.; Choudhary, S.; Harding, N.; Kratz, A.; Fang, Z.; Kleinkauf, R.; Timm, H.; Khan, A.; Cock, P.J.A.; Seiler, E.; Nguyen, H.; Brislawn, C.; Stovner, E.B.; Johnson, J.E.; Hägglund, E.; Ewels, P.; Chambers, M.; Pruesse, E.; Guimera, R.V.; Ye, S.; Dunn, W.A.; Parsons, L.; Cornwell, M.; Reynolds, A.; Bargull, M.; Grassi, E.; Koppstein, D.; Patro, R.; Wohlers, I.; Stoler, N.; Blankenberg, D.; He, G.; Freeberg, M.; Farouini, R.; Junge, A.; Bogema, D.R.; Singh, S.; Cumbo, F.; Larson, D.E.; Wang, L.; Workentine, M.L.; Devisetty, U.K.; Laurent, S.; Garnier, X.; Agren, R.; Roger, P.; Eppley, J.M.; Li, W.; Rausch, R.; Chande, A.T.; Taylor, J.; Stöcker, B.K.; Milne, I.; Wright, P.R.; Taranto, A.P.; Chicco, D.; Abdennur, N.; Sennblad, B.; Baaijens, J.A.; Gopez, M.; Enache, O.M.; Pinello, L.; Srivastava, A.; de Bruijn, I.; Kensche, P.R.; Blin, K.; Pirola, Y.; Preussner, J.; Knudsen, M.; Bendall, M.L.; rai, V.; Gonnella, G.; Stahl, C.; Miles, A.; Waters, N.R.; Hiltemann, S.; Boursin, Y.; Perez-Riverol, Y.; Schmeier, S.; Clarke, E.; Arvai, K.; Jung, M.; Stephen, G.; Domenico, T.; seiler, J.; Rasche, E.; Kornobis, E.; Beisser, D.; Rahmann, S.; Mikheyev, A.S.; Tran, C.; Capellades, J.; Moskalenko, O.; Schröder, C.; Dirmeier, S.; Webster, T.H.; Salatino, A.E.; Urgese, G.; Köster, J. (2018) Bioconda: A sustainable and comprehensive software distribution for the life sciences., Nature Methods, 15, 475-476.
- Nascimento, F.; Vicente, C.; Cock, P.; Tavares, M.; Rossi, M.; Hasegawa, K.; Mota, M. (2018) From plants to nematodes: Serratia grimesii BXF1 genome reveals an adaptation to the modulation of multi-species interactions., Microbial Genomics, 4, Article No. 000178.
- Eves-van den Akker, S.; Laetsch, D.R.; Thorpe, P.; Lilley, C.J.; Danchin, E.G.J.; Da Rocha, M.; Rancurel, C.; Holroyd, N.E.; Cotton, J.A.; Szitenberg, A.; Grenier, E.; Montarry, J.; Mimee, B.; Duceppe, M.O.; 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 insights into the basis of parasitism and virulence., Genome Biology, 17, Article No. 124.
- Vicente, C.S.L.; Nascimento, F.X.; Ikuyo, Y.; Cock, P.J.A.; Mota, M.; Hasegawa, K. (2016) The genome and genetics of a high oxidative stress tolerant Serratia sp LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus., BMC Genomics, 17, Article No. 301.
- Vicente, C.S.L.; Nascimento, F.X.; Barbosa, P.; Ke, H.M.; Tsai, I.J.; Hirao, T.; Cock, P.J.A.; Kikuchi, T.; Hasegawa, K.; Mota, M. (2016) Evidence for an opportunistic and endophytic lifestyle of the Bursaphelenchus xylophilus-associated bacteria Serratia marcescens PWN146 isolated from wilting Pinus pinaster., Microbial Ecology, 72, 669-681.
- Thorpe, P.; Cock, P.J.A.; Bos, J. (2016) Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets., BMC Genomics, 17, Article No. 172.
- Espada, M.; Silva, A.C.; Eves-van den Akker, S.; Cock, P.J.A.; Mota, M.; Jones, J.T. (2016) Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy., Molecular Plant Pathology, 17, 286-295.
- Palomares-Rius, J.E.; Hedley, P.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Blok, V.C. (2016) Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate., PeerJ, 4, Article No. e1654.
- Harris, N.L.; Cock, P.J.A.; Lapp, H.; Chapman, B.; Davey, R.; Fields, C.; Hokamp, K.; Munoz-Torres, M. (2016) The 2015 Bioinformatics Open Source Conference (BOSC 2015)., PLoS Computational Biology, 12, Article No. e1004691.
- Bolleman, J.T.; Mungall, C.J.; Strozzi, F.; Baran, J.; Dumontier, M.; Bonnal, R.J.P.; Buels, R.; Hoehndorf, R.; Fujisawa, T.; Katayama, T.; Cock, P.J.A. (2016) FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation., Journal of Biomedical Semantics, 7, Article No. 39.
- Eves-van den Akker, S.; Lilley, C.J.; Reid, A.; Pickup, J.; Anderson, E.; Cock, P.J.A.; Blaxter, M.; Urwin, P.E.; Jones, J.T.; Blok, V.C. (2015) A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual., Molecular Ecology, 24, 5842-5851.
- Lu, Y.W.; McGavin, W.; Cock, P.J.A.; Schnettler, E.; Yan, F.; Chen, J.P.; MacFarlane, S.A. (2015) Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins., Journal of General Virology, 96, 3432-3439.
- Cock, P.J.A.; Chilton, J.M.; Gruning, B.; Johnson, J.E.; Soranzo, N. (2015) NCBI BLASTplus integrated into Galaxy. Technical note., GigaScience, 4, Article No. 39.
- Reavy, B.; Swanson, M.M.; Cock, P.J.A.; Dawson, L.A.; Freitag, T.E.; Singh, B.K.; Torrance, L.; Mushegain, A.R.; Taliansky, M. (2015) Distinct circular single-stranded DNA viruses exist in different soil types., Applied and Environmental Microbiology, 81, 3934-3945.
- Cock, P.J.A.; Bonfield, J.; Chevreux, B.; Li, H. (2015) SAM/BAM format v1.5 extensions for de novo assemblies., bioRxiv, 29 May 2015, 3pp.
- Eves-van den Akker, S.; Lilley, C.J.; Danchin, E.G.J.; Rancurel, C.; Cock, P.J.A.; Urwin, P.E.; Jones, J.T. (2014) The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes., Genome Biology and Evolution, 6, 2181-2194.
- Thorpe, P.; Mantelin, S.; Cock, P.J.A.; Blok, V.C.; Coke M.C.; van Den Akker, S.E.; Guzeeva, E.; Lilley, C.J.; Smant, G.; Reid, A.J.; Wright, K.M.; Urwin, P.E.; Jones, J.T. (2014) Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida., BMC Genomics, 15, Article No. 923.
- Cotton, J.A.; Lilley, C.J.; Jones, L.M.; Kikuchi, T.; Reid, A.J.; Thorpe, P.; Tsai, I.J.; Beasley, H.; Blok, V.C.; Cock, P.J.A.; Eves-van den Akker, S.; Holroyd, N.; Hunt, M.; Mantelin, S.; Naghra, H.; Pain, A.; Palomares-Rius, J.E.; Zarowiecki, M.; Berriman, M.; Jones, J.T.; Urwin, P.E. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode., Genome Biology, 15, Article No. R43.
- Kikuchi, T.; Cock, P.J.A.; Helder, J.; Jones, J.T. (2014) Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase., Nematology, 16, 99-107.
- Moller, S.; Afgan, E.; Banck, M.; Bonnal, R.J.P.; Booth, T.; Chilton, J.; Cock, P.J.A.; Gumbel, M.; Harris, N.; Holland, R.; Kalas, M.; Kajan, L.; Kibukawa, E.; Powel, D.R.; Prins, P.; Quinn, J.; Sallou, O.; Strozzi, F.; Seemann, T.; Sloggett, C.; Soiland-Reyes, S.; Spooner, W.; Steinbiss, S.; Tille, A.; Travis, A.J.; Guimera, R.V.; Katayama, T.; Chapman, B.A. (2014) Community-driven development for computational biology at Sprints, Hackathons and Codefests., BMC Bioinformatics, 15(Suppl 14), S7.
- Katayama, T.; Wilkinson, M.D.; Aoki-Kinoshita, K.F.; Kawashima, S.; Yamamoto, Y.; Yamaguchi, A.; Okamoto, S.; Kawano, S.; Kim, J.D.; Wang, Y.; Wu, H.Y.; Kano, Y.; Ono, H.; Bono, H.; Kocbek, S.; Aerts, J.; Akune, Y.; Antezana, E.; Arakawa, K.; Aranda, B.; Baran, J.; Bolleman, J.; Bonnal, R.J.P.; Buttigieg, P.L.; Campbell, M.P.; Chen, Y.A.; Chiba, H.; Cock, P.J.A.; Cohen, K.B.; Constantin, A.; Duck, G.; Dumontier, M.; Fujisawa, T.; Fujiwara, T.; Goto, N.; Hoehndorf, R.; Igarashi, Y.; Itaya, H.; Ito, M.; Iwasaki, W.; Kalas, M.; Katoda, T.; Kim, T.; Kokubu, A.; Komiyama, Y.; Kotera, M.; Laibe, C.; Lapp, H.; Lutteke, T.; Marshall, M.S.; Mori, T.; Mori, H.; Morita, M.; Murakami, K.; Nakao, M.; Narimatsu, H.; Nishide, H.; Nishimura, Y.; Nystrom-Persson, J.; Ogishima, S.; Okamura, Y.; Okuda, S.; Oshita, K.; Packer, N.H.; Prins, P.; Ranzinger, R.; Rocca-Serra, P.; Sansone, S.; Sawaki, H.; Shin, S.H.; Splendiani, A.; Strozzi, F.; Tadaka, S.; Toukach, P.; Uchiyama, I.; Umezaki, M.; Vos, R.; Whetzel, P.L.; Yamada, I.; Yamasaki, C.; Yamashita, R.; York, W.S.; Zmasek, C.M.; Kawamoto, S.; Takagi, T. (2014) BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains., Journal of Biomedical Semantics, 5, Article No.5.
- Jupe, F.; Witek, K.; Verweij, W.; Sliwka, J.; Pritchard, L.; Etherington, G.J.; Maclean, D.; Cock, P.J.; Leggett, R.M.; Bryan, G.J.; Cardle, L.; Hein, I.; Jones, J.D.G. (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations., Plant Journal, 76, 530-544.
- Cock, P.J.A.; Gruning, B.A.; Paszkiewicz, K.; Pritchard, L. (2013) Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology., Peer J, 1, Article No. e167.
- Kamei, H.; Cock, P.J.A. (2013) Computation of balanced equivalence relations and their lattice for a coupled cell network., Siam Journal on Applied Dynamical Systems, 12, 352-382.
- Palomares-Rius, J.E.; Jones, J.T.; Cock, P.J.; Castillo, P.; Blok, V.C. (2013) Activation of hatching in diapaused and quiescent Globodera pallida., Parasitology, 140, 445-454.
- Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F. (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
- Katayama, T.; Wilkinson, M.D.; Micklem, G.; Kawashima, S.; Yamaguchi, A.; Nakao, M.; Yamamoto, Y.; Okamoto, S.; Oouchida, K.; Hong-Woo ,C.; Aerts, J.; Afzal, H.; Antezana, E.; Arakawa, K.; Aranda, B.; Belleau, F.; Bolleman, J.; Bonnal, R.J.P.; Chapman, B.; Cock, P.J.A.; Eriksson, T.; Gordon, P.M.K.; Goto, N.; Hayashi, K.: Horn, H.; Ishiwata, R.; Kaminuma, E.; Kasprzyk, A.; Kawaji, H.; Kido, N.; Kim, Y-J.; Kinjo, A.R.; Konishi, F.; Kwon, K-H.; Labarga, A.; Lamprecht, A-L.; Lin, Y.; Lindenbaum, P.; McCarthy, L.; Morita, H.; Murakami, K.; Nagao, K.; Nishida, K.; Nishimura, K.; Nishizawa, K.; Ogishima, S.; Ono, K.; Oshita, K.; Park, K-J.; Prins, P.; Saito, T.L.; Samwald, M.; Satagopam, V.P.; Shigemoto, Y.; Smith, R.; Splendiani, A.; Sugawara, H.; Taylor, J.; Vos, R.A.; Withers, D.; Yamasaki, C.; Zmasek, C.M.; Kawamoto, S.; Okubo, K.; Asai K.; Takagi, T. (2013) The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies., Journal of Biomedical Semantics, 4(6).
- Talevich, E.; Invergo, B.M.; Cock, P.J.A.; Chapman, B.A. (2012) Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biophyton., BMC Bioinformatics, 13, 209.
- Swanson, M.M.; Reavy, B.; Makarova, K.S.; Cock, P.J.; 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, Article No. e40683.
- Palomares-Rius, J.E.; Hedley, P.E.; Cock, P.J.A.; 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., Molecular Plant Pathology, 13, 1120-1134.
- Wang, D.P.; Qi, M.S.; Calla, B.; Korban, S.S.; Clough, S.J.; Cock, P.J.A.; Sundin, G.W.; Toth, I.K.; Zhao, Y.F. (2012) Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora., Molecular Plant-Microbe Interactions, 25, 6-17.
- McNally, R.R.; Toth, I.K.; Cock, P.J.A.; Pritchard, L.; Hedley, P.E.; Morris, J.A.; Zhao, Y.F.; Sundin, G.W. (2012) Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors., Molecular Plant Pathology, 13, 160-173.
- Jupe, F.; Pritchard, L.; Etherington, G.; MacKenzie, K.; Cock, P.J.A.; Wright, F.; Sharma, S.K.; Bolser, D.; Bryan, G.J.; Jones, J.; Hein, I. (2012) Identification and localisation of the NB-LRR gene family within the potato genome., BMC Genomics,13, 1-14.
- McGavin, W.J.; Mitchell, C.; Cock, P.J.A.; Wright, K.M.; 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, 430-437.
- 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.; 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.
- 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.
- 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.
