PhytoPath, an infrastructure for hundreds of plant pathogen genomes
Project (past)
| Project dates | 31 May 2014 to end of 30 May 2017 |
|---|---|
| Researchers | |
| Principal Investigator | Kim Hammond-Kosack |
| Funder | Biotechnology and Biological Sciences Research Council |
| Project number | S5310 |
| 5310 | |
| Department | Biointeractions and Crop Protection |
| Research fish code | BB/K020056/1 |
| Grant ID | BB/K020056/1 |
Outputs
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PHI-base - the Pathogen–Host Interactions database
A - Papers appearing in refereed journals
Urban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., De Silva, N., Venkatesh, S. Y, Martinez, M. C., Pedro, H., Yates, A. D., Hassani-Pak, K. and Hammond-Kosack, K. E. 2020. PHI-base - the Pathogen–Host Interactions database . Nucleic Acids Research. 48 (Database issue D1), pp. D613-D620. https://doi.org/10.1093/nar/gkz904
PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets
A - Papers appearing in refereed journals
Janowska-Seja, E. I., Lysenko, A., Urban, M., Rawlings, C. J., Toska, S. and Hammond-Kosack, K. E. 2019. PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. Frontiers in Microbiology. 10 (2721). https://doi.org/10.3389/fmicb.2019.02721
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
A - Papers appearing in refereed journals
Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., Mcdowall, M. D., Maheswari, U., Naamati, G., Newman, V., Ong, C. K., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R. D., Urban, M., Hammond-Kosack, K. E., Bolser, D. M., De Silva, N., Howe, K. L., Langridge, N., Maslen, G., Staines, D. M. and Yates, A. 2018. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Research. 46 (D1), pp. D802-D808. https://doi.org/10.1093/nar/gkx1011
Effects of variety, year of cultivation and sulphur supply on the accumulation of free asparagine in the grain of commercial wheat varieties
A - Papers appearing in refereed journals
Curtis, T., Powers, S. J., Wang, R. and Halford, N. G. 2018. Effects of variety, year of cultivation and sulphur supply on the accumulation of free asparagine in the grain of commercial wheat varieties. Food Chemistry. 239 (15 January), pp. 304-313. https://doi.org/10.1016/j.foodchem.2017.06.113
Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum
A - Papers appearing in refereed journals
King, R., Brown, N. A., Urban, M. and Hammond-Kosack, K. E. 2018. Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. BMC Genomics. 19, p. 269. https://doi.org/10.1186/s12864-018-4612-2
Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb)
A - Papers appearing in refereed journals
Baldwin, T. T., Basenko, E., Harb, O., Brown, N. A., Urban, M., Hammond-Kosack, K. E. and Bregitzer, P. P. 2018. Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb). Fungal Genetics and Biology. 115 (June), pp. 90-93. https://doi.org/10.1016/j.fgb.2018.01.002
RNAi as an emerging approach to control Fusarium Head Blight disease and mycotoxin contamination in cereals
A - Papers appearing in refereed journals
Machado, A., Brown, N. A., Urban, M., Kanyuka, K. and Hammond-Kosack, K. E. 2017. RNAi as an emerging approach to control Fusarium Head Blight disease and mycotoxin contamination in cereals. Pest Management Science. 74 (4), pp. 790-799. https://doi.org/10.1002/ps.4748
A spatial temporal analysis of the Fusarium graminearum transcriptome during symptomless and symptomatic wheat infection
A - Papers appearing in refereed journals
Brown, N. A., Evans, J., Mead, A. and Hammond-Kosack, K. E. 2017. A spatial temporal analysis of the Fusarium graminearum transcriptome during symptomless and symptomatic wheat infection. Molecular Plant Pathology. 18 (9), pp. 1295-1312. https://doi.org/10.1111/mpp.12564
The Gsp-1 genes encode the wheat arabinogalactan peptide
C2 - Non-edited contributions to conferences
Wilkinson, M. D., Tosi, P., Lovegrove, A., Corol, D. I., Ward, J. L., Palmer, R., Powers, S., Passmore, D., Webster, G., Marcus, S. E., Knox, J. P. and Shewry, P. R. 2017. The Gsp-1 genes encode the wheat arabinogalactan peptide. Quality and Nutrition at MonoGram 2017, 4-6 April 2017, University of Bristol, Bristol , UK (oral presentation). pp. p10
cis-jasmone elicits aphid-induced stress signalling in potatoes
A - Papers appearing in refereed journals
Sobhy, I. S., Woodcock, C. M., Powers, S. J., Caulfield, J. C., Pickett, J. A. and Birkett, M. A. 2017. cis-jasmone elicits aphid-induced stress signalling in potatoes. Journal of Chemical Ecology. 43 (1), pp. 39-52. https://doi.org/10.1007/s10886-016-0805-9
PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database
A - Papers appearing in refereed journals
Urban, M., Cuzick, A., Rutherford, K., Irvine, A. G., Pedro, H., Pant, R., Sadanadan, V., Khamari, L., Billal, S., Mohanty, Sagar and Hammond-Kosack, K. E. 2017. PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database. Nucleic Acids Research. 45 (D1), pp. D604-D610. https://doi.org/10.1093/nar/gkw1089
Changes in the arabinoxylan fraction of wheat grain during alcohol production
A - Papers appearing in refereed journals
Kosik, O., Powers, S. J., Chatzifragkou, A., Prabhakumari, P. C., Charalampopoulos, D., Hess, L., Brosnan, J., Shewry, P. R. and Lovegrove, A. 2017. Changes in the arabinoxylan fraction of wheat grain during alcohol production. Food Chemistry. 221 (15 April), pp. 1754-1762. https://doi.org/10.1016/j.foodchem.2016.10.109
Acrylamide-forming potential of potatoes grown at different locations, and the ratio of free asparagine to reducing sugars at which free asparagine becomes a limiting factor for acrylamide formation
A - Papers appearing in refereed journals
Muttucumaru, N., Powers, S. J., Elmore, J. S., Dodson, A., Briddon, A., Mottram, D. S. and Halford, N. G. 2017. Acrylamide-forming potential of potatoes grown at different locations, and the ratio of free asparagine to reducing sugars at which free asparagine becomes a limiting factor for acrylamide formation. Food Chemistry. 220 (1 April), pp. 76-86. https://doi.org/10.1016/j.foodchem.2016.09.199
Mass seasonal bioflows of high-flying insect migrants
A - Papers appearing in refereed journals
Hu, G., Lim, K. S., Horvitz, N., Clark, S. J., Reynolds, D. R., Sapir, N. and Chapman, J. W. 2016. Mass seasonal bioflows of high-flying insect migrants. Science - AAAS. 354 (6319), pp. 1584-1587. https://doi.org/10.1126/science.aah4379
Using the phenotypic information in the pathogen-host interactions database (PHI-BASE) to explore Fusarium and Magnaporthe genomes, transcriptomes and proteomes
C1 - Edited contributions to conferences/learned societies
Urban, M., Irvine, A., Cuzick, A. and Hammond-Kosack, K. E. 2016. Using the phenotypic information in the pathogen-host interactions database (PHI-BASE) to explore Fusarium and Magnaporthe genomes, transcriptomes and proteomes. Proceedings 5th ISFHB - 2nd IWWB Symposium, 5-10, Florianopolis, Brasil.
Effects of fungicide treatment on free amino acid concentration and acrylamide-forming potential in wheat
A - Papers appearing in refereed journals
Curtis, T. Y., Powers, S. J. and Halford, N. G. 2016. Effects of fungicide treatment on free amino acid concentration and acrylamide-forming potential in wheat. Journal of Agricultural and Food Chemistry - JAFC. 64 (51), pp. 9689-9696. https://doi.org/10.1021/acs.jafc.6b04520
The genome of the emerging barley pathogen Ramularia collo-cygni
A - Papers appearing in refereed journals
McGrann, G. R. D., Andongabo, A. E., Sjokvist, E., Trivedi, U., Dussart, F., Kaczmarek, M., Mackenzie, A., Fountaine, J. M., Taylor, J. M. G., Paterson, L. J., Gorniak, K., Burnett, F., Kanyuka, K., Hammond-Kosack, K. E., Rudd, J. J., Blaxter, M. and Havis, N. D. 2016. The genome of the emerging barley pathogen Ramularia collo-cygni. BMC Genomics. 17 (1), p. 584. https://doi.org/10.1186/s12864-016-2928-3
The natural plant stress elicitor cis-jasmone causes cultivar-dependent reduction in growth of the stink bug, Euschistus heros and associated changes in flavonoid concentrations in soybean, Glycine max
A - Papers appearing in refereed journals
Da Graca, J. P., Ueda, T. E., Janegitz, T., Vieira, S. S., Salvador, M. C., De Oliveira, M. C., Zingaretti, S. M., Powers, S. J., Pickett, J. A., Birkett, M. A. and Hoffmann-Campo, C. B. 2016. The natural plant stress elicitor cis-jasmone causes cultivar-dependent reduction in growth of the stink bug, Euschistus heros and associated changes in flavonoid concentrations in soybean, Glycine max. Phytochemistry. 131 (November), pp. 84-91. https://doi.org/10.1016/j.phytochem.2016.08.013
Quantification of brown dog tick repellents, 2-hexanone and benzaldehyde, and release from tick-resistant beagles, Canis lupus familiaris.
A - Papers appearing in refereed journals
De Oliveira Filho, J. G., Sarria, A. L. F., Ferreira, L. L., Caulfield, J. C., Powers, S. J., Pickett, J. A., De Leon, A. A., Birkett, M. A. and Borges, L. M. F. 2016. Quantification of brown dog tick repellents, 2-hexanone and benzaldehyde, and release from tick-resistant beagles, Canis lupus familiaris. Journal Of Chromatography B. 1022 (1 June 2016), pp. 64-69. https://doi.org/10.1016/j.jchromb.2016.03.014
RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose
A - Papers appearing in refereed journals
Brown, N. A., Ries, L. N. A., Reis, T. F., Rajendran, R., Correa dos Santos, R. A., Ramage, G., Riano-Pachon, D. M. and Goldman, G. H. 2016. RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose. Biotechnology for Biofuels. 9, p. 145. https://doi.org/10.1186/s13068-016-0558-2
Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneal synthase - a potential target to reduce Fusarium head blight disease
A - Papers appearing in refereed journals
Bresso, E., Leroux, V., Urban, M., Hammond-Kosack, K. E., Maigret, B. and Martins, N. F. 2016. Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneal synthase - a potential target to reduce Fusarium head blight disease. Journal Of Molecular Modeling. 22, p. 163. https://doi.org/10.1007/s00894-016-3021-1
Publishing FAIR data: an exemplar methodology utilizing PHI-base
A - Papers appearing in refereed journals
Rodriguez-Iglesias, A., Rodriguez-Gonzales, A., Irvine, A. G., Sesma, A., Urban, M., Hammond-Kosack, K. E. and Wilkinson, M. D. 2016. Publishing FAIR data: an exemplar methodology utilizing PHI-base. Frontiers in Plant Science. 7, p. 641. https://doi.org/10.3389/fpls.2016.00641
The contribution of Aspergillus fumigatus stress responses to virulence and antifungal resistance
A - Papers appearing in refereed journals
Brown, N. A. and Goldman, G. H. 2016. The contribution of Aspergillus fumigatus stress responses to virulence and antifungal resistance. Journal of Microbiology. 54, pp. 243-253. https://doi.org/10.1007/s12275-016-5510-4
PhytoPath: an integrative resource for plant pathogen genomics
A - Papers appearing in refereed journals
Pedro, H., Maheswari, U., Urban, M., Irvine, A. G., Cuzick, A., Mcdowall, M. D., Staines, D. M., Kulesha, E., Hammond-Kosack, K. E. and Kersey, P. J. 2016. PhytoPath: an integrative resource for plant pathogen genomics. Nucleic Acids Research. 44 (D1), pp. D688-D693. https://doi.org/10.1093/nar/gkv1052
Dedicated biomass crops can enhance biodiversity in the arable landscape
A - Papers appearing in refereed journals
Haughton, A. J., Bohan, D. A., Clark, S. J., Mallott, M. D., Mallott, V., Sage, R. and Karp, A. 2016. Dedicated biomass crops can enhance biodiversity in the arable landscape. Global Change Biology. Bioenergy. 8 (6), pp. 1071-1081. https://doi.org/10.1111/gcbb.12312
The trans-kingdom identification of negative regulators of pathogen hypervirulence
A - Papers appearing in refereed journals
Brown, N. A., Urban, M. and Hammond-Kosack, K. E. 2016. The trans-kingdom identification of negative regulators of pathogen hypervirulence. FEMS Microbiology Reviews. 40 (1), pp. 19-40. https://doi.org/10.1093/femsre/fuv042
G‐protein coupled receptor‐mediated nutrient sensing and developmental control in Aspergillus nidulans
A - Papers appearing in refereed journals
Brown, N. A., Dos Reis, T. F., Ries, L. N. A., Caldana, C., Mah, J-H., Yu, J-H., Macdonald, J. M. and Goldman, G. H. 2015. G‐protein coupled receptor‐mediated nutrient sensing and developmental control in Aspergillus nidulans. Molecular Microbiology. 98 (3), pp. 420-439. https://doi.org/10.1111/mmi.13135
Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence
A - Papers appearing in refereed journals
Urban, M., Irvine, A. G., Cuzick, A. and Hammond-Kosack, K. E. 2015. Using the pathogen-host interactions database (PHI-base) to investigate plant pathogen genomes and genes implicated in virulence. Frontiers in Plant Science. 6, p. 605. https://doi.org/10.3389/fpls.2015.00605
The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum
A - Papers appearing in refereed journals
King, R., Urban, M., Hammond-Kosack, M. C. U., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum. BMC Genomics. 16, p. 544. https://doi.org/10.1186/s12864-015-1756-1
The Pathogen-Host Interactions database (PHI-base): additions and future developments
A - Papers appearing in refereed journals
Urban, M., Pant, R., Raghunath, A., Irvine, A. G., Pedro, H. and Hammond-Kosack, K. E. 2015. The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Research. 43, pp. D645-D655. https://doi.org/10.1093/nar/gku1165
Sequestration of C in soils under Miscanthus can be marginal and is affected by genotype-specific root distribution
A - Papers appearing in refereed journals
Richter, G. M., Agostini, F., Redmile-Gordon, M. A., White, Robin P. and Goulding, K. W. T. 2015. Sequestration of C in soils under Miscanthus can be marginal and is affected by genotype-specific root distribution. Agriculture, Ecosystems & Environment. 200, pp. 169-177. https://doi.org/10.1016/j.agee.2014.11.011
Wheat root growth responses to horizontal stratification of fertiliser in a water-limited environment
A - Papers appearing in refereed journals
Jin, K., Shen, J., Ashton, R. W., White, Robin P., Dodd, I. C., Parry, M. A. J. and Whalley, W. R. 2015. Wheat root growth responses to horizontal stratification of fertiliser in a water-limited environment. Plant and Soil. 386, pp. 77-88. https://doi.org/10.1007/s11104-014-2249-8
Classification of molecular sequence data using Bayesian phylogenetic mixture models
A - Papers appearing in refereed journals
Loza-Reyes, E., Hurn, M. A. and Robinson, A. 2014. Classification of molecular sequence data using Bayesian phylogenetic mixture models. Computational Statistics & Data Analysis. 75, pp. 81-95. https://doi.org/10.1016/j.csda.2014.01.008
The efficacy of flufenacet based herbicides on Alopecurus myosuroides (black-grass): analysis of data from 375 field trials
C1 - Edited contributions to conferences/learned societies
Hull, R. I., Clark, S. J., Westrup, L. and Moss, S. R. 2014. The efficacy of flufenacet based herbicides on Alopecurus myosuroides (black-grass): analysis of data from 375 field trials. Crop production in Southern Britain: precision decisions for profitable cropping. Aspects of Applied Biology 127 . Association of Applied Biologists (AAB) Wellesbourne Warwick . pp. 49-56