CAS: Genomics and Bioinformatics
| Title | CAS: Genomics and Bioinformatics |
|---|---|
| Type | Research cluster |
Outputs
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Mutation scanning in wheat by exon capture and next-generation sequencing
A - Papers appearing in refereed journals
King, R., Bird, N., Ramirez-Gonzalez, R., Coghill, J. A., Patil, A., Hassani-Pak, K., Uauy, C. and Phillips, A. L. 2015. Mutation scanning in wheat by exon capture and next-generation sequencing. PLOS ONE. 10, p. e0137549. https://doi.org/10.1371/journal.pone.0137549
Resequencing at >40-fold depth of the parental genomes of a Solanum lycopersicum x S. pimpinellifolium recombinant inbred line population and characterization of frame-shift InDels that are highly likely to perturb protein function
A - Papers appearing in refereed journals
Kevei, Z., King, R., Mohareb, F., Sergeant, M. J., Awan, S. Z. and Thompson, A. J. 2015. Resequencing at >40-fold depth of the parental genomes of a Solanum lycopersicum x S. pimpinellifolium recombinant inbred line population and characterization of frame-shift InDels that are highly likely to perturb protein function. G3: Genes, Genomes, Genetics. 5, pp. 971-981. https://doi.org/10.1534/g3.114.016121
G-fibre cell wall development in willow stems during tension wood induction
A - Papers appearing in refereed journals
Gritsch, C., Wan, Y., Mitchell, R. A. C., Shewry, P. R., Hanley, S. J. and Karp, A. 2015. G-fibre cell wall development in willow stems during tension wood induction. Journal of Experimental Botany. 66 (20), pp. 6447-6459. https://doi.org/10.1093/jxb/erv358
Efficient method for rapid multiplication of clean and healthy willow clones via in vitro propagation with broad genotype applicability
A - Papers appearing in refereed journals
Palomo-Rios, E., Macalpine, W. J., Shield, I. F., Amey, J. S., Karaoglu, C., West, J., Hanley, S. J., Krygier, R., Karp, A. and Jones, H. D. 2015. Efficient method for rapid multiplication of clean and healthy willow clones via in vitro propagation with broad genotype applicability. Canadian Journal Of Forest Research. 45 (11), pp. 1662-1667. https://doi.org/10.1139/cjfr-2015-0055
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
Characterisation of the willow phenylalanine ammonia-lyase (Pal) gene family reveals expression differences compared with poplar
A - Papers appearing in refereed journals
De Jong, F., Hanley, S. J., Beale, M. H. and Karp, A. 2015. Characterisation of the willow phenylalanine ammonia-lyase (Pal) gene family reveals expression differences compared with poplar. Phytochemistry. 117 (September), pp. 90-97. https://doi.org/10.1016/j.phytochem.2015.06.005
Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions
A - Papers appearing in refereed journals
Urban, M., King, R., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions. BMC Genomics. 16, p. 261. https://doi.org/10.1186/s12864-015-1412-9
Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition
A - Papers appearing in refereed journals
Rudd, J. J., Kanyuka, K., Hassani-Pak, K., Derbyshire, M., Andongabo, A. E., Devonshire, J., Lysenko, A., Saqi, M., Desai, N. M., Powers, S. J., Hooper, J., Ambroso, L., Bharti, A., Farmer, A., Hammond-Kosack, K. E., Dietrich, R. A. and Courbot, M. 2015. Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition. Plant Physiology. 167 (3), pp. 1158-1185. https://doi.org/10.1104/pp.114.255927
Climate change increases risk of fusarium wheat ear blight on wheat in central China
A - Papers appearing in refereed journals
Zhang, X., Halder, J., White, Robin P., Hughes, D. J., Ye, Z., Wang, C., Xu, R., Gan, B. and Fitt, B. D. L. 2014. Climate change increases risk of fusarium wheat ear blight on wheat in central China. Annals of Applied Biology - AAB. 164 (3), pp. 384-395. https://doi.org/10.1111/aab.12107
Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)
A - Papers appearing in refereed journals
Berlin, S., Trybush, S. O., Fogelqvist, J., Gyllenstrand, N., Hallingback, H. R., Ahman, I., Nordh, N-E., Shield, I. F., Powers, S. J., Weih, M., Lagercrantz, U., Ronnberg-Wastljung, A-C., Karp, A. and Hanley, S. J. 2014. Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae). Tree Genetics & Genomes. 10 (6), pp. 1595-1610. https://doi.org/10.1007/s11295-014-0782-5
A tale of one fungal pathogen of wheat: how it evades host surveillance and then hijacks host defences
C2 - Non-edited contributions to conferences
Kanyuka, K., Lysenko, A., Saqi, M., Derbyshire, M., Andongabo, A. E., Hassani-Pak, K., Hammond-Kosack, K. E., Courbot, M. and Rudd, J. J. 2014. A tale of one fungal pathogen of wheat: how it evades host surveillance and then hijacks host defences. Abstracts 16th International Congress on Molecular Plant-Microbe Interactions (IS-MPMI 2014), Rhodes, 6-10 July 2014 . pp. P069
Identification and analysis of differentially expressed genes in the wheat- Zymoseptoria tritici interaction
C2 - Non-edited contributions to conferences
Kanyuka, K., Andongabo, A. E., Hassani-Pak, K., Powers, S. J., Lysenko, A., Saqi, M., Derbyshire, M., Lee, W-S., Hammond-Kosack, K. E., Courbot, M. and Rudd, J. J. 2014. Identification and analysis of differentially expressed genes in the wheat- Zymoseptoria tritici interaction. Abstracts Plant Genomics Congress, London, 12-13 May 2014 .
A query suggestion workflow for life science IR-systems
A - Papers appearing in refereed journals
Esch, M., Chen, J., Weise, S., Hassani-Pak, K., Scholz, U. and Lange, M. 2014. A query suggestion workflow for life science IR-systems. Journal of Integrative Bioinformatics. 11, p. 237. https://doi.org/10.2390/biecoll-jib-2014-237
Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing response gene
A - Papers appearing in refereed journals
Salmon, J., Ward, S. P., Hanley, S. J., Leyser, O. and Karp, A. 2014. Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing response gene. Plant Biotechnology Journal. 12 (4), pp. 480-491. https://doi.org/10.1111/pbi.12154
Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems
A - Papers appearing in refereed journals
Wan, Y., Gritsch, C., Tryfona, T., Ray, M. J., Andongabo, A. E., Hassani-Pak, K., Jones, H. D., Dupree, P., Karp, A., Shewry, P. R. and Mitchell, R. A. C. 2014. Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems. Planta. 239, pp. 1041-1053. https://doi.org/10.1007/s00425-014-2034-1
Ondex Web: web-based visualization and exploration of heterogeneous biological networks
A - Papers appearing in refereed journals
Taubert, J., Hassani-Pak, K., Castells-Brooke, N. I. D. and Rawlings, C. J. 2014. Ondex Web: web-based visualization and exploration of heterogeneous biological networks. Bioinformatics. 30, pp. 1034-1035. https://doi.org/10.1093/bioinformatics/btt740
Genetics, genomics and crop modelling: integrative approaches to the improvement of biomass willows
B - Book chapters etc edited externally
Karp, A., Richter, G. M., Shield, I. F. and Hanley, S. J. 2014. Genetics, genomics and crop modelling: integrative approaches to the improvement of biomass willows. in: McCann, M. C. (ed.) Plants and bioenergy. Advances in Plant Biology, Vol 4 Springer, New York. pp. 107-130
Genetic strategies for dissecting complex traits in biomass willows (Salix spp.)
A - Papers appearing in refereed journals
Hanley, S. J. and Karp, A. 2014. Genetic strategies for dissecting complex traits in biomass willows (Salix spp.). Tree Physiology. 34 (11), pp. 1167-1180. https://doi.org/10.1093/treephys/tpt089
Insights into nitrogen allocation and recycling from nitrogen elemental analysis and 15N isotope labelling in 14 genotypes of willow
A - Papers appearing in refereed journals
Brereton, N. J. B., Pitre, F. E., Shield, I. F., Hanley, S. J., Ray, M. J., Murphy, R. J. and Karp, A. 2014. Insights into nitrogen allocation and recycling from nitrogen elemental analysis and 15N isotope labelling in 14 genotypes of willow. Tree Physiology. 34 (11), pp. 1252-1262. https://doi.org/10.1093/treephys/tpt081
Near infrared spectroscopy (NIRS) for screening condensed tannins in a willow germplasm collection
C2 - Non-edited contributions to conferences
Klongsiriwet, C., Karp, A., Hanley, S. J., Barnes, R., Falchero, L. and Mueller-Harvey, I. 2013. Near infrared spectroscopy (NIRS) for screening condensed tannins in a willow germplasm collection. Thieme. https://doi.org/10.1055/s-0033-1352230
Arable crop disease control, climate change and food security
C2 - Non-edited contributions to conferences
Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J. and West, J. S. 2013. Arable crop disease control, climate change and food security.
Using Arabidopsis to study shoot branching in biomass willow
A - Papers appearing in refereed journals
Ward, S. P., Salmon, J., Hanley, S. J., Karp, A. and Leyser, O. 2013. Using Arabidopsis to study shoot branching in biomass willow. Plant Physiology. 162 (June), pp. 800-811. https://doi.org/10.1104/pp.113.218461
The presence of two different target-site resistance mechanisms in individual plants of Alopecurus myosuroides Huds., identified using a quick molcular test for the characterisation of six ALS and seven ACCase SNPs
A - Papers appearing in refereed journals
Marshall, R., Hanley, S. J., Hull, R. I. and Moss, S. R. 2013. The presence of two different target-site resistance mechanisms in individual plants of Alopecurus myosuroides Huds., identified using a quick molcular test for the characterisation of six ALS and seven ACCase SNPs. Pest Management Science. 69 (6), pp. 727-737. https://doi.org/10.1002/ps.3429
A SNaPshot assay for the rapid and simple detection of known point mutations conferring resistance to ACCase-inhibiting herbicides in Lolium spp.
A - Papers appearing in refereed journals
Reverte, R. A., Hanley, S. J., Kaundun, S. S., Karp, A. and Moss, S. R. 2013. A SNaPshot assay for the rapid and simple detection of known point mutations conferring resistance to ACCase-inhibiting herbicides in Lolium spp. Weed Research. 53 (1), pp. 12-20. https://doi.org/10.1111/wre.12002
High levels of genetic diversity in Salix viminalis of the Czech Republic as revealed by microsatellite markers
A - Papers appearing in refereed journals
Trybush, S. O., Jahodova, S., Cizkova, L., Karp, A. and Hanley, S. J. 2012. High levels of genetic diversity in Salix viminalis of the Czech Republic as revealed by microsatellite markers. BioEnergy Research. 5 (4), pp. 969-977. https://doi.org/10.1007/s12155-012-9212-4
Population genetics of Tuberolachnus salignus, an obligate parthenogenetic aphid
A - Papers appearing in refereed journals
Aradottir, G. I., Hanley, S. J., Collins, C. M., Dawson, K. J., Karp, A., Leather, S. R., Shield, I. F. and Harrington, R. 2012. Population genetics of Tuberolachnus salignus, an obligate parthenogenetic aphid. Agricultural and Forest Entomology. 14 (2), pp. 197-205. https://doi.org/10.1111/j.1461-9563.2011.00559.x
Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits
C1 - Edited contributions to conferences/learned societies
Defoin-Platel, M., Hassani-Pak, K. and Rawlings, C. J. 2011. Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. Systems Approaches to Crop Improvement. Aspects of Applied Biology 107 . Association of Applied Biologists (AAB) Wellesbourne Warwick . pp. 79-87
Condensed tannins in willow (Salix spp.): a first step to evaluate novel feeds for nutritionally improved animal products
C1 - Edited contributions to conferences/learned societies
Falchero, L., Brown, R. H., Mueller-Harvey, I., Hanley, S. J., Shield, I. F. and Karp, A. 2011. Condensed tannins in willow (Salix spp.): a first step to evaluate novel feeds for nutritionally improved animal products. Hopkins, A., Krautzer, B. and Potsch, E. M. (ed.) Proceedings 16th Symposium of the European Grassland Federation: Grassland Farming and Land Management Systems in Mountainous Regions, Gumpenstein, 29-31 August 2011 . Wallig Ennstaler Druckerei und Verlag, Grobming. pp. 434-436
The structural diversity of condensed tannins in willows (salix spp.): a first screening to improve the nutritional quality of ruminant products
C2 - Non-edited contributions to conferences
Falchero, L., Brown, R., Hanley, S. J., Karp, A., Shield, I. F. and Mueller-Harvey, I. 2011. The structural diversity of condensed tannins in willows (salix spp.): a first screening to improve the nutritional quality of ruminant products.
BSBEC-BioMASS - selecting traits to optimise biomass yield of SRC willow
A - Papers appearing in refereed journals
Cunniff, J., Shield, I. F., Barraclough, T. J. P., Castle, M., Hanley, S. J., Andralojc, P. J., Richter, G. M., Cerasuolo, M., Purdy, S., Clifton-Brown, J., Maddison, A., Jones, L., Donnison, I. and Karp, A. 2011. BSBEC-BioMASS - selecting traits to optimise biomass yield of SRC willow. Aspects of Applied Biology. 112.
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory
A - Papers appearing in refereed journals
Splendiani, A., Gundel, M., Austyn, J. M., Cavalieri, D., Scognamiglio, C. and Brandizi, M. 2011. Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. Briefings in Bioinformatics. 12, pp. 562-575. https://doi.org/10.1093/bib/bbr051
Climate change and arable crop disease control: mitigation and adaptation
C1 - Edited contributions to conferences/learned societies
Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J., Madgwick, J. W., Jeger, M. J., Townsend, J. A., Turner, J. A. and West, J. S. 2011. Climate change and arable crop disease control: mitigation and adaptation. Deising, H. B., Lyr, H., Russell, P. E., Kuck, K. H., Gisi, U. and Dehne, H. W. (ed.) Modern Fungicides and Antifungal Compounds VI: Proceedings 16th Reinhardsbrunn Symposium, Friedrichroda, 25-29 April 2010 . Deutsche Phytomedizinische Gesellschaft, Braunschweig. pp. 17-26
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis
A - Papers appearing in refereed journals
Lysenko, A., Defoin-Platel, M., Hassani-Pak, K., Taubert, J., Hodgman, C., Rawlings, C. J. and Saqi, M. 2011. Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics. 12, p. 203 (14pp). https://doi.org/10.1186/1471-2105-12-203
Willow
B - Book chapters etc edited externally
Hanley, S. J. 2011. Willow. in: Karp, A. and Halford, N. G. (ed.) Energy crops Royal Society of Chemistry (RSC), Cambridge. pp. 259-274
Disease control on UK winter oilseed rape contributes to climate change mitigation
C2 - Non-edited contributions to conferences
Mahmuti, M., West, J. S., Watts, J., Gladders, P., Hughes, D. J. and Fitt, B. D. L. 2011. Disease control on UK winter oilseed rape contributes to climate change mitigation. Abstracts 13th International Rapeseed Congress, Prague, 5-9 June 2011 . pp. 1330-1333
Effects of disease control by fungicides on greenhouse gas emissions by UK arable crop production
A - Papers appearing in refereed journals
Hughes, D. J., West, J. S., Atkins, S. D., Gladders, P., Jeger, M. J. and Fitt, B. D. L. 2011. Effects of disease control by fungicides on greenhouse gas emissions by UK arable crop production. Pest Management Science. 67 (9), pp. 1082-1092. https://doi.org/10.1002/ps.2151
Resistance to Pyrenopeziza brassicae (light leaf spot) in Brassica napus (oilseed rape) stops asexual but not sexual sporulation
C2 - Non-edited contributions to conferences
Boys, E. F., Roques, S., West, J. S., Werner, C. P., King, G. J., Dyer, P. S., Hughes, D. J. and Fitt, B. D. L. 2011. Resistance to Pyrenopeziza brassicae (light leaf spot) in Brassica napus (oilseed rape) stops asexual but not sexual sporulation. Abstracts 13th International Rapeseed Congress, Prague, 5-9 June 2011 .
Genetic mapping of rust resistance loci in biomass willow
A - Papers appearing in refereed journals
Hanley, S. J., Pei, M. H., Powers, S. J., Ruiz, C., Mallott, M. D., Barker, J. H. A. and Karp, A. 2011. Genetic mapping of rust resistance loci in biomass willow. Tree Genetics & Genomes. 7 (3), pp. 597-608. https://doi.org/10.1007/s11295-010-0359-x
Genetic improvement of willow for bioenergy and biofuels
A - Papers appearing in refereed journals
Karp, A., Hanley, S. J., Trybush, S. O., Macalpine, W. J., Pei, M. H. and Shield, I. F. 2011. Genetic improvement of willow for bioenergy and biofuels. Journal of Integrative Plant Biology. 53 (2), pp. 151-165. https://doi.org/10.1111/j.1744-7909.2010.01015.x
Arable crop disease control, climate change and food security
C1 - Edited contributions to conferences/learned societies
Fitt, B. D. L., Evans, N., Gladders, P., Hughes, D. J., Jeger, M. J., Turner, J. A. and West, J. S. 2011. Arable crop disease control, climate change and food security. Crop protection in Southern Britain. Aspects of Applied Biology 106 . pp. 161-169