Research
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Software development: Design of TOPALi application for phylogenetic, positive selection, and recombination detection analyses.
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Statistics methodology: Methods to analyse of multiple sequence alignments, particularly to detect evidence of recombination.
Collaboration/Consultancy/Training:
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Application of statistical/evolutionary methods to molecular sequence data and genomics data.
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Providing training in molecular phylogenetics.
Areas of Expertise:
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Computational Molecular Biology.
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Molecular Sequence Analysis.
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Phylogenetics.
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Genomic Sequence Analysis.
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Systems Biology.
Publications
The following Publications have not yet been migrated to the James Hutton Institute's Pure service and relate to the research outputs from the two legacy organisations: The Macaulay Land Use Research Institute and The Scottish Crop Research Institute.
Journals
- Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F. (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
- Wheelhouse, N.; Katzer, F.; Wright, F.; Longbottom, D. (2010) Novel chlamydia-like organisms as cause of bovine abortions, UK., Emerging Infectious Diseases, 16, 1323-1324.
- Ballingall, K.T.; Rocchi, M.; McKeever, D.J.; Wright, F. (2010) Trans-species polymorphism and selection in the MHC class II DRA genes of domestic sheep., PLoS ONE, 5, 1-10.
- Milne, I.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F. (2010) Tablet – next generation sequence assembly visualization., Bioinformatics, 26, 401-402.
- Milne, I.; Lindner, D.; Bayer, M.M.; Husmeier, D.; McGuire, G.; Marshall, D.F.; Wright, F. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops., Bioinformatics, 25, 126-127.
- Ducreux, L.J.M.; Morris, W.L.; Prosser, I.M.; Morris, J.A.; Beale, M.H.; Wright, F.; Shepherd, T.; Bryan, G.J.; Hedley, P.E.; Taylor, M.A. (2008) Expression profiling of potato germplasm differentiated in quality traits leads to the identification of candidate flavour and texture genes., Journal of Experimental Botany, 59, 4219-4231.
- Opik, M.; Moora, M.; Zobel, M.; Saks, U.; Wheatley, R.E.; Wright, F.; Daniell, T.J. (2008) High diversity of arbuscular mycorrhizal fungi in a boreal, herb-rich, coniferous forest., New Phytologist, 179, 867-876.
- Liu, Z.; Bos, J.I.B.; Armstrong, M.R.; Whisson, S.C.; da Cunha, L.; Torto-Alalibo, T.; Win, J.; Avrova, A.O.; Wright, F.; Birch, P.R.J.; Kamoun, S. (2005) Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans., Molecular Biology and Evolution, 22, 659-572.
- Husmeier, D.; Wright, F.; Milne, I. (2005) Detecting interspecific recombination with a pruned probabilistic divergence measure., Bioinformatics, 21, 1797-1806.
- Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D.; McGuire, G. (2004) TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments., Bioinformatics, 20, 1806-1807.
- Oliveira, C.M.G.; Hubschen, J.; Brown, D.J.F.; Ferraz, C.C.B.; Wright, F.; Neilson, R. (2004) Phylogenetic relationships among Xiphinema and Xiphidorus nematode species from Brazil inferred from 18S rDNA gene sequences., Journal of Nematology, 36, 153-159.
- Husmeier, D.; Wright, F. (2002) A Bayesian approach to discriminate between alternative DNA sequence segmentations., Bioinformatics, 18, 226-234.
- Husmeier, D.; Wright, F. (2001) Detection of recombination in DNA multiple alignments with hidden Markov models., Journal of Computational Biology, 8, 401-427.
- Taylor, M.A.; Ross, H.A.; McRae, D.; Wright, F.; Viola, R.; Davies, H.V. (2001) Copy-DNA cloning and characterisation of a potato alpha-glucosidase: expression in Esherichia coli and effects of down-regulation in transgenic potato., Planta, 213, 258-264.
- Husmeier, D.; Wright, F. (2001) Probabilistic divergence measures for detecting interspecies recombination., Bioinformatics, 1, 1-8
- Taylor, M.A.; Ross, H.A.; McRae, D.; Stewart, D.; Roberts, I.M.; Duncan, G.H.; Wright, F.; Millam, S.; Davies, H.V. (2000) A potato alpha-glucosidase gene encodes a glycoprotein processing alpha-glucosidase II-like activity. Demonstration of enzyme activity and effects of down-regulation in transgenic plants., Plant Journal, 24, 305-316.
- Provan, J.; Lawrence, P.; Young, G.; Wright, F.; Bird, R.; Paglia, G.; Cattonaro, F.; Morgante, M.; Powell, W. (1999) Analysis of the genusZea (Poaceae) using polymorphic chloroplast simple sequence repeats., Plant Systematics and Evolution, 218, 245-256.
- Hopkins, R.J.; Wright, F.; Birch, A.N.E.; McKinlay, R.G. (1999) The decision to reject an oviposition site: sequential analysis of the post-alighting behaviour of Delia floralis., Physiological Entomology, 24, 41-50.
- Fennell, S.R.; Powell, W.; Wright, F.; Ramsay, G.; Waugh, R. (1998) Phylogenetic relationships between Vicia faba (Fabaceae) and related species inferred from chloroplast trnL sequences., Plant Systematics and Evolution, 212, 247-259.
Technical / contract reports
- Wright, F. (2011) Phylogenetic trees and molecular evolution., Annual Report of the Scottish Crop Research Institute for 2010, p54.
Conference papers
- Opik, M.; Moora, M.; Saks, U.; Wheatley, R.E.; Wright, F.; Daniell, T.J.; Zobel, M. (2008) Boreo-nemoral herb-rich forest – a new biodiversity hotspot for arbuscular mycorrhizal fungi., Joint Meeting: European Ecological Federation and the Ecological Societies of Germany, Austria and Switzerland EURECO-GFOE 2008, Leipzig, Germany, 15-19 September 2008.
- Ghasemi, S.; Wright, F.; Torrance, L.; Izadpanah, K. (2005) Detection and classification of potyviruses causing mosaic disease of sugarcane in Iran using molecular approaches., Second Asian Conference on Plant Pathology, Singapore, 25-28 June 2005.
- Milne, I.; Wright, F.; Rowe, G.; Marshall, D.F.; Husmeier, D. (2004) TOPALi – Software for detecting recombinants in DNA multiple alignments., Plant and Animal Genome Conference (PAG) XII Proceedings, San Diego, California, 10-12 January 2004.
- Lazarova, S.S.; Brown, D.J.F.; Malloch, G.; Oliveira, C.M.G.; Vandekerkhove, T.M.; Fenton, B.; Wright, F.; Lamberti, F.; Barsi, L.; Neilson, R. (2004) Phylogenetic relationships of the endosymbiont bacteria of Xiphinema americanum-Group nematodes., European Society of Nematologists Meeting, Rome, 14-18 June 2004.
- Oliveira, C.M.G.; Hobschen, J.; Brown, D.J.F.; Monteiro, A.R.; Ferraz, L.C.C.B.; Wright, F.; Neilson, R. (2003) Taxonomic relationships of selected Xiphinema and Xiphidorus nematode species from Brazil., 16th Symposium of the Nematological Society of Southern Africa, South Africa, 30 June – 4 July 2003.
- Oliveira, C.M.G.; Hubschen, J.; Brown, D.J.F.; Monteiro, A.R.; Ferraz, C.C.B.; Wright, F.; Neilson, R. (2003) Taxonomic relationships of selected Xiphinema and Xiphidorus nematode species from Brazil based on morphometrics and 18S rDNA gene sequences., Proceedings of the 55th International Symposium on Crop Protection, Ghent, Belgium, 6 May 2003.
- Husmeier, D.; Wright, F. (2000) Detection of recombination in phylogenetic data sets with hidden Markov models., Mathematical and Statistical Aspects of Molecular Biology, Newton Institute, Cambridge, 4-5 April 2000.
- Husmeier, D.; Wright, F. (2000) Detecting recombination with hidden Markov models., International Conference on Intelligent Systems for Molecular Biology (ISMB), La Jolla, California, 20-23 August 2000.
- Husmeier, D.; Wright, F. (2000) Detecting sporadic recombination in DNA alignments with hidden Markov models., Proceedings of the 15th German Conference on Bioinformatics, Heidelberg, Germany, 5-7 October 2000, pp19-26.
Conference posters / abstracts
- Milne, I.; Lindner, D.; Wright, F. (2007) TOPAi v2: Extended multiple sequence alignment analysis software using web services and cluster computing., ISMB 2007, Vienna, 21-25 July 2007 (Poster).
- Milne, I.; Wright, F. (2004) A simple algorithm to automatically detect recombinants in DNA/RNA sequence alignments., ISMB/ECCB 2004. Glasgow, 31 July – 4 August 2004. (Poster).
