Biomathematics & Statistics Scotland

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Published:

Category: "Refereed journal"

Milne, I., Bayer, M.M., Cardle, L., Shaw, P., Stephen, G., Wright, F. and 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. and Wright, F. (2009). TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25(1), 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. and 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 Biology 59, 4219-4231.

Husmeier, D., Wright, F. and Milne, I. (2005). Detecting interspecific recombination with a pruned probabilistic divergence measure. Bioinformatics 21, 1797-1806.

Liu, Z., Bos, J.I.B., Armstrong, M., Whisson, S.C., da Cunha, L., Torto-Alalibo, T., Win, J., Avrova, A.V., Wright, F., Birch, P.R.J. and Kamoun, S. (2005). Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans. Molecular Biology and Evolution 22, 659-672.

Oliviera, C.M.G., Hubschen, J., Brown, D.J.F., Ferraz, L.C.C.B., Wright, F. and Neilson, R. (2004). Phylogenetic relationships among Xiphinema and Xiphidorus nematode species from Brazil inferred from 18S rDNA sequences. Journal of Nematology 36, 153-159.

Milne, I., Wright, F., Rowe, G., Marshall, D., Husmeier, D. and McGuire, G. (2004). TOPALi: Software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20, 1806-1807.

Husmeier, D. and Wright, F. (2002). A Bayesian approach to discriminate between alternative DNA sequence segmentations. Bioinformatics 18, 226-234.

Stevenson, K., Hughes, V.M., De Juan, L., Inglis, N.F., Wright, F. and Sharp, J.M. (2002). Molecular characterization of pigmented and nonpigmented isolates of Mycobacterium avium subsp. paratuberculosis. Journal of Clinical Microbiology 40, 1798-1804.

Taylor, M.A., Ross, H.A., McRae, D., Wright, F., Viola, R. and Davies, H.V. (2001). Copy-DNA cloning and characterisation of a potato alpha-glucosidase: expression in Escherichia coli and effects of down-regulation in transgenic potato. Planta 213, 258-264.

Husmeier, D. and Wright, F. (2001). Detection of recombination in DNA multiple alignments with hidden Markov models. Journal of Computational Biology 8, 401-427.

Husmeier, D. and Wright, F. (2001). Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics 17, S123-S131.

McGuire, G., Wright, F. and Prentice, M.J. (2000). A bayesian model for detecting past recombination events in DNA multiple alignments. Journal of Computational Biology 7, 159-170.

Taylor, M.A., Ross, H.R., George, L.A., McRae, D., Stewart, D., Roberts, I.M., Duncan, J., Wright, F. and Davies, H.V. (2000). A potato alpha-glucosidase gene in codes glycoprotein processing alpha-glucosidase II-like activity. Demonstration of enzyme activity and effects of down-regulation in transgenic plants. The Plant Journal 24, 305-316.

Provan, J., Lawrence, P., Young, G., Wright, F., Bid, R., Paglia, G., Cattonaro, F., Morgante, M. and Powell, W. (1999). Analysis of the genus Zea (Poaceae) using polymorphic chloroplast simple sequence repeats. Plant Systematics and Evolution 218: 245-256, 218:245-256.

McGuire, G., Prentice, M.J. and Wright, F. (1999). Improved error bounds for genetic distances from DNA sequences. Biometrics 55, 1064-1070.

Horgan, G.W., Elston, D.A., Franklin, M.F., Glasbey, C.A., Hunter, E.A., Talbot, M., Kempton, R.A., McNicol, J.W. and Wright, F. (1999). Teaching statistics to biological research scientists. Journal of the Royal Statistical Society, Series A Series D,48, 393-400.

Hopkins, R.J., Wright, F., Birch, A.N.E. and McKinlay, R.G. (1999). The decision to oviposit: a sequential analysis of the post-alighting behaviour of Delia floralis. Physiological Entomology 24, 41-50.

McGuire, G. and Wright, F. (1999). TOPAL 2.0: improved detecting of mosaic sequences within multiple alignments. Bioinformatics 16, 130-134.

Kirby, J., Wright, F. and Flint, H.J. (1998). A cysteine desulphurase gene from the cellulolytic rumen anaerobe Ruminococcus flavefaciens. Biochimica et Biophysica Acta 1386, 233-237.

Harrier, L.A., Wright, F. and Hooker, J.E. (1998). Isolation of the 3-phosphoglycerate kinase gene of the arbuscular mycorrhizal fungus Glomus mosseal (Nicol. & Gerd.) Gerdemann & Trappe. Current Genetics 34, 386-392.

Fennell, S.R., Powell, W., Wright, F., Ramsay, G. and Waugh, R. (1998). Phylogenetic relationships between Vicia faba (Fabaceae) and related species inferred from chloroplast trnL sequences. Plant Systematics and Evolution 212, 247-259.

McGuire, G. and Wright, F. (1998). TOPAL: recombination detection in DNA and protein sequences. Bioinformatics 14, 219-220.

McGuire, G., Wright, F. and Prentice, M.J. (1997). A graphical method for detecting recombination in phylogenetic data sets. Molecular Biology and Evolution 14, 1125-1131.

Hopkins, R.J., Wright, F., McKinlay, R.G. and Birch, A.N.E. (1996). Analysis of sequential behaviour patterns: the oviposition decision of the turnip root fly, Delia floralis. Entomologia Experimentalis et Applicata 80, 93-96.

Wood, A.R., Lainson, F.A., Wright, F., Baird, G.D. and Donachie, W. (1995). A native plasmid of Pasteurella haemolytica serotype A1: DNA sequence analysis and investigation of its potential as a vector. Research in Veterinary Science 58, 163-168.

Wright, H., Redmond, J., Wright, F. and Ballingall, K.T. (1995). The nucleotide sequence of the sheep MHC class II DNA gene. Immunogenetics 41, 131-133.

Glasbey, C.A. and Wright, F. (1994). An algorithm for unwarping multitrack electrophoretic gels. Electrophoresis 15, 143-148.

Taylor, M.A., Wright, F. and Davies, H.V. (1994). Characterisation of the cDNA clones of two B-tubulin genes and their expression in the potato plant (S. tuberosum L.). Plant Molecular Biology 26, 1013-1018.

McInnis, C.J., Logan, M., Haig, D. and Wright, F. (1994). Cloning of a cDNA encoding ovine interleukin-3. Gene 139, 289-290.

Augustin, G., Wright, F. and Flint, H.J. (1994). Genetic diversity and phylogenetic relationships among strains of Prevotella (Bacteroides) ruminicola from the rumen. International Journal of Systematic Bacteriology 44, 246-255.

Baxter, F., Wright, F., Chalmers, R.H., Low, J.C. and Donachie, W. (1993). Characterisation by multilocus enzyme electrophoresis of Listeria monocytogenes isolates involved in ovine listeriosis outbreaks in Scotland during 1989-91. Applied and Environmental Microbiology 59, 3126-3129.

Low, J.C., Donachie, W., Wright, F. and McLauchlan, J. (1993). Serotyping and distribution of Listeria isolates from cases of ovine listeriosis. Veterinary Record 133, 165-166.

Lally, N.C., Baird, D.G., McQuay, S.J., Wright, F. and Oliver, J.J. (1992). A 2359bp DNA fragment from Cryptosporidium parvum encoding a repetitive oocyst protein. Molecular and Biochemical Parasitology 56, 69-78.

Wright, F. and Bibb, M.J. (1992). Codon usage in the G + C rich Streptomyces genome. Gene 113, 55-65.

Wright, F. (1990). The effective number of codons used in a gene. Gene 87, 23-29.

Sharp, P.M., Cowe, E., Higgins, D.G., Shields, D.C., Wolfe, K.H. and Wright, F. (1988). Codon usage patterns in E. coli, B. subtilis, S. cerevisiae, S. pombe, D. melanogaster, and H. Sapiens. A review of the considerable within-species diversity. Nucleic Acids Research 16, 8207-8211.

Shields, D.C., Sharp, P.M., Higgins, D.G. and Wright, F. (1988). Silent sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons. Molecular Biology and Evolution 5, 704-716.

Category: "Book Chapter"

Husmeier, D. and Wright, F. (2005). Detecting recombination in DNA sequence alignments. In "Probabilistic Modeling in Bioinformatics and Medical Informatics", 147-190. Eds. Husmeier, D., Dybowski, R. & Roberts, S.. Springer Verlag.