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Computational identification and analysis of protein short linear motifs.
Davey NE, Edwards RJ, Shields DC. Davey NE, et al. Front Biosci (Landmark Ed). 2010 Jun 1;15:801-25. doi: 10.2741/3647. Front Biosci (Landmark Ed). 2010. PMID: 20515727 Review.
GASP: Gapped Ancestral Sequence Prediction for proteins.
Edwards RJ, Shields DC. Edwards RJ, et al. BMC Bioinformatics. 2004 Sep 6;5:123. doi: 10.1186/1471-2105-5-123. BMC Bioinformatics. 2004. PMID: 15350199 Free PMC article.
A sequence sub-sampling algorithm increases the power to detect distant homologues.
Johnston CR, Shields DC. Johnston CR, et al. Nucleic Acids Res. 2005 Jul 8;33(12):3772-8. doi: 10.1093/nar/gki687. Print 2005. Nucleic Acids Res. 2005. PMID: 16006623 Free PMC article.
Human tissue profiling with multidimensional protein identification technology.
Cagney G, Park S, Chung C, Tong B, O'Dushlaine C, Shields DC, Emili A. Cagney G, et al. J Proteome Res. 2005 Sep-Oct;4(5):1757-67. doi: 10.1021/pr0500354. J Proteome Res. 2005. PMID: 16212430
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent.
Davey NE, Shields DC, Edwards RJ. Davey NE, et al. Nucleic Acids Res. 2006 Jul 19;34(12):3546-54. doi: 10.1093/nar/gkl486. Print 2006. Nucleic Acids Res. 2006. PMID: 16855291 Free PMC article.
Absolute net charge and the biological activity of oligopeptides.
Parthasarathi L, Devocelle M, S√łndergaard C, Baran I, O'Dushlaine CT, Davey NE, Edwards RJ, Moran N, Kenny D, Shields DC. Parthasarathi L, et al. J Chem Inf Model. 2006 Sep-Oct;46(5):2183-90. doi: 10.1021/ci0600760. J Chem Inf Model. 2006. PMID: 16995748
Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication.
Johnston CR, O'Dushlaine C, Fitzpatrick DA, Edwards RJ, Shields DC. Johnston CR, et al. Mol Biol Evol. 2007 Jan;24(1):315-23. doi: 10.1093/molbev/msl162. Epub 2006 Oct 25. Mol Biol Evol. 2007. PMID: 17065596
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