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M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O'Sullivan O, Higgins DG, Notredame C. Wallace IM, et al. Among authors: higgins dg. Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. doi: 10.1093/nar/gkl091. Print 2006. Nucleic Acids Res. 2006. PMID: 16556910 Free PMC article.
Between-group analysis of microarray data.
Culhane AC, Perrière G, Considine EC, Cotter TG, Higgins DG. Culhane AC, et al. Among authors: higgins dg. Bioinformatics. 2002 Dec;18(12):1600-8. doi: 10.1093/bioinformatics/18.12.1600. Bioinformatics. 2002. PMID: 12490444
Multiple sequence alignment with the Clustal series of programs.
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Chenna R, et al. Among authors: higgins dg. Nucleic Acids Res. 2003 Jul 1;31(13):3497-500. doi: 10.1093/nar/gkg500. Nucleic Acids Res. 2003. PMID: 12824352 Free PMC article.
3DCoffee: combining protein sequences and structures within multiple sequence alignments.
O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. O'Sullivan O, et al. Among authors: higgins dg. J Mol Biol. 2004 Jul 2;340(2):385-95. doi: 10.1016/j.jmb.2004.04.058. J Mol Biol. 2004. PMID: 15201059
Evaluation of iterative alignment algorithms for multiple alignment.
Wallace IM, O'Sullivan O, Higgins DG. Wallace IM, et al. Among authors: higgins dg. Bioinformatics. 2005 Apr 15;21(8):1408-14. doi: 10.1093/bioinformatics/bti159. Epub 2004 Nov 25. Bioinformatics. 2005. PMID: 15564300
MADE4: an R package for multivariate analysis of gene expression data.
Culhane AC, Thioulouse J, Perrière G, Higgins DG. Culhane AC, et al. Among authors: higgins dg. Bioinformatics. 2005 Jun 1;21(11):2789-90. doi: 10.1093/bioinformatics/bti394. Epub 2005 Mar 29. Bioinformatics. 2005. PMID: 15797915
Multiple sequence alignments.
Wallace IM, Blackshields G, Higgins DG. Wallace IM, et al. Among authors: higgins dg. Curr Opin Struct Biol. 2005 Jun;15(3):261-6. doi: 10.1016/j.sbi.2005.04.002. Curr Opin Struct Biol. 2005. PMID: 15963889 Review.
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.
Jeffery IB, Higgins DG, Culhane AC. Jeffery IB, et al. Among authors: higgins dg. BMC Bioinformatics. 2006 Jul 26;7:359. doi: 10.1186/1471-2105-7-359. BMC Bioinformatics. 2006. PMID: 16872483 Free PMC article.
Analysis and comparison of benchmarks for multiple sequence alignment.
Blackshields G, Wallace IM, Larkin M, Higgins DG. Blackshields G, et al. Among authors: higgins dg. In Silico Biol. 2006;6(4):321-39. In Silico Biol. 2006. PMID: 16922695
APDB: a web server to evaluate the accuracy of sequence alignments using structural information.
Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C. Armougom F, et al. Among authors: higgins dg. Bioinformatics. 2006 Oct 1;22(19):2439-40. doi: 10.1093/bioinformatics/btl404. Bioinformatics. 2006. PMID: 17032685
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