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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. 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.
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.
O'Sullivan O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C. O'Sullivan O, et al. Bioinformatics. 2003;19 Suppl 1:i215-21. doi: 10.1093/bioinformatics/btg1029. Bioinformatics. 2003. PMID: 12855461
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. 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. Bioinformatics. 2005 Apr 15;21(8):1408-14. doi: 10.1093/bioinformatics/bti159. Epub 2004 Nov 25. Bioinformatics. 2005. PMID: 15564300
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions.
Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW. Claesson MJ, et al. Nucleic Acids Res. 2010 Dec;38(22):e200. doi: 10.1093/nar/gkq873. Epub 2010 Sep 29. Nucleic Acids Res. 2010. PMID: 20880993 Free PMC article.
Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon.
Rea MC, Dobson A, O'Sullivan O, Crispie F, Fouhy F, Cotter PD, Shanahan F, Kiely B, Hill C, Ross RP. Rea MC, et al. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1(Suppl 1):4639-44. doi: 10.1073/pnas.1001224107. Epub 2010 Jun 29. Proc Natl Acad Sci U S A. 2011. PMID: 20616009 Free PMC article.
In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria.
Marsh AJ, O'Sullivan O, Ross RP, Cotter PD, Hill C. Marsh AJ, et al. BMC Genomics. 2010 Nov 30;11:679. doi: 10.1186/1471-2164-11-679. BMC Genomics. 2010. PMID: 21118552 Free PMC article.
Genome mining for radical SAM protein determinants reveals multiple sactibiotic-like gene clusters.
Murphy K, O'Sullivan O, Rea MC, Cotter PD, Ross RP, Hill C. Murphy K, et al. PLoS One. 2011;6(7):e20852. doi: 10.1371/journal.pone.0020852. Epub 2011 Jul 8. PLoS One. 2011. PMID: 21760885 Free PMC article.
Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese.
Quigley L, O'Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. Quigley L, et al. Int J Food Microbiol. 2011 Nov 1;150(2-3):81-94. doi: 10.1016/j.ijfoodmicro.2011.08.001. Epub 2011 Aug 8. Int J Food Microbiol. 2011. PMID: 21868118 Review.
Genome sequence of the phage clP1, which infects the beer spoilage bacterium Pediococcus damnosus.
Kelly D, O'Sullivan O, Mills S, McAuliffe O, Ross RP, Neve H, Coffey A. Kelly D, et al. Gene. 2012 Aug 1;504(1):53-63. doi: 10.1016/j.gene.2012.04.085. Epub 2012 May 4. Gene. 2012. PMID: 22564705
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