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CellMix: a comprehensive toolbox for gene expression deconvolution.
Gaujoux R, Seoighe C. Gaujoux R, et al. Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3. Bioinformatics. 2013. PMID: 23825367
Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK, Geeleher P, Seoighe C. Korir PK, et al. BMC Bioinformatics. 2015 Sep 4;16:286. doi: 10.1186/s12859-015-0712-z. BMC Bioinformatics. 2015. PMID: 26338512 Free PMC article.
Gene-set analysis is severely biased when applied to genome-wide methylation data.
Geeleher P, Hartnett L, Egan LJ, Golden A, Raja Ali RA, Seoighe C. Geeleher P, et al. Bioinformatics. 2013 Aug 1;29(15):1851-7. doi: 10.1093/bioinformatics/btt311. Epub 2013 Jun 3. Bioinformatics. 2013. PMID: 23732277
CONTACT: cathal.seoighe@nuigalway.ie SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: cathal.seoighe@nuigalway.ie SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
Robust inference of positive selection from recombining coding sequences.
Scheffler K, Martin DP, Seoighe C. Scheffler K, et al. Bioinformatics. 2006 Oct 15;22(20):2493-9. doi: 10.1093/bioinformatics/btl427. Epub 2006 Aug 7. Bioinformatics. 2006. PMID: 16895925
FRAGS: estimation of coding sequence substitution rates from fragmentary data.
Swart EC, Hide WA, Seoighe C. Swart EC, et al. BMC Bioinformatics. 2004 Jan 29;5:8. doi: 10.1186/1471-2105-5-8. BMC Bioinformatics. 2004. PMID: 15005802 Free PMC article.
A flexible R package for nonnegative matrix factorization.
Gaujoux R, Seoighe C. Gaujoux R, et al. BMC Bioinformatics. 2010 Jul 2;11:367. doi: 10.1186/1471-2105-11-367. BMC Bioinformatics. 2010. PMID: 20598126 Free PMC article.
Investigating the effect of paralogs on microarray gene-set analysis.
Faure AJ, Seoighe C, Mulder NJ. Faure AJ, et al. BMC Bioinformatics. 2011 Jan 24;12:29. doi: 10.1186/1471-2105-12-29. BMC Bioinformatics. 2011. PMID: 21261946 Free PMC article.
Models of coding sequence evolution.
Delport W, Scheffler K, Seoighe C. Delport W, et al. Brief Bioinform. 2009 Jan;10(1):97-109. doi: 10.1093/bib/bbn049. Epub 2008 Oct 29. Brief Bioinform. 2009. PMID: 18971241 Free PMC article. Review.
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