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LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.
Yu Y, Ceredig R, Seoighe C. Yu Y, et al. Among authors: seoighe c. Nucleic Acids Res. 2016 Feb 29;44(4):e31. doi: 10.1093/nar/gkv1016. Epub 2015 Oct 7. Nucleic Acids Res. 2016. PMID: 26446988 Free PMC article.
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development.
Seoighe C, Korir PK. Seoighe C, et al. BMC Bioinformatics. 2011 Oct 5;12 Suppl 9(Suppl 9):S16. doi: 10.1186/1471-2105-12-S9-S16. BMC Bioinformatics. 2011. PMID: 22151910 Free PMC article.
Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts.
Nguyen TT, Seoighe C. Nguyen TT, et al. Among authors: seoighe c. PLoS One. 2013 Nov 18;8(11):e79627. doi: 10.1371/journal.pone.0079627. eCollection 2013. PLoS One. 2013. PMID: 24260269 Free PMC article.
Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models.
Lacerda M, Moore PL, Ngandu NK, Seaman M, Gray ES, Murrell B, Krishnamoorthy M, Nonyane M, Madiga M, Wibmer CK, Sheward D, Bailer RT, Gao H, Greene KM, Karim SS, Mascola JR, Korber BT, Montefiori DC, Morris L, Williamson C, Seoighe C; CAVD-NSDP Consortium. Lacerda M, et al. Among authors: seoighe c. Virol J. 2013 Dec 2;10:347. doi: 10.1186/1743-422X-10-347. Virol J. 2013. PMID: 24295501 Free PMC article.
RESULTS: We applied our method to ID50 neutralization data generated from seven HIV-1 subtype C serum samples with neutralization breadth that had been tested against a multi-clade panel of 225 pseudoviruses for which envelope sequences were also available. ...
RESULTS: We applied our method to ID50 neutralization data generated from seven HIV-1 subtype C serum samples with neutralization bre …
Inference of allele-specific expression from RNA-seq data.
Korir PK, Seoighe C. Korir PK, et al. Among authors: seoighe c. Methods Mol Biol. 2014;1112:49-69. doi: 10.1007/978-1-62703-773-0_4. Methods Mol Biol. 2014. PMID: 24478007
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.
Keane P, Ceredig R, Seoighe C. Keane P, et al. Among authors: seoighe c. Bioinformatics. 2015 Apr 1;31(7):986-90. doi: 10.1093/bioinformatics/btu785. Epub 2014 Nov 25. Bioinformatics. 2015. PMID: 25429061
Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy.
O'Reilly P, Ortutay C, Gernon G, O'Connell E, Seoighe C, Boyce S, Serrano L, Szegezdi E. O'Reilly P, et al. Among authors: seoighe c. BMC Genomics. 2014 Dec 19;15(1):1144. doi: 10.1186/1471-2164-15-1144. BMC Genomics. 2014. PMID: 25527049 Free PMC article.
Seq-ing improved gene expression estimates from microarrays using machine learning.
Korir PK, Geeleher P, Seoighe C. Korir PK, et al. Among authors: seoighe c. BMC Bioinformatics. 2015 Sep 4;16:286. doi: 10.1186/s12859-015-0712-z. BMC Bioinformatics. 2015. PMID: 26338512 Free PMC article.
Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization.
Yang H, Seoighe C. Yang H, et al. Among authors: seoighe c. PLoS One. 2016 Oct 14;11(10):e0164880. doi: 10.1371/journal.pone.0164880. eCollection 2016. PLoS One. 2016. PMID: 27741311 Free PMC article.
Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells.
Martin G, Selcuklu SD, Schouest K, Nembaware V, McKeown PC, Seoighe C, Spillane C. Martin G, et al. Among authors: seoighe c. Gene. 2017 Jan 20;598:107-112. doi: 10.1016/j.gene.2016.11.004. Epub 2016 Nov 5. Gene. 2017. PMID: 27826023
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