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Items: 1 to 20 of 72

1.

Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells.

Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ.

Physiol Genomics. 2016 Apr;48(4):257-73. doi: 10.1152/physiolgenomics.00046.2015. Epub 2016 Jan 26.

PMID:
26812987
2.

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships.

Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM.

Epigenetics Chromatin. 2015 Nov 16;8:46. doi: 10.1186/s13072-015-0040-6. eCollection 2015.

3.

LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.

Yu Y, Ceredig R, Seoighe C.

Nucleic Acids Res. 2016 Feb 29;44(4):e31. doi: 10.1093/nar/gkv1016. Epub 2015 Oct 7.

4.

Seq-ing improved gene expression estimates from microarrays using machine learning.

Korir PK, Geeleher P, Seoighe C.

BMC Bioinformatics. 2015 Sep 4;16:286. doi: 10.1186/s12859-015-0712-z.

5.

A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations.

Chimusa ER, Meintjies A, Tchanga M, Mulder N, Seoighe C, Soodyall H, Ramesar R.

PLoS Genet. 2015 Mar 26;11(3):e1005052. doi: 10.1371/journal.pgen.1005052. eCollection 2015 Mar. Erratum in: PLoS Genet. 2015 Jul;11(7):e1005363. Seioghe, Cathal [corrected to Seoighe, Cathal].

6.

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.

BMC Genomics. 2014 Dec 19;15:1144. doi: 10.1186/1471-2164-15-1144.

7.

Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.

Keane P, Ceredig R, Seoighe C.

Bioinformatics. 2015 Apr 1;31(7):986-90. doi: 10.1093/bioinformatics/btu785. Epub 2014 Nov 25.

8.

Population genetics inference for longitudinally-sampled mutants under strong selection.

Lacerda M, Seoighe C.

Genetics. 2014 Nov;198(3):1237-50. doi: 10.1534/genetics.114.167957. Epub 2014 Sep 10. Erratum in: Genetics. 2015 Mar;199(3):885.

9.

A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing.

Korir PK, Roberts L, Ramesar R, Seoighe C.

BMC Res Notes. 2014 Jun 27;7:401. doi: 10.1186/1756-0500-7-401.

10.

The miRNAome of the postpartum dairy cow liver in negative energy balance.

Fatima A, Lynn DJ, O'Boyle P, Seoighe C, Morris D.

BMC Genomics. 2014 Apr 12;15:279. doi: 10.1186/1471-2164-15-279.

11.

Inference of allele-specific expression from RNA-seq data.

Korir PK, Seoighe C.

Methods Mol Biol. 2014;1112:49-69. doi: 10.1007/978-1-62703-773-0_4.

PMID:
24478007
12.

Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle.

Fatima A, Waters S, O'Boyle P, Seoighe C, Morris DG.

BMC Genomics. 2014 Jan 15;15:28. doi: 10.1186/1471-2164-15-28.

13.

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.

Virol J. 2013 Dec 2;10:347. doi: 10.1186/1743-422X-10-347.

14.
15.

The shared genomic architecture of human nucleolar organizer regions.

Floutsakou I, Agrawal S, Nguyen TT, Seoighe C, Ganley AR, McStay B.

Genome Res. 2013 Dec;23(12):2003-12. doi: 10.1101/gr.157941.113. Epub 2013 Aug 29.

16.

CellMix: a comprehensive toolbox for gene expression deconvolution.

Gaujoux R, Seoighe C.

Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3.

17.

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.

Bioinformatics. 2013 Aug 1;29(15):1851-7. doi: 10.1093/bioinformatics/btt311. Epub 2013 Jun 3.

18.

Comparison of viral Env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design.

Ping LH, Joseph SB, Anderson JA, Abrahams MR, Salazar-Gonzalez JF, Kincer LP, Treurnicht FK, Arney L, Ojeda S, Zhang M, Keys J, Potter EL, Chu H, Moore P, Salazar MG, Iyer S, Jabara C, Kirchherr J, Mapanje C, Ngandu N, Seoighe C, Hoffman I, Gao F, Tang Y, Labranche C, Lee B, Saville A, Vermeulen M, Fiscus S, Morris L, Karim SA, Haynes BF, Shaw GM, Korber BT, Hahn BH, Cohen MS, Montefiori D, Williamson C, Swanstrom R; CAPRISA Acute Infection Study and the Center for HIV-AIDS Vaccine Immunology Consortium.

J Virol. 2013 Jul;87(13):7218-33. doi: 10.1128/JVI.03577-12. Epub 2013 Apr 24.

19.

Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression.

Abrahams MR, Treurnicht FK, Ngandu NK, Goodier SA, Marais JC, Bredell H, Thebus R, de Assis Rosa D, Mlisana K, Seoighe C, Karim SA, Gray CM, Williamson C.

AIDS. 2013 Feb 20;27(4):507-18. doi: 10.1097/QAD.0b013e32835cab64. Erratum in: AIDS. 2013 Jun 1;27(9):1525.

20.

The regulatory effect of miRNAs is a heritable genetic trait in humans.

Geeleher P, Huang SR, Gamazon ER, Golden A, Seoighe C.

BMC Genomics. 2012 Aug 10;13:383. doi: 10.1186/1471-2164-13-383.

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