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Results: 1 to 20 of 65

1.

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.

PMID:
25213172
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24969741
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24725334
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
24428929
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
24295501
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PLoS One. 2013 Nov 18;8(11):e79627. doi: 10.1371/journal.pone.0079627. eCollection 2013.

PMID:
24260269
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23990606
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23825367
[PubMed - indexed for MEDLINE]
Free Article
10.

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.

PMID:
23732277
[PubMed - indexed for MEDLINE]
Free Article
11.

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.

PMID:
23616655
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23370465
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23272639
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The hidden geometries of the Arabidopsis thaliana epidermis.

Staff L, Hurd P, Reale L, Seoighe C, Rockwood A, Gehring C.

PLoS One. 2012;7(9):e43546. doi: 10.1371/journal.pone.0043546. Epub 2012 Sep 11.

PMID:
22984433
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Evidence for intron length conservation in a set of mammalian genes associated with embryonic development.

Seoighe C, Korir PK.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S16. doi: 10.1186/1471-2105-12-S9-S16.

PMID:
22151910
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Is there evidence of optimisation for carbon efficiency in plant proteomes?

Jankovic B, Seoighe C, Alqurashi M, Gehring C.

Plant Biol (Stuttg). 2011 Nov;13(6):831-4. doi: 10.1111/j.1438-8677.2011.00494.x. Epub 2011 Jul 25.

PMID:
21973021
[PubMed - indexed for MEDLINE]
17.

Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study.

Gaujoux R, Seoighe C.

Infect Genet Evol. 2012 Jul;12(5):913-21. doi: 10.1016/j.meegid.2011.08.014. Epub 2011 Sep 10.

PMID:
21930246
[PubMed - indexed for MEDLINE]
18.

Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor.

Millane RC, Kanska J, Duffy DJ, Seoighe C, Cunningham S, Plickert G, Frank U.

Development. 2011 Jun;138(12):2429-39. doi: 10.1242/dev.064931.

PMID:
21610024
[PubMed - indexed for MEDLINE]
Free Article
19.

Immune and Genetic Correlates of Vaccine Protection Against Mucosal Infection by SIV in Monkeys.

Letvin NL, Rao SS, Montefiori DC, Seaman MS, Sun Y, Lim SY, Yeh WW, Asmal M, Gelman RS, Shen L, Whitney JB, Seoighe C, Lacerda M, Keating S, Norris PJ, Hudgens MG, Gilbert PB, Buzby AP, Mach LV, Zhang J, Balachandran H, Shaw GM, Schmidt SD, Todd JP, Dodson A, Mascola JR, Nabel GJ.

Sci Transl Med. 2011 May 4;3(81):81ra36. doi: 10.1126/scitranslmed.3002351.

PMID:
21543722
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Inhibition of human BK polyomavirus replication by small noncoding RNAs.

Tikhanovich I, Liang B, Seoighe C, Folk WR, Nasheuer HP.

J Virol. 2011 Jul;85(14):6930-40. doi: 10.1128/JVI.00547-11. Epub 2011 May 4.

PMID:
21543481
[PubMed - indexed for MEDLINE]
Free PMC Article

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