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Items: 1 to 20 of 113

1.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JF, Ritchie ME, Lynch AG, Tavaré S.

Nucleic Acids Res. 2010 Jan;38(3):e17. doi: 10.1093/nar/gkp942. Epub 2009 Nov 18.

2.

lumi: a pipeline for processing Illumina microarray.

Du P, Kibbe WA, Lin SM.

Bioinformatics. 2008 Jul 1;24(13):1547-8. doi: 10.1093/bioinformatics/btn224. Epub 2008 May 8.

PMID:
18467348
3.

BeadArray expression analysis using bioconductor.

Ritchie ME, Dunning MJ, Smith ML, Shi W, Lynch AG.

PLoS Comput Biol. 2011 Dec;7(12):e1002276. doi: 10.1371/journal.pcbi.1002276. Epub 2011 Dec 1.

4.

Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

Arloth J, Bader DM, Röh S, Altmann A.

PLoS One. 2015 Oct 1;10(10):e0139516. doi: 10.1371/journal.pone.0139516. eCollection 2015.

5.

OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes.

Wernersson R, Nielsen HB.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W611-5.

6.
7.

Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.

Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P.

Nucleic Acids Res. 2005 Oct 19;33(18):5914-23. Print 2005.

8.

Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments.

Benovoy D, Kwan T, Majewski J.

Nucleic Acids Res. 2008 Aug;36(13):4417-23. doi: 10.1093/nar/gkn409. Epub 2008 Jul 2.

9.

Development and application of bovine and porcine oligonucleotide arrays with protein-based annotation.

Garbe JR, Elsik CG, Antoniou E, Reecy JM, Clark KJ, Venkatraman A, Kim JW, Schnabel RD, Michael Dickens C, Wolfinger RD, Fahrenkrug SC, Taylor JF.

J Biomed Biotechnol. 2010;2010:453638. doi: 10.1155/2010/453638. Epub 2010 Dec 14.

10.

ProbeLynx: a tool for updating the association of microarray probes to genes.

Roche FM, Hokamp K, Acab M, Babiuk LA, Hancock RE, Brinkman FS.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W471-4.

11.

Single nucleotide mismatch analysis using oligonucleotide probes synthesized on bacterial magnetic particle.

Ota H, Arakaki A, Tanaka T, Takeyama H, Matsunaga T.

Biomol Eng. 2003 Jul;20(4-6):305-9.

PMID:
12919813
12.

BASH: a tool for managing BeadArray spatial artefacts.

Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG.

Bioinformatics. 2008 Dec 15;24(24):2921-2. doi: 10.1093/bioinformatics/btn557. Epub 2008 Oct 25.

13.

Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays.

Li J, Spletter ML, Johnson JA.

Physiol Genomics. 2005 Mar 21;21(1):43-58. Epub 2004 Dec 21.

14.

OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling.

Tolstrup N, Nielsen PS, Kolberg JG, Frankel AM, Vissing H, Kauppinen S.

Nucleic Acids Res. 2003 Jul 1;31(13):3758-62.

15.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J.

BMC Genomics. 2008 Nov 7;9:529. doi: 10.1186/1471-2164-9-529. Erratum in: BMC Genomics. 2009 Mar 23;10. doi: 10.1186/1471-2164-10-121.

16.

Statistical methods of background correction for Illumina BeadArray data.

Xie Y, Wang X, Story M.

Bioinformatics. 2009 Mar 15;25(6):751-7. doi: 10.1093/bioinformatics/btp040. Epub 2009 Feb 4.

17.

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data.

Yin J, McLoughlin S, Jeffery IB, Glaviano A, Kennedy B, Higgins DG.

BMC Genomics. 2010 Jan 20;11:50. doi: 10.1186/1471-2164-11-50.

19.

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.

Dufour YS, Wesenberg GE, Tritt AJ, Glasner JD, Perna NT, Mitchell JC, Donohue TJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W321-5. doi: 10.1093/nar/gkq517. Epub 2010 Jun 6.

20.

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.

Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F.

Nucleic Acids Res. 2005 Nov 10;33(20):e175.

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