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Items: 1 to 20 of 88

1.

Model-based analysis of two-color arrays (MA2C).

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS.

Genome Biol. 2007;8(8):R178.

2.

Analysis of the quality of contact-pin fabricated oligonucleotide microarrays.

Yang AX, Mejido J, Bhattacharya B, Petersen D, Han J, Kawasaki ES, Puri RK.

Mol Biotechnol. 2006 Nov;34(3):303-15.

PMID:
17284778
3.

Error-correcting properties of the SOLiD Exact Call Chemistry.

Massingham T, Goldman N.

BMC Bioinformatics. 2012 Jun 22;13:145. doi: 10.1186/1471-2105-13-145.

4.

CGHPRO -- a comprehensive data analysis tool for array CGH.

Chen W, Erdogan F, Ropers HH, Lenzner S, Ullmann R.

BMC Bioinformatics. 2005 Apr 5;6:85.

5.

Assessing the need for sequence-based normalization in tiling microarray experiments.

Royce TE, Rozowsky JS, Gerstein MB.

Bioinformatics. 2007 Apr 15;23(8):988-97. Epub 2007 Mar 25.

PMID:
17387113
6.

Normalization and centering of array-based heterologous genome hybridization based on divergent control probes.

Darby BJ, Jones KL, Wheeler D, Herman MA.

BMC Bioinformatics. 2011 May 21;12:183. doi: 10.1186/1471-2105-12-183.

7.

Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays.

Lahti L, Elo LL, Aittokallio T, Kaski S.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):217-25. doi: 10.1109/TCBB.2009.38.

PMID:
21071809
8.

Efficient oligonucleotide probe selection for pan-genomic tiling arrays.

Phillippy AM, Deng X, Zhang W, Salzberg SL.

BMC Bioinformatics. 2009 Sep 16;10:293. doi: 10.1186/1471-2105-10-293.

9.

The distribution and deposition algorithm for multiple oligo nucleotide arrays.

Ning K, Leong HW.

Genome Inform. 2006;17(2):89-99.

PMID:
17503382
10.

Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods.

GuhaThakurta D, Palomar L, Stormo GD, Tedesco P, Johnson TE, Walker DW, Lithgow G, Kim S, Link CD.

Genome Res. 2002 May;12(5):701-12. Erratum in: Genome Res 2002 Aug;12(8):1301.

11.

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.

Kauffmann A, Gentleman R, Huber W.

Bioinformatics. 2009 Feb 1;25(3):415-6. doi: 10.1093/bioinformatics/btn647. Epub 2008 Dec 23.

12.

Functional normalization of 450k methylation array data improves replication in large cancer studies.

Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD.

Genome Biol. 2014 Dec 3;15(12):503. doi: 10.1186/s13059-014-0503-2.

13.

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.

McCall MN, Jaffee HA, Irizarry RA.

Bioinformatics. 2012 Dec 1;28(23):3153-4. doi: 10.1093/bioinformatics/bts588. Epub 2012 Oct 7.

14.

HAT: a novel statistical approach to discover functional regions in the genome.

Taskesen E, Wouters B, Delwel R.

Methods Mol Biol. 2013;1067:125-41. doi: 10.1007/978-1-62703-607-8_9.

PMID:
23975790
15.

TiArA: a virtual appliance for the analysis of Tiling Array data.

Greenbaum JA, Assarsson E, Chung JL, Head S, Sette A, Peters B.

PLoS One. 2010 Apr 1;5(4):e9993. doi: 10.1371/journal.pone.0009993.

16.

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ, Smith L, Greenfield A, Tiganescu A, Buckle V, Ventress N, Ayyub H, Salhan A, Pedraza-Diaz S, Broxholme J, Ragoussis J, Higgs DR, Flint J, Knight SJ.

Nucleic Acids Res. 2005 Jun 16;33(11):3455-64. Print 2005.

18.

Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays.

Thomassen GO, Rowe AD, Lagesen K, Lindvall JM, Rognes T.

PLoS One. 2009 Jun 17;4(6):e5943. doi: 10.1371/journal.pone.0005943.

19.

Comparison of sequence-dependent tiling array normalization approaches.

Chung HR, Vingron M.

BMC Bioinformatics. 2009 Jun 30;10:204. doi: 10.1186/1471-2105-10-204.

20.

Microarray data quality control improves the detection of differentially expressed genes.

Kauffmann A, Huber W.

Genomics. 2010 Mar;95(3):138-42. doi: 10.1016/j.ygeno.2010.01.003. Epub 2010 Jan 14. Review.

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