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Linear model for fast background subtraction in oligonucleotide microarrays.

Kroll KM, Barkema GT, Carlon E.

Algorithms Mol Biol. 2009 Nov 16;4:15.PMID: 19917117 [PubMed]Free PMC ArticleFree textRelated citations

The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.

Hooyberghs J, Van Hummelen P, Carlon E.

Nucleic Acids Res. 2009 Apr;37(7):e53. Epub 2009 Mar 6.PMID: 19270064 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modeling background intensity in DNA microarrays.

Kroll KM, Barkema GT, Carlon E.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jun;77(6 Pt 1):061915. Epub 2008 Jun 18.PMID: 18643308 [PubMed - indexed for MEDLINE]Related citations

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.

Fasold M, Stadler PF, Binder H.

BMC Bioinformatics. 2010 Apr 27;11:207.PMID: 20423484 [PubMed - in process]Free PMC ArticleFree textRelated citations

Non-linear analysis of GeneChip arrays.

Abdueva D, Skvortsov D, Tavaré S.

Nucleic Acids Res. 2006;34(15):e105. Epub 2006 Aug 26.PMID: 16936321 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Background correction using dinucleotide affinities improves the performance of GCRMA.

Gharaibeh RZ, Fodor AA, Gibas CJ.

BMC Bioinformatics. 2008 Oct 23;9:452.PMID: 18947404 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data.

Chen Z, McGee M, Liu Q, Kong M, Deng Y, Scheuermann RH.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S19.PMID: 19594878 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.

Furusawa C, Ono N, Suzuki S, Agata T, Shimizu H, Yomo T.

Bioinformatics. 2009 Jan 1;25(1):36-41. Epub 2008 Oct 31.PMID: 18977779 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

A competitive hybridization model predicts probe signal intensity on high density DNA microarrays.

Li S, Pozhitkov A, Brouwer M.

Nucleic Acids Res. 2008 Nov;36(20):6585-91. Epub 2008 Oct 18.PMID: 18931378 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization.

Binder H, Brücker J, Burden CJ.

J Phys Chem B. 2009 Mar 5;113(9):2874-95.PMID: 19708217 [PubMed - indexed for MEDLINE]Related citations

Nonspecific Hybridization Scaling of Microarray Expression Estimates: A Physicochemical Approach for Chip-to-Chip Normalization.

Binder H, Brücker J, J Burden C.

J Phys Chem B. 2009 Feb 9. [Epub ahead of print]PMID: 19203216 [PubMed - as supplied by publisher]Related citations

On the relationship between perfect matches and mismatches in Affymetrix Genechips.

Ferrantini A, Carlon E.

Gene. 2008 Oct 1;422(1-2):1-6. Epub 2008 Jun 14.PMID: 18621117 [PubMed - indexed for MEDLINE]Related citations

Inverse Langmuir method for oligonucleotide microarray analysis.

Mulders GC, Barkema GT, Carlon E.

BMC Bioinformatics. 2009 Feb 20;10:64.PMID: 19232092 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Physical-chemistry-based analysis of affymetrix microarray data.

Heim T, Tranchevent LC, Carlon E, Barkema GT.

J Phys Chem B. 2006 Nov 16;110(45):22786-95.PMID: 17092029 [PubMed - indexed for MEDLINE]Related citations

Incorporating pathway information into boosting estimation of high-dimensional risk prediction models.

Binder H, Schumacher M.

BMC Bioinformatics. 2009 Jan 13;10:18.PMID: 19144132 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

"Hook"-calibration of GeneChip-microarrays: theory and algorithm.

Binder H, Preibisch S.

Algorithms Mol Biol. 2008 Aug 29;3:12.PMID: 18759985 [PubMed]Free PMC ArticleFree textRelated citations

Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data.

Gray DM, Gray CW, Yoo BH, Lou TF.

BMC Bioinformatics. 2010 May 14;11:252.PMID: 20470414 [PubMed - in process]Free PMC ArticleFree textRelated citations

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution.

Silver JD, Ritchie ME, Smyth GK.

Biostatistics. 2009 Apr;10(2):352-63. Epub 2008 Dec 8.PMID: 19068485 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Model-based probe set optimization for high-performance microarrays.

Leparc GG, Tüchler T, Striedner G, Bayer K, Sykacek P, Hofacker IL, Kreil DP.

Nucleic Acids Res. 2009 Feb;37(3):e18. Epub 2008 Dec 22.PMID: 19103659 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Fast minimization of structural risk by nearest neighbor rule.

Karacali B, Krim H.

IEEE Trans Neural Netw. 2003;14(1):127-37.PMID: 18237996 [PubMed - in process]Related citations