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

Binder H, Preibisch S.

Algorithms Mol Biol. 2008 Aug 29;3:12.PMID: 18759985 [PubMed]Related articlesFree article

"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures.

Binder H, Krohn K, Preibisch S.

Algorithms Mol Biol. 2008 Aug 29;3:11.PMID: 18759984 [PubMed]Related articlesFree article

Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays.

Binder H, Preibisch S, Kirsten T.

Langmuir. 2005 Sep 27;21(20):9287-302.PMID: 16171364 [PubMed - indexed for MEDLINE]Related articles

Calibration of microarray gene-expression data.

Binder H, Preibisch S, Berger H.

Methods Mol Biol. 2010;576:375-407.PMID: 19882273 [PubMed - indexed for MEDLINE]Related articles

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 articles

Specific and nonspecific hybridization of oligonucleotide probes on microarrays.

Binder H, Preibisch S.

Biophys J. 2005 Jul;89(1):337-52. Epub 2005 Apr 15.PMID: 15834006 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimation and correction of non-specific binding in a large-scale spike-in experiment.

Schuster EF, Blanc E, Partridge L, Thornton JM.

Genome Biol. 2007;8(6):R126.PMID: 17594493 [PubMed - indexed for MEDLINE]Related articlesFree article

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 articles

Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips.

Wang Y, Miao ZH, Pommier Y, Kawasaki ES, Player A.

Bioinformatics. 2007 Aug 15;23(16):2088-95. Epub 2007 Jun 6.PMID: 17553856 [PubMed - indexed for MEDLINE]Related articlesFree article

Quantitative oligonucleotide microarray data analysis with an artificial standard probe strategy.

Hwang BH, Cha HJ.

Biosens Bioelectron. 2008 Jun 15;23(11):1738-44. Epub 2008 Feb 7.PMID: 18337080 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

Mismatch and G-stack modulated probe signals on SNP microarrays.

Binder H, Fasold M, Glomb T.

PLoS One. 2009 Nov 17;4(11):e7862.PMID: 19924253 [PubMed - in process]Related articlesFree article

Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.

Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD.

PLoS One. 2009;4(3):e4702. Epub 2009 Mar 11.PMID: 19277110 [PubMed - indexed for MEDLINE]Related articlesFree article

A white-box approach to microarray probe response characterization: the BaFL pipeline.

Thompson KJ, Deshmukh H, Solka JL, Weller JW.

BMC Bioinformatics. 2009 Dec 29;10:449.PMID: 20040098 [PubMed - in process]Related articlesFree article

Explaining differences in saturation levels for Affymetrix GeneChip arrays.

Skvortsov D, Abdueva D, Curtis C, Schaub B, Tavaré S.

Nucleic Acids Res. 2007;35(12):4154-63. Epub 2007 Jun 12.PMID: 17567617 [PubMed - indexed for MEDLINE]Related articlesFree article

Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays.

Burden CJ, Binder H.

Phys Biol. 2009 Dec 21;7(1):016004.PMID: 20026877 [PubMed - indexed for MEDLINE]Related articles

Statistical analysis of adsorption models for oligonucleotide microarrays.

Burden CJ, Pittelkow YE, Wilson SR.

Stat Appl Genet Mol Biol. 2004;3:Article35. Epub 2004 Dec 9.PMID: 16646815 [PubMed]Related articlesFree article

Thermodynamic scaling behavior in genechips.

Ferrantini A, Allemeersch J, Van Hummelen P, Carlon E.

BMC Bioinformatics. 2009 Jan 6;10:3.PMID: 19123958 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article