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

Physical Biology

Volumn 7, Issue 1, 2010, Pages

  Burden, Conrad J ^a   Binder, Hans ^b  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL MODEL; DNA MICROARRAY; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; PHYSICAL CHEMISTRY;

MODELS, CHEMICAL; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYSICOCHEMICAL PHENOMENA;

EID: 75449110420     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/7/1/016004     Document Type: Article

References (30)

1. http://www.affymetrix.com/support/technical/sample-data/datasets.affx
2. http://cran.r-project.org/
3. http://wwwmaths.anu.edu.au/cbis/̃conrad/Spike-in-Isotherms
4. http://www.izbi.uni-leipzig.de/englisch/downloads-links/programs/hook. php?group=links
5. Binder H 2006 Thermodynamics of competitive surface adsorption on DNA microarrays J. Phys.: Condens. Matter 18 S491-523
6. Binder H, Brückner J and Burden C J 2009 Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization J. Phys. Chem. B 113 2874-95
7. Binder H, Kirsten T, Loeffler M and Stadler P F 2004 Sensitivity of microarray oligonucleotide probes: variability and effect of base composition J. Phys. Chem. 108 18003-14
8. Binder H, Krohn K and Preibisch S 2008 'Hook'-calibration of genechip microarrays: chip characteristics and expression measures Algorithms Mol. Biol. 3 11
9. Binder H and Preibisch S 2005 Specific and nonspecific hybridization of oligonucleotide probes on microarrays Biophys. J. 89 337-52
10. Binder H and Preibisch S 2006 Genechip microarrays-signal intensities, RNA concentrations and probe intensities J. Phys.: Condens. Matter 18 S537-66
11. Binder H and Preibisch S 2008 'Hook'-calibration of genechip microarrays: theory and algorithm Algorithms Mol. Biol. 3 12
12. Binder H, Preibisch S and Berger H 2009 Calibration of microarray gene-expression data Methods Mol. Biol. 576 375-407
13. Burden C J 2009 Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed Phys. Biol. 5 016004
14. Burden C J, Pittelkow Y E and Wilson S R 2004 Statistical analysis of adsorption models for oligonucleotide microarrays Stat. Appl. Genet. Mol. Biol. 3 Article 35
15. Burden C J, Pittelkow Y E and Wilson S R 2006 Adsorption models of hybridisation and post-hybridisation behaviour on oligonucleotide microarrays J. Phys.: Condens. Matter 18 5545-65
16. Carlon E and Heim T 2006 Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays Physica A 362 433-49
17. Heim T, Tranchevent L-C, Carlon E and Barkema G T 2006 Physical-chemistry-based analysis of Affymetrix microarray data J. Phys. Chem. B 110 22786-95
18. Heim T, Wolterink J Klein, Carlon E and Barkema G T 2006 Effective affinities in microarray data J. Phys.: Condens. Matter 18 S525-36
19. Hekstra D, Taussig A R, Magnasco M and Naef F 2003 Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays Nucleic Acids Res. 31 1962-8
20. Held G A, Grinstein G and Tu Y 2003 Modeling of DNA microarray data by using physical properties of hybridization Proc. Natl Acad. Sci. 100 7575-80
21. Held G A, Grinstein G and Tu Y 2006 Relationship between gene expression and observed intensities in DNA microarrays-a model study Nucleic Acids Res. 34 e70
22. Kroll K M, Barkema G T and Carlon E 2008 Modeling background intensity in DNA microarrays Phys. Rev. E 77 061915
23. Li S, Pozhitkov A and Brouwer M 2008 A competitive hybridization model predicts probe signal intensity on high density DNA micorarrays Nucleic Acids Res. 36 6585-91
24. McCullagh P and Nelder J A 1989 Generalized Linear Models 2nd edn (London: Chapman and Hall)
25. Mulders G C W M, Barkema G T and Carlon E 2009 Inverse langmuir method for oligonucleotide microarray analysis BMC Bioinformatics 10 64
26. Nguyen K 2009 Extended investigations in the physics of oligonucleotide microarrays ANU Undergrad. Res. J. 1 29-38
27. Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, Shimizu H and Yomo T 2008 An improved physico-chemical model of hybridization on high-density oligonuclotide micoarrays Bioinformatics 24 1278-85
28. SantaLucia J 1998 A unified view of polymer, dumbbell and oligonucleotide DNA nearest neighbour thermodynamics Proc. Natl. Acad. Sci. 95 1460-5
29. Skvortsov D, Abdueva D, Curtis C, Schaub B and Tavaré S 2007 Explaining differences in saturation levels for Affymetrix Genechiparrays Nucleic Acids Res. 35 4154-63
30. Suzuki S, Ono N, Furusawa C, Kashiwagi A and Yomo T 2007 Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays BMC Genomics 8 373