Relevant Publications

1. Arteaga-Salas JM, Harrison AP, Upton GJ. Reducing spatial flaws in oligonucleotide arrays by using neighborhood information.  Stat Appl Genet Mol Biol. 2008. 7:29. [pdf]

2. Arteaga-Salas JM, Zuzan H, Langdon WB, Upton GJ, Harrison AP. An overview of image-processing methods for Affymetrix GeneChips.  Brief Bioinform. 2007. 9:25-33. [pdf]

3. Auburn, RP; Kreil, DP; Meadows, LA; Fischer, B; Matilla, SS; Russell, S. Robotic spotting of cDNA and oligonucleotide microarrays.  Trends in Biotechnology. 2005. 23:374-379. [pdf]

4. Binder H, Brücker J, Burden CJ. Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization.  J Phys Chem B. 2009. 113:2874-2895. [pdf]

5. Binder H, Fasold M, Glomb T. Mismatch and G-stack modulated probe signals on SNP microarrays.  PLoS One. 2009. 4:e7862. [pdf]

6. Binder H, Krohn K, Burden CJ. Washing scaling of GeneChip microarray expression.  BMC Bioinformatics. 2010. 11:291. [pdf]

7. Binder H, Preibisch S, Berger H. Calibration of microarray gene-expression data.  Methods Mol Biol. 2007. 576:375-407. [pdf]

8. Binder H, Preibisch S. Hook-calibration of GeneChip-microarrays: theory and algorithm.  Algorithms Mol Biol. 2008. 3:12. [pdf]

9. Binder H, Preibisch S. Hook-calibration of GeneChip-microarrays: Chip characteristic and expression measures.  Algorithms Mol Biol. 2008. 3:11. [pdf]

10. Binder H, Wirth H, Galle J. Gene expression density profiles characterize modes of genomic regulation: Theory and experiment.  J Biotechnol. 2010 149:98-114. [pdf]

11. Burden C, Pittlekow Y, Wilson S. Adsorption models of hybridisation and post-hybridisation behaviour on oligonucleotide microarrays.  Journal of Physics: Condensed Matter 2006, 18:5545 - 5565. [pdf]

12. Burden CJ, Binder H. Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays.  Phys Biol. 2009. 7:016004. [pdf]

13. Burden CJ, Pittelkow YE, Wilson SR. Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays.  Stat App in Gen and Mol Biol 2004. 3:35. [pdf]

14. Burden CJ. Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed.  Physical Biology 2008, 5:016004. [pdf]

15. Carlon E, Heim T, Wolterink JK, Barkema GT. Comment on "Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays".  Phys Rev E Stat Nonlin Soft Matter Phys. 2006. 73:063901. [pdf]

16. Carlon E, Heim T. Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays.  Physica A 2006. 362:433–449. [pdf]

17. Dandy DS, Wu P, Grainger DW. Array feature size influences nucleic acid surface capture in DNA microarrays.  Proc Natl Acad Sci U S A. 2007. 104:8223-8. [pdf]

18. Fasold M, Stadler PF, Binder H. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.  BMC Bioinformatics. 2010. 11:207. [pdf]

19. Ferrantini A, Allemeersch J, Van Hummelen P, Carlon E. Thermodynamic scaling behavior in genechips.  BMC Bioinformatics. 2009. 10:3. [pdf]

20. Ferrantini A, Carlon E. On the relationship between perfect matches and mismatches in Affymetrix Genechips.  Gene. 2008. 422:1-6. [pdf]

21. Fuchs J, Dell'Atti D, Buhot A, Calemczuk R, Mascini M, Livache T. Effects of formamide on the thermal stability of DNA duplexes on biochips.  Anal Biochem. 2010. 397:132-4. [pdf]

22. Fuchs J, Fiche JB, Buhot A, Calemczuk R, Livache T. Salt concentration effects on equilibrium melting curves from DNA microarrays.  Biophys J. 2010. 99:1886-95. [pdf]

23. Gong P, Harbers GM, Grainger DW. Multi-technique Comparison of Immobilized and Hybridized Oligonucleotide Surface Density on Commercial Amine-Reactive Microarray Slides.  Anal. Chem. 2006. 78:2342-2351. [pdf]

24. Gong P, Levicky R. DNA surface hybridization regimes.  Proc Natl Acad Sci U S A. 2008. 105:5301-5306. [pdf]

25. Gong P, Wang K, Liu Y, Shepard K, Levicky R. Molecular mechanisms in morpholino-DNA surface hybridization.  J Am Chem Soc. 2010. 132:9663-9671. [pdf]

26. Halperin A, Buhot A, Zhulina EB. 2005. Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines.  Biophys J. 89:796-811. [pdf]

27. Halperin A, Buhot A, Zhulina EB. Hybridization at a surface: the role of spacers in DNA microarrays.  Langmuir. 2006. 22:11290-11304. [pdf]

28. Halperin A, Buhot A, Zhulina EB. Hybridization isotherms of DNA microarrays and the quantification of mutation studies.  Clin Chem. 2004. 50:2254-2262. [pdf]

29. Halperin A, Buhot A, Zhulina EB. On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions.  J. Phys.: Condens. Matter 2006. 18: S463–S490. [pdf]

30. Halperin A, Buhot A, Zhulina EB. Sensitivity, specificity, and the hybridization isotherms of DNA chips.  Biophys J. 2004. 86:718-730. [pdf]

31. Halperin A, Zhulina EB. Atomic force microscopy of polymer brushes: colloidal versus sharp tips.  Langmuir. 2010. 26:8933-8940. [pdf]

32. Harrison AP, Johnston CE, Orengo CA. Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips.  BMC Bioinformatics. 2007. 8:195. [pdf]

33. Harrison AP, Rowsell J, da Silva Camargo R, Langdon WB, Stalteri M, Upton GJ, Arteaga-Salas JM. The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA.  Biochem Soc Trans. 2008. 36:511-513. [pdf]

34. Heim T, Tranchevent LC, Carlon E, Barkema GT. Physical-chemistry-based analysis of affymetrix microarray data.  J Phys Chem B. 2006. 110:22786-22795. [pdf]

35. Heim T, Wolterink JK, Carlon E, Barkema GT. Effective affinities in microarray data.  J Phys Cond. Matter. 2006. 18:S525-S536. [pdf]

36. Hooyberghs J, Baiesi M, Ferrantini A, Carlon E. Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays.  Phys Rev E Stat Nonlin Soft Matter Phys. 2010. 81:012901. [pdf]

37. Hooyberghs J, Van Hummelen P, Carlon E. The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.  Nucleic Acids Res. 2009. 37:e53. [pdf]

38. Howard JJ, Perkyns JS, Pettitt BM. The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge.  J Phys Chem B. 2010. 114:6074-6083. [pdf]

39. Huang TC, Paul S, Gong P, Levicky R, Kymissis J, Amundson SA, Shepard KL. Gene expression analysis with an integrated CMOS microarray by time-resolved fluorescence detection.  Biosens Bioelectron. 2010. [pdf]

40. Huang TC, Sorgenfrei S, Gong P, Levicky R, Shepard KL. A 0.18-microm CMOS Array Sensor for Integrated Time-Resolved Fluorescence Detection.  IEEE J Solid-State Circuits. 2009. 44:1644-1654. [pdf]

41. Huettel B, Kreil DP, Matzke M, Matzke AJ. Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.  PLoS Genet. 2008. 4:e1000226. [pdf]

42. Irving D, Gong P, Levicky R. DNA surface hybridization: comparison of theory and experiment.  J Phys Chem B. 2010. 114:7631-7640. [pdf]

43. Kreil, DP; Karp, NA; Lilley, KS. DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results.  Bioinformatics. 2004. 20:2026-2034. [pdf]

44. Kreil, DP, Russell, RR, Inference Grp. There is no silver bullet - a guide to low-level data transforms and normalisation methods for microarray data.  Briefings In Bioinformatics. 2005, 6:86-97. [pdf]

45. Kroll KM, Barkema GT, Carlon E. Linear model for fast background subtraction in oligonucleotide microarrays.  Algorithms Mol Biol. 2009. 4:15. [pdf]

46. Kroll KM, Barkema GT, Carlon E. Modeling background intensity in DNA microarrays.  Phys Rev E Stat Nonlin Soft Matter Phys. 2008. 77:061915. [pdf]

47. Langdon WB, Upton GJ, Harrison AP. Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips.  Brief Bioinform. 2009. 10:259-277. [pdf]

48. Lee CY, Harbers GM, Grainger DW, Gamble LJ, Castner DG. Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays.  J Am Chem Soc. 2007. 129:9429-38. [pdf]

49. Leparc GG, Tuechler T, Striedner G, Bayer K, Sykacek P, Hofacker IL, Kreil DP. Model-based probe set optimization for high-performance microarrays.  Nucleic Acids Research. 2009. 37 (3):Article No.: e18. [pdf]

50. Levicky R, Horgan A. Physicochemical perspectives on DNA microarray and biosensor technologies.  Trends Biotechnol. 2005. 23:143-149. [pdf]

51. Levine PM, Gong P, Levicky R, Shepard KL. Real-time, multiplexed electrochemical DNA detection using an active complementary metal-oxide-semiconductor biosensor array with integrated sensor electronics.  Biosens Bioelectron. 2009. 24:1995-2001. [pdf]

52. Li S, Pozhitkov A, Brouwer M. A competitive hybridization model predicts signal intensity on high density DNA microarrays.  Nucl Acids Res 2008. 20:6585-6591. [pdf]

53. Memon FN, Owen AM, Sanchez-Graillet O, Upton GJ, Harrison AP. Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.  J Integr Bioinform. 2010. 7:111. [pdf]

54. Michel W, Mai T, Naiser T, Ott A. Optical study of DNA surface hybridization reveals DNA surface density as a key parameter for microarray hybridization kinetics.  Biophys J. 2007. 92:999-1004. [pdf]

55. Mueckstein U, Leparc GG, Posekany A, Hofacker I, Kreil DP. Hybridization thermodynamics of NimbleGen Microarrays.  BMC Bioinformatics 2010, 11, art.no.-35. [pdf]

56. Mulders GC, Barkema GT, Carlon E. Inverse Langmuir method for oligonucleotide microarray analysis.  BMC Bioinformatics. 2009. 10:64. [pdf]

57. Naiser T, Ehler O, Kayser J, Mai T, Michel W, Ott A. Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: comparison of single base mismatches and base bulges.  BMC Biotechnol. 2008. 8:48. [pdf]

58. Naiser T, Kayser J, Mai T, Michel W, Ott A. Position dependent mismatch discrimination on DNA microarrays - experiments and model.  BMC Bioinformatics. 2008. 9:509. [pdf]

59. Naiser T, Kayser J, Mai T, Michel W, Ott A. Stability of a surface-bound oligonucleotide duplex inferred from molecular dynamics: a study of single nucleotide defects using DNA microarrays.  Phys Rev Lett. 2009. 102:218301. [pdf]

60. Pozhitkov A, Chernov B, Yershov G, Noble PA. Evaluation of gel-pad oligonucleotide microarray technology using artificial neural networks.  Appl Environ Microbiol 2005. 71:8663-8676. [pdf]

61. Pozhitkov A, Noble PA, Domazet-Loso T, Nolte AW, Sonnenberg R, Staehler P, Beier M, Tautz D. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted.  Nucl. Acids Res. 2006. 34:e66. [pdf]

62. Pozhitkov AE, Bailey KD, Noble PA. Development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays.  J Microbiol Methods 2007. 70:292-300. [pdf]

63. Pozhitkov AE, Boube I, Brouwer MH, Noble PA. Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.  Nucl Acids Res 2010. 38:e28. [pdf]

64. Pozhitkov AE, Nies G, Kleinhenz B, Tautz D, Noble PA. Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of information.  J Microbiol Methods 2008. 75:92-102. [pdf]

65. Pozhitkov AE, Noble PA. Comment on "Discrimination of shifts in a soil microbial community associated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays".  Environ Sci Technol 2007. 41:1797-1798. [pdf]

66. Pozhitkov AE, Noble PA. High variability in melting profiles from gel pad arrays.  Environ Microbiol 2007. 9:1865. [pdf]

67. Pozhitkov AE, Rule RA, Stedtfeld RD, Hashsham SA, Noble PA. Concentration dependency of nonequilibrium thermal dissociation curves in complex target samples.  J Microbiol Methods 2008. 74:82-88. [pdf]

68. Pozhitkov AE, Stedtfeld RD, Hashsham SA, Noble PA. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays.  Nucleic Acids Res 2007. 35:e70. [pdf]

69. Pozhitkov AE, Tautz D, Noble PA. Oligonucleotide microarrays: widely applied-poorly understood.  Brief Funct Genomic Proteomic 2007. 6:141-148. [pdf]

70. Pozhitkov AE. Scanner calibration revisited.  BMC Bioinformatics 2011. 11: 361. [pdf]

71. Qamhieh K, Wong KY, Lynch GC, Pettitt BM. The melting mechanism of DNA techered to a surface.  Int J Numer Anal Model. 2009. 6:474-488. [pdf]

72. Rowsell J, da Silva Camargo R, Langdon WB, Stalteri MA, Harrison AP. Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips.  J Integr Bioinform. 2010. 7: doi: 10.2390/biecoll-jib-2010-137. [pdf]

73. Rule RA, Pozhitkov AE, Noble PA. Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixtures.  J Microbiol Methods 2009. 76:188-195. [pdf]

74. Sanchez-Graillet O, Rowsell J, Langdon WB, Stalteri M, Arteaga-Salas JM, Upton GJ, Harrison AP. Widespread existence of uncorrelated probe intensities from within the same probeset on Affymetrix GeneChips.  J Integr Bioinform. 2008. 5: doi: 10.2390/biecoll-jib-2008-98. [pdf]

75. Sanchez-Graillet O, Stalteri MA, Rowsell J, Upton GJ, Harrison AP. Using surveys of Affymetrix GeneChips to study antisense expression.  J Integr Bioinform. 2010. 7: doi: 10.2390/biecoll-jib-2010-114. [pdf]

76. Shen G, Anand MF, Levicky R. X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides.  Nucleic Acids Res. 2004. 32:5973-5980. [pdf]

77. Shen G, Tercero N, Gaspar MA, Varughese B, Shepard K, Levicky R. Charging behavior of single-stranded DNA polyelectrolyte brushes.  J Am Chem Soc. 2006. 128:8427-8433. [pdf]

78. Stalteri MA, Harrison AP. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips.  BMC Bioinformatics. 2007. 8:13. [pdf]

79. Tercero N, Wang K, Gong P, Levicky R. Morpholino monolayers: preparation and label-free DNA analysis by surface hybridization.  J Am Chem Soc. 2009. 131:4953-4961. [pdf]

80. Tercero N, Wang K, Levicky R. Capacitive Monitoring of Morpholino-DNA Surface hybridization: experimental and theoretical analysis.  Langmuir. 2010. 114:7631–7640. [pdf]

81. Upton GJ, Langdon WB, Harrison AP. G-spots cause incorrect expression measurement in Affymetrix microarrays.  BMC Genomics. 2008. 9:613. [pdf]

82. Upton GJ, Sanchez-Graillet O, Rowsell J, Arteaga-Salas JM, Graham NS, Stalteri MA, Memon FN, May ST, Harrison AP. On the causes of outliers in Affymetrix GeneChip data.  Brief Funct Genomic Proteomic. 2009. 8:199-212. [pdf]

83. Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays.  Appl Environ Microbiol 2003. 69:2848-2856. [pdf]

84. Urakawa H, Noble PA, El Fantroussi S, Kelly JJ, Stahl DA. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses.  Appl Environ Microbiol 2002. 68:235-244. [pdf]

85. Vainrub A, Pettitt BM. Sensitive quantitative nucleic acid detection using oligonucleotide microarrays.  J Am Chem Soc. 2003. 125:7798-7799. [pdf]

86. Vainrub A, Pettitt BM. Surface electrostatic effects in oligonucleotide microarrays: Control and optimization of binding thermodynamics.  Biopolymers. 2003. 68:265-270. [pdf]

87. Vainrub A, Pettitt BM. Theoretical aspects of genomic variation screening using DNA microarrays.  Biopolymers. 2004. 73:614-620. [pdf]

88. Weckx S, Carlon E, DeVuyst L, Van Hummelen P. Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model.  J Phys Chem B. 2007. 111:13583-13590. [pdf]

89. Wu P, Castner DG, Grainger DW. Diagnostic devices as biomaterials: a review of nucleic acid and protein microarray surface performance issues.  J Biomater Sci Polym Ed. 2008. 19:725-53. [pdf]