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. 2008:629–657. doi: 10.1007/978-0-387-75113-9_23

Oligonucleotide and DNA Microarrays: Versatile Tools for Rapid Bacterial Diagnostics

Tanja Kostic 4, Patrice Francois 5, Levente Bodrossy 4, Jacques Schrenzel 6
Editors: Mohammed Zourob1, Souna Elwary2, Anthony Turner3
PMCID: PMC7121292

Abstract

The rapid and unambiguous detection and identification of microorganisms, historically a major challenge of clinical microbiology, gained additional importance in the fields of public health and biodefence. These requirements cannot be well addressed by classical culture-based approaches. Therefore, a wide range of molecular approaches has been suggested. Microarrays are molecular tools that can be used for simultaneous identification of microorganisms in clinical and environmental samples. Main advantages of microarrays are high throughput, parallelism and miniaturization of the detection system. Furthermore, they allow for both high specificity and high sensitivity of the detection.

Microarrays consist of set of probes immobilized on a solid surface. Even though the first application of the microarrays can be seen as relatively recent (Schena et al. 1995), the technology developed rapidly reaching the milestone of 5,000 published papers in 2004 (Holzman and Kolker 2004). This development encompasses both the successful transfer of various technological aspects as well as the expansion of the application scope. The most important technological elements of custom-made platforms as well as the characteristics of the commercially available formats are reviewed in this chapter. Furthermore, application potential is presented together with considerations about quality control.

Keywords: Oligonucleotide Microarrays, Oligonucleotide Array, Resonance Light Scattering, Massively Parallel Signature Sequencing, Appl Environ

Contributor Information

Mohammed Zourob, Email: m.zourob@biophagepharma.net.

Souna Elwary, Email: selwary@yahoo.com.

Anthony Turner, Email: a.p.turner@cranfield.ac.uk.

References

  1. Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol. 2003;69:6875–6887. doi: 10.1128/AEM.69.11.6875-6887.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ahn HJ, La HJ, Forney LJ. System for determining the relative fitness of multiple bacterial populations without using selective markers. Appl Environ Microbiol. 2006;72:7383–7385. doi: 10.1128/AEM.01246-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Aitman TJ. DNA microarrays in medical practice. BMJ. 2001;323:611–615. doi: 10.1136/bmj.323.7313.611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Albert TJ, Norton J, Ott M, Richmond T, Nuwaysir K, Nuwaysir EF, Stengele KP, Green RD. Light-directed 5′ → 3′ synthesis of complex oligonucleotide microarrays. Nucleic Acids Res. 2003;31:e35. doi: 10.1093/nar/gng035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Lu L, Jr, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503–511. doi: 10.1038/35000501. [DOI] [PubMed] [Google Scholar]
  6. Allawi HT, SantaLucia J., Jr Nearest-neighbor thermodynamics of internal AC mismatches in DNA: sequence dependence and pH effects. Biochemistry. 1998;37:9435–9444. doi: 10.1021/bi9803729. [DOI] [PubMed] [Google Scholar]
  7. Anthony RM, Brown TJ, French GL. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol. 2000;38:781–788. doi: 10.1128/jcm.38.2.781-788.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Aoyagi K, Tatsuta T, Nishigaki M, Akimoto S, Tanabe C, Omoto Y, Hayashi S, Sakamoto H, Sakamoto M, Yoshida T, Terada M, Sasaki H. A faithful method for PCR-mediated global mRNA amplification and its integration into microarray analysis on laser-captured cells. Biochem Biophys Res Commun. 2003;300:915–920. doi: 10.1016/S0006-291X(02)02967-4. [DOI] [PubMed] [Google Scholar]
  9. Armitage BA. The impact of nucleic acid secondary structure on PNA hybridization. Drug Discov Today. 2003;8:222–228. doi: 10.1016/S1359-6446(03)02611-4. [DOI] [PubMed] [Google Scholar]
  10. Bae JW, Rhee SK, Nam YD, Park YH. Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes. Nucleic Acids Res. 2005;33:e113. doi: 10.1093/nar/gni112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Bailly X, Bena G, Lajudie P, de Lenief P, Avarre JC. Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae. J Microbiol Methods. 2006;67:114–124. doi: 10.1016/j.mimet.2006.03.006. [DOI] [PubMed] [Google Scholar]
  12. Bains W, Smith GC. A novel method for nucleic acid sequence determination. J Theor Biol. 1988;135:303–307. doi: 10.1016/S0022-5193(88)80246-7. [DOI] [PubMed] [Google Scholar]
  13. Baldeschwieler JD, Gamble RC, Thierault TP. Method and apparatus for performing multiple sequential reactions on a matrix. USA: WO9525116; 1995. [Google Scholar]
  14. Ballmer K, Korczak BM, Kuhnert P, Slickers P, Ehricht R, Hachler H. Fast DNA-serotyping of Escherichia coli by oligonucleotide microarray. J Clin Microbiol. 2007;45:370–379. doi: 10.1128/JCM.01361-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ. Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res. 2003;13:1775–1785. doi: 10.1101/gr.1048803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Bavykin SG, Akowski JP, Zakhariev VM, Barsky VE, Perov AN, Mirzabekov AD. Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl Environ Microbiol. 2001;67:922–928. doi: 10.1128/AEM.67.2.922-928.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Bekal S, Brousseau R, Masson L, Prefontaine G, Fairbrother J, Harel J. Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNA microarrays. J Clin Microbiol. 2003;41:2113–2125. doi: 10.1128/JCM.41.5.2113-2125.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Blanchard AP, Friend SH. Cheap DNA arrays—it’s not all smoke and mirrors. Nat Biotechnol. 1999;17:953. doi: 10.1038/13644. [DOI] [PubMed] [Google Scholar]
  19. Blanchard AP, Kaiser RJ, Hood LE. High-density oligonucleotide arrays. Biosensors & Bioelectronics. 1996;11:687–690. doi: 10.1016/0956-5663(96)83302-1. [DOI] [Google Scholar]
  20. Bo T, Jonassen I. New feature subset selection procedures for classification of expression profiles. Genome Biol. 2002;3:RESEARCH0017. doi: 10.1186/gb-2002-3-4-research0017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Bodrossy L. Diagnostic oligonucleotide microarrays for microbiology. In: Blalock E, editor. A Beginner’s Guide to Microarrays. New York: Kluwer Academic Publishers; 2003. pp. 43–92. [Google Scholar]
  22. Bodrossy L, Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol. 2004;7:245–254. doi: 10.1016/j.mib.2004.04.005. [DOI] [PubMed] [Google Scholar]
  23. Bodrossy L, Stralis-Pavese N, Konrad-Koszler M, Weilharter A, Reichenauer TG, Schofer D, Sessitsch A. mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol. 2006;72:1672–1676. doi: 10.1128/AEM.72.2.1672-1676.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol. 2003;5:566–582. doi: 10.1046/j.1462-2920.2003.00450.x. [DOI] [PubMed] [Google Scholar]
  25. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt L, Brown PO, Relman DA. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A. 2002;99:972–977. doi: 10.1073/pnas.231625398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Borucki MK, Krug MJ, Muraoka WT, Call DR. Discrimination among Listeria monocytogenes isolates using a mixed genome DNA microarray. Vet Microbiol. 2003;92:351–362. doi: 10.1016/S0378-1135(02)00423-6. [DOI] [PubMed] [Google Scholar]
  27. Borucki MK, Reynolds J, Call DR, Ward TJ, Page B, Kadushin J. Suspension microarray with dendrimer signal amplification allows direct and high-throughput subtyping of Listeria monocytogenes from genomic DNA. J Clin Microbiol. 2005;43:3255–3259. doi: 10.1128/JCM.43.7.3255-3259.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Brennan TM, Heinecker H (1995) Methods and compositions for determining the sequence of nucleic acids. 5′474′796, USA, Ref Type: Patent
  29. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. 2000;18:630–634. doi: 10.1038/76469. [DOI] [PubMed] [Google Scholar]
  30. Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol. 2006;72:6288–6298. doi: 10.1128/AEM.00246-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Call DR, Bakko MK, Krug MJ, Roberts MC. Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob Agents Chemother. 2003;47:3290–3295. doi: 10.1128/AAC.47.10.3290-3295.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Call DR, Borucki MK, Loge FJ. Detection of bacterial pathogens in environmental samples using DNA microarrays. J Microbiol Methods. 2003;53:235–243. doi: 10.1016/S0167-7012(03)00027-7. [DOI] [PubMed] [Google Scholar]
  33. Case-Green SC, Southern EM. Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides. Nucleic Acids Res. 1994;22:131–136. doi: 10.1093/nar/22.2.131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Cassat JE, Dunman PM, McAleese F, Murphy E, Projan SJ, Smeltzer MS. Comparative genomics of Staphylococcus aureus musculoskeletal isolates. J Bacteriol. 2005;187:576–592. doi: 10.1128/JB.187.2.576-592.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Charbonnier Y, Gettler BM, Francois P, Bento M, Renzoni A, Vaudaux P, Schlegel W, Schrenzel J. A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics. 2005;6:95. doi: 10.1186/1471-2164-6-95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Chizhikov V, Rasooly A, Chumakov K, Levy DD. Microarray analysis of microbial virulence factors. Appl Environ Microbiol. 2001;67:3258–3263. doi: 10.1128/AEM.67.7.3258-3263.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Couzinet S, Jay C, Barras C, Vachon R, Vernet G, Ninet B, Jan I, Minazio MA, Francois P, Lew D, Troesch A, Schrenzel J. High-density DNA probe arrays for identification of staphylococci to the species level. J Microbiol Methods. 2005a;61:201–208. doi: 10.1016/j.mimet.2004.11.019. [DOI] [PubMed] [Google Scholar]
  38. Couzinet S, Yugueros J, Barras C, Visomblin N, Francois P, Lacroix B, Vernet G, Lew D, Troesch A, Schrenzel J, Jay C. Evaluation of a high-density oligonucleotide array for characterization of grlA, grlB, gyrA and gyrB mutations in fluoroquinolone resistant Staphylococcus aureus isolates. J Microbiol Methods. 2005b;60:275–279. doi: 10.1016/j.mimet.2004.09.015. [DOI] [PubMed] [Google Scholar]
  39. Debouck C, Goodfellow PN. DNA microarrays in drug discovery and development. Nat Genet. 1999;21:48–50. doi: 10.1038/4475. [DOI] [PubMed] [Google Scholar]
  40. Denef VJ, Park J, Rodrigues JL, Tsoi TV, Hashsham SA, Tiedje JM. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol. 2003;5:933–943. doi: 10.1046/j.1462-2920.2003.00490.x. [DOI] [PubMed] [Google Scholar]
  41. Diehl F, Grahlmann S, Beier M, Hoheisel JD. Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res. 2001;29:E38. doi: 10.1093/nar/29.7.e38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Dorrell N, Hinchliffe SJ, Wren BW. Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol. 2005;8:620–626. doi: 10.1016/j.mib.2005.08.012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Drmanac R, Crkvenjakov R (1993) Method of sequencing of genomes by hybridization of oligonucleotide probes. US1991000723712 USA, Ref Type: Patent
  44. Drmanac R, Drmanac S. cDNA screening by array hybridization. Methods Enzymol. 1999;303:165–78. doi: 10.1016/S0076-6879(99)03013-X. [DOI] [PubMed] [Google Scholar]
  45. Drmanac R, Drmanac S, Strezoska Z, Paunesku T, Labat I, Zeremski M, Snoddy J, Funkhouser WK, Koop B, Hood L. DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science. 1993;260:1649–1652. doi: 10.1126/science.8503011. [DOI] [PubMed] [Google Scholar]
  46. Drmanac S, Kita D, Labat I, Hauser B, Schmidt C, Burczak JD, Drmanac R. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat Biotechnol. 1998;16:54–58. doi: 10.1038/nbt0198-54. [DOI] [PubMed] [Google Scholar]
  47. Dunbar SA, Vander Zee CA, Oliver KG, Karem KL, Jacobson JW. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J Microbiol Methods. 2003;53:245–252. doi: 10.1016/S0167-7012(03)00028-9. [DOI] [PubMed] [Google Scholar]
  48. Duveneck GL, Bopp MA, Ehrat M, Balet LP, Haiml M, Keller U, Marowsky G, Soria S. Two-photon fluorescence excitation of macroscopic areas on planar waveguides. Biosens Bioelectron. 2003;18:503–510. doi: 10.1016/S0956-5663(03)00006-X. [DOI] [PubMed] [Google Scholar]
  49. Epstein JR, Ferguson JA, Lee KH, Walt DR. Combinatorial decoding: an approach for universal DNA array fabrication. J Am Chem Soc. 2003a;125:13753–13759. doi: 10.1021/ja0365577. [DOI] [PubMed] [Google Scholar]
  50. Epstein JR, Leung AP, Lee KH, Walt DR. High-density, microsphere-based fiber optic DNA microarrays. Biosens Bioelectron. 2003b;18:541–546. doi: 10.1016/S0956-5663(03)00021-6. [DOI] [PubMed] [Google Scholar]
  51. Epstein JR, Walt DR. Fluorescence-based fibre optic arrays: a universal platform for sensing. Chem Soc Rev. 2003;32:203–214. doi: 10.1039/b300617d. [DOI] [PubMed] [Google Scholar]
  52. Ericsson O, Sivertsson A, Lundeberg J, Ahmadian A. Microarray-based resequencing by apyrase-mediated allele-specific extension. Electrophoresis. 2003;24:3330–3338. doi: 10.1002/elps.200305583. [DOI] [PubMed] [Google Scholar]
  53. Fan J, Chen Y, Chan HM, Tam PK, Ren Y. Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells. Proc Natl Acad Sci U S A. 2005;102:17751–17756. doi: 10.1073/pnas.0509175102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Fan J, Tam P, Woude GV, Ren Y. Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine. Proc Natl Acad Sci U S A. 2004;101:1135–1140. doi: 10.1073/pnas.0307557100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz RJ, Lockhart DJ, Chakravarti A. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 2000;10:853–860. doi: 10.1101/gr.10.6.853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Ferguson JA, Steemers FJ, Walt DR. High-density fiber-optic DNA random microsphere array. Anal Chem. 2000;72:5618–5624. doi: 10.1021/ac0008284. [DOI] [PubMed] [Google Scholar]
  57. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL. Multiplexed biochemical assays with biological chips. Nature. 1993;364:555–556. doi: 10.1038/364555a0. [DOI] [PubMed] [Google Scholar]
  58. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 1991;251:767–773. doi: 10.1126/science.1990438. [DOI] [PubMed] [Google Scholar]
  59. Francois P, Bento M, Vaudaux P, Schrenzel J. Comparison of fluorescence and resonance light scattering for highly sensitive microarray detection of bacterial pathogens. J Microbiol Methods. 2003;55:755–762. doi: 10.1016/j.mimet.2003.08.008. [DOI] [PubMed] [Google Scholar]
  60. Francois P, Charbonnier Y, Jaquet J, Utinger D, Bento M, Lew DP, Kresbach G, Schlegel W, Schrenzel J. Rapid bacterial identification using evanescent waveguide oligonucleotide microarray classification. J Microbiol Methods. 2005;65:390–403. doi: 10.1016/j.mimet.2005.08.012. [DOI] [PubMed] [Google Scholar]
  61. Francois P, Garzoni C, Bento M, Schrenzel J. Comparison of amplification methods for transcriptomic analysis of low abundance prokaryotic RNA sources. J Microbiol Methods. 2007;68(2):385–91. doi: 10.1016/j.mimet.2006.09.022. [DOI] [PubMed] [Google Scholar]
  62. Franke-Whittle IH, Klammer SH, Mayrhofer S, Insam H. Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization. J Microbiol Methods. 2006;65:117–126. doi: 10.1016/j.mimet.2005.06.011. [DOI] [PubMed] [Google Scholar]
  63. Fredericks DN, Relman DA. Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin Microbiol Rev. 1996;9:18–33. doi: 10.1128/cmr.9.1.18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Garaizar J, Rementeria A, Porwollik S. DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens? FEMS Immunol Med Microbiol. 2006;47:178–189. doi: 10.1111/j.1574-695X.2006.00081.x. [DOI] [PubMed] [Google Scholar]
  65. Garzoni C, Francois P, Couzinet S, Tapparel C, Charbonnier Y, Huyghe A, Renzoni A, Lucchini S, Lew DP, Vaudaux P, Kelley WL, Schrenzel J. A global view of the Staphylococcus aureus whole genome expression upon internalization in human epithelial cells. BMC Genomics. 2007;14:171. doi: 10.1186/1471-2164-8-171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000;11:4241–4257. doi: 10.1091/mbc.11.12.4241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Gill RT, Katsoulakis E, Schmitt W, Taroncher-Oldenburg G, Misra J, Stephanopoulos G. Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp strain PCC 6803. J Bacteriol. 2002;184:3671–3681. doi: 10.1128/JB.184.13.3671-3681.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Gillepsie D, Spiegelman SA. A quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane. J Mol Biol. 1965;12:829–842. doi: 10.1016/S0022-2836(65)80331-X. [DOI] [PubMed] [Google Scholar]
  69. Gingeras TR, Ghandour G, Wang E, Berno A, Small PM, Drobniewski F, Alland D, Desmond E, Holodniy M, Drenkow J. Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res. 1998;8:435–448. doi: 10.1101/gr.8.5.435. [DOI] [PubMed] [Google Scholar]
  70. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999;286:531–537. doi: 10.1126/science.286.5439.531. [DOI] [PubMed] [Google Scholar]
  71. Grifantini R, Bartolini E, Muzzi A, Draghi M, Frigimelica E, Berger J, Ratti G, Petracca R, Galli G, Agnusdei M, Giuliani MM, Santini L, Brunelli B, Tettelin H, Rappuoli R, Randazzo F, Grandi G. Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol. 2002;20:914–921. doi: 10.1038/nbt728. [DOI] [PubMed] [Google Scholar]
  72. Guschin D, Yershov G, Zaslavsky A, Gemmell A, Shick V, Proudnikov D, Arenkov P, Mirzabekov A. Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal Biochem. 1997;250:203–211. doi: 10.1006/abio.1997.2209. [DOI] [PubMed] [Google Scholar]
  73. Hacia JG. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet. 1999;21:42–47. doi: 10.1038/4469. [DOI] [PubMed] [Google Scholar]
  74. Halperin A, Buhot A, Zhulina EB. Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines. Biophys J. 2005;89:796–811. doi: 10.1529/biophysj.105.063479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U, Davis RW. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol. 2003;21:673–678. doi: 10.1038/nbt821. [DOI] [PubMed] [Google Scholar]
  76. Hardenbol P, Yu F, Belmont J, Mackenzie J, Bruckner C, Brundage T, Boudreau A, Chow S, Eberle J, Erbilgin A, Falkowski M, Fitzgerald R, Ghose S, Iartchouk O, Jain M, Karlin-Neumann G, Lu X, Miao X, Moore B, Moorhead M, Namsaraev E, Pasternak S, Prakash E, Tran K, Wang Z, Jones HB, Davis RW, Willis TD, Gibbs RA. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 2005;15:269–275. doi: 10.1101/gr.3185605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Hashsham SA, Wick LM, Rouillard JM, Gulari E, Tiedje JM. Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. Biosens Bioelectron. 2004;20:668–683. doi: 10.1016/j.bios.2004.06.032. [DOI] [PubMed] [Google Scholar]
  78. Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X. Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics. 2004;5:53. doi: 10.1186/1471-2164-5-53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Holzman T, Kolker E. Statistical analysis of global gene expression data: some practical considerations. Curr Opin Biotechnol. 2004;15:52–57. doi: 10.1016/j.copbio.2003.12.004. [DOI] [PubMed] [Google Scholar]
  80. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Ziman M, Meyer MR, Kobayashi S, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 2001;19:342–347. doi: 10.1038/86730. [DOI] [PubMed] [Google Scholar]
  81. Jaeger J, Spang R. Selecting normalization genes for small diagnostic microarrays. BMC Bioinformatics. 2006;7:388. doi: 10.1186/1471-2105-7-388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Joyce EA, Chan K, Salama NR, Falkow S. Redefining bacterial populations: a post-genomic reformation. Nat Rev Genet. 2002;3:462–473. doi: 10.1038/nrg820. [DOI] [PubMed] [Google Scholar]
  83. Kafatos FC, Jones CW, Efstratiadis A. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res. 1979;7:1541–1552. doi: 10.1093/nar/7.6.1541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Kajiyama T, Miyahara Y, Kricka LJ, Wilding P, Graves DJ, Surrey S, Fortina P. Genotyping on a thermal gradient DNA chip. Genome Res. 2003;13:467–475. doi: 10.1101/gr.790603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Kakinuma K, Fukushima M, Kawaguchi R. Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol Bioeng. 2003;83:721–728. doi: 10.1002/bit.10709. [DOI] [PubMed] [Google Scholar]
  86. Kelly JJ, Chernov BK, Tovstanovsky I, Mirzabekov AD, Bavykin SG. Radical-generating coordination complexes as tools for rapid and effective fragmentation and fluorescent labeling of nucleic acids for microchip hybridization. Anal Biochem. 2002;311:103–118. doi: 10.1016/S0003-2697(02)00388-3. [DOI] [PubMed] [Google Scholar]
  87. Kessler N, Ferraris O, Palmer K, Marsh W, Steel A. Use of the DNA flow-thru chip, a three-dimensional biochip, for typing and subtyping of influenza viruses. J Clin Microbiol. 2004;42:2173–2185. doi: 10.1128/JCM.42.5.2173-2185.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Knight J. When the chips are down. Nature. 2001;410:860–861. doi: 10.1038/35073680. [DOI] [PubMed] [Google Scholar]
  89. Koessler T, Francois P, Charbonnier Y, Huyghe A, Bento M, Dharan S, Renzi G, Lew D, Harbarth S, Pittet D, Schrenzel J. Use of oligoarrays for characterization of community-onset methicillin-resistant Staphylococcus aureus. J Clin Microbiol. 2006;44:1040–1048. doi: 10.1128/JCM.44.3.1040-1048.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Korczak B, Frey J, Schrenzel J, Pluschke G, Pfister R, Ehricht R, Kuhnert P. Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J Clin Microbiol. 2005;43:1024–1031. doi: 10.1128/JCM.43.3.1024-1031.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. Kostic T, Weilharter A, Rubino S, Delogu G, Rudi K, Sessitsch A, Bodrossy L. A microbial diagnostic microarray technique for the detection and identification of pathogenic bacteria in a background of non-pathogens. Anal Biochem. 2007;360:244–254. doi: 10.1016/j.ab.2006.09.026. [DOI] [PubMed] [Google Scholar]
  92. Kothapalli R, Yoder SJ, Mane S, Loughran TP., Jr Microarray results: how accurate are they? BMC Bioinformatics. 2002;3:22. doi: 10.1186/1471-2105-3-22. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Kroll TC, Wolfl S. Ranking: a closer look on globalisation methods for normalisation of gene expression arrays. Nucleic Acids Res. 2002;30:e50. doi: 10.1093/nar/30.11.e50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  94. Li J, Pankratz M, Johnson JA. Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci. 2002;69:383–390. doi: 10.1093/toxsci/69.2.383. [DOI] [PubMed] [Google Scholar]
  95. Li W. How many genes are needed for early detection of breast cancer, based on gene expression patterns in peripheral blood cells? Breast Cancer Res. 2005;7:E5. doi: 10.1186/bcr1295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  96. Lima WF, Monia BP, Ecker DJ, Freier SM. Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry. 1992;31:12055–12061. doi: 10.1021/bi00163a013. [DOI] [PubMed] [Google Scholar]
  97. Lindroos HL, Mira A, Repsilber D, Vinnere O, Naslund K, Dehio M, Dehio C, Andersson SG. Characterization of the genome composition of Bartonella koehlerae by microarray comparative genomic hybridization profiling. J Bacteriol. 2005;187:6155–6165. doi: 10.1128/JB.187.17.6155-6165.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Lindroos K, Liljedahl U, Raitio M, Syvanen AC. Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries. Nucleic Acids Res. 2001;29:E69. doi: 10.1093/nar/29.13.e69. [DOI] [PMC free article] [PubMed] [Google Scholar]
  99. Lindroos K, Sigurdsson S, Johansson K, Ronnblom L, Syvanen AC. Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res. 2002;30:e70. doi: 10.1093/nar/gnf069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet. 1999;21:20–24. doi: 10.1038/4447. [DOI] [PubMed] [Google Scholar]
  101. Lipshutz RJ, Morris D, Chee M, Hubbell E, Kozal MJ, Shah N, Shen N, Yang R, Fodor SP. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques. 1995;19:442–447. [PubMed] [Google Scholar]
  102. Liu M, Popper SJ, Rubins KH, Relman DA. Early days: genomics and human responses to infection. Curr Opin Microbiol. 2006;9:312–319. doi: 10.1016/j.mib.2006.04.006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  103. Liu WT, Guo H, Wu JH. Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays. Appl Environ Microbiol. 2007;73:73–82. doi: 10.1128/AEM.01468-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. Liu WT, Mirzabekov AD, Stahl DA. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol. 2001;3:619–629. doi: 10.1046/j.1462-2920.2001.00233.x. [DOI] [PubMed] [Google Scholar]
  105. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996;14:1675–1680. doi: 10.1038/nbt1296-1675. [DOI] [PubMed] [Google Scholar]
  106. Lodes MJ, Suciu D, Elliott M, Stover AG, Ross M, Caraballo M, Dix K, Crye J, Webby RJ, Lyon WJ, Danley DL, McShea A. Use of semiconductor-based oligonucleotide microarrays for influenza A virus subtype identification and sequencing. J Clin Microbiol. 2006;44:1209–1218. doi: 10.1128/JCM.44.4.1209-1218.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Loge FJ, Thompson DE, Call DR. PCR detection of specific pathogens in water: a risk-based analysis. Environ Sci Technol. 2002;36:2754–2759. doi: 10.1021/es015777m. [DOI] [PubMed] [Google Scholar]
  108. Loy A, Bodrossy L. Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta. 2006;363:106–119. doi: 10.1016/j.cccn.2005.05.041. [DOI] [PubMed] [Google Scholar]
  109. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol. 2002;68:5064–5081. doi: 10.1128/AEM.68.10.5064-5081.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales.". Appl Environ Microbiol. 2005;71:1373–1386. doi: 10.1128/AEM.71.3.1373-1386.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Lucchini S, Liu H, Jin Q, Hinton JC, Yu J. Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen. Infect Immun. 2005;73:88–102. doi: 10.1128/IAI.73.1.88-102.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Lucchini S, Thompson A, Hinton JC. Microarrays for microbiologists. Microbiology. 2001;147:1403–1414. doi: 10.1099/00221287-147-6-1403. [DOI] [PubMed] [Google Scholar]
  113. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH. ARB: a software environment for sequence data. Nucleic Acids Res. 2004;32:1363–1371. doi: 10.1093/nar/gkh293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Lynch JL, deSilva CJ, Peeva VK, Swanson NR. Comparison of commercial probe labeling kits for microarray: towards quality assurance and consistency of reactions. Anal Biochem. 2006;355:224–231. doi: 10.1016/j.ab.2006.04.052. [DOI] [PubMed] [Google Scholar]
  115. Macevicz SC. Nucleic acid sequence determination by multiple mixed oligonucleotide probes. Patent: US1988000261702 USA Ref Type; 1991. [Google Scholar]
  116. Malanoski GJ, Samore MH, Pefanis A, Karchmer AW. Staphylococcus aureus catheter-associated bacteremia. Minimal effective therapy and unusual infectious complications associated with arterial sheath catheters. Arch Intern Med. 1995;155:1161–1166. doi: 10.1001/archinte.155.11.1161. [DOI] [PubMed] [Google Scholar]
  117. Marcelino LA, Backman V, Donaldson A, Steadman C, Thompson JR, Preheim SP, Lien C, Lim E, Veneziano D, Polz MF. Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci U S A. 2006;103:13629–13634. doi: 10.1073/pnas.0601476103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  118. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Nature. 2005;437:376–380. doi: 10.1038/nature03959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  119. Maskos U, Southern EM. A novel method for the parallel analysis of multiple mutations in multiple samples. Nucleic Acids Res. 1993a;21:2269–2270. doi: 10.1093/nar/21.9.2269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  120. Maskos U, Southern EM. A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesised on a glass support. Nucleic Acids Res. 1993b;21:4663–4669. doi: 10.1093/nar/21.20.4663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Matveeva OV, Shabalina SA, Nemtsov VA, Tsodikov AD, Gesteland RF, Atkins JF. Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res. 2003;31:4211–4217. doi: 10.1093/nar/gkg476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Mikulowska-Mennis A, Taylor TB, Vishnu P, Michie SA, Raja R, Horner N, Kunitake ST. High-quality RNA from cells isolated by laser capture microdissection. Biotechniques. 2002;33:176–179. doi: 10.2144/02331md06. [DOI] [PubMed] [Google Scholar]
  123. Mir KU, Southern EM. Determining the influence of structure on hybridization using oligonucleotide arrays. Nat Biotechnol. 1999;17:788–792. doi: 10.1038/11732. [DOI] [PubMed] [Google Scholar]
  124. Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci U S A. 2001;98:9853–9858. doi: 10.1073/pnas.171178898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  125. Naef F, Magnasco MO. Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys. 2003;68:011906. doi: 10.1103/PhysRevE.68.011906. [DOI] [PubMed] [Google Scholar]
  126. Nguyen HK, Southern EM. Minimising the secondary structure of DNA targets by incorporation of a modified deoxynucleoside: implications for nucleic acid analysis by hybridisation. Nucleic Acids Res. 2000;28:3904–3909. doi: 10.1093/nar/28.20.3904. [DOI] [PMC free article] [PubMed] [Google Scholar]
  127. Pasternack RF, Collings PJ. Resonance light scattering: a new technique for studying chromophore aggregation. Science. 1995;269:935–939. doi: 10.1126/science.7638615. [DOI] [PubMed] [Google Scholar]
  128. Pawlak M, Schick E, Bopp MA, Schneider MJ, Oroszlan P, Ehrat M. Zeptosens’ protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics. 2002;2:383–393. doi: 10.1002/1615-9861(200204)2:4<383::AID-PROT383>3.0.CO;2-E. [DOI] [PubMed] [Google Scholar]
  129. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994;91:5022–5026. doi: 10.1073/pnas.91.11.5022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  130. Peplies J, Glockner FO, Amann R. Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol. 2003;69:1397–1407. doi: 10.1128/AEM.69.3.1397-1407.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Perou CM, Sorlie T, Eisen MB, Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D. Molecular portraits of human breast tumours. Nature. 2000;406:747–752. doi: 10.1038/35021093. [DOI] [PubMed] [Google Scholar]
  132. Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J. Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J Clin Microbiol. 2005;43:2291–2302. doi: 10.1128/JCM.43.5.2291-2302.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Peterson AW, Heaton RJ, Georgiadis RM. The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 2001;29:5163–5168. doi: 10.1093/nar/29.24.5163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  134. Phimister B. Chipping forecast: going global. Nat Genet. 1999;21:1. [Google Scholar]
  135. Porwollik S, Frye J, Florea LD, Blackmer F, McClelland M. A non-redundant microarray of genes for two related bacteria. Nucleic Acids Res. 2003;31:1869–1876. doi: 10.1093/nar/gkg298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  136. Pozhitkov A, Chernov B, Yershov G, Noble PA. Evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks. Appl Environ Microbiol. 2005;71:8663–8676. doi: 10.1128/AEM.71.12.8663-8676.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. 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. Nucleic Acids Res. 2006;34:e66. doi: 10.1093/nar/gkl133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Proudnikov D, Mirzabekov A. Chemical methods of DNA and RNA fluorescent labeling. Nucleic Acids Res. 1996;24:4535–4542. doi: 10.1093/nar/24.22.4535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Puskas LG, Zvara A, Hackler L, Hummelen P. RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques. 2002;32:1330–4. doi: 10.2144/02326mt04. [DOI] [PubMed] [Google Scholar]
  140. Raman R, Raguram S, Venkataraman G, Paulson JC, Sasisekharan R. Glycomics: an integrated systems approach to structure-function relationships of glycans. Nat Methods. 2005;2:817–824. doi: 10.1038/nmeth807. [DOI] [PubMed] [Google Scholar]
  141. Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol. 2004;70:4303–4317. doi: 10.1128/AEM.70.7.4303-4317.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Rimour S, Hill D, Militon C, Peyret P. GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics. 2005;21:1094–1103. doi: 10.1093/bioinformatics/bti112. [DOI] [PubMed] [Google Scholar]
  143. Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol. 1998;16:939–945. doi: 10.1038/nbt1098-939. [DOI] [PubMed] [Google Scholar]
  144. Rudi K, Flateland SL, Hanssen JF, Bengtsson G, Nissen H. Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl Environ Microbiol. 2002;68:1146–1156. doi: 10.1128/AEM.68.3.1146-1156.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  145. Rudi K, Treimo J, Nissen H, Vegarud G. Protocols for 16S rDNA array analyses of microbial communities by sequence-specific labeling of DNA probes. ScientificWorldJournal. 2003;3:578–584. doi: 10.1100/tsw.2003.44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A. 2000;97:14668–14673. doi: 10.1073/pnas.97.26.14668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Sanguin H, Herrera A, Oger-Desfeux C, Dechesne A, Simonet P, Navarro E, Vogel T M, Moenne-Loccoz Y, Grundmann X, Nesme GL. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ Microbiol. 2006;8:289–307. doi: 10.1111/j.1462-2920.2005.00895.x. [DOI] [PubMed] [Google Scholar]
  148. SantaLucia J., Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998;95:1460–1465. doi: 10.1073/pnas.95.4.1460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  149. SantaLucia JJ, Allawi HT, Seneviratne PA. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry. 1996;35:3555–3562. doi: 10.1021/bi951907q. [DOI] [PubMed] [Google Scholar]
  150. Santos SR, Ochman H. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol. 2004;6:754–759. doi: 10.1111/j.1462-2920.2004.00617.x. [DOI] [PubMed] [Google Scholar]
  151. Schadt EE, Li C, Ellis B, Wong WH. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl Suppl. 2001;37:120–125. doi: 10.1002/jcb.10073. [DOI] [PubMed] [Google Scholar]
  152. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  153. Scherl A, Francois P, Charbonnier Y, Deshusses JM, Koessler T, Huyghe A, Bento M, Stahl-Zeng J, Fischer A, Masselot A, Gallé F, Renzoni A, Vaudaux P, Lew D, Zimmermann-Ivol CG, Binz PA, Sanchez JC, Hochstrasser DF, Schrenzel J. Exploring glycopeptide resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance related markers. BMC Genomics. 2006;7:-296. doi: 10.1186/1471-2164-7-296. [DOI] [PMC free article] [PubMed] [Google Scholar]
  154. Schrenzel J, Hibbs J. Non-cognate hybridization system (NCHS) Patent: 00/75377 A2 Ref Type; 2003. [Google Scholar]
  155. Sergeev N, Distler M, Courtney S, Al Khaldi SF, Volokhov D, Chizhikov V, Rasooly A. Multipathogen oligonucleotide microarray for environmental and biodefense applications. Biosens Bioelectron. 2004;20:684–698. doi: 10.1016/j.bios.2004.04.030. [DOI] [PubMed] [Google Scholar]
  156. Shchepinov MS, Case-Green SC, Southern EM. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 1997;25:1155–1161. doi: 10.1093/nar/25.6.1155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  157. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JM, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Slikker W, Shi L, Reid LH. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006;24:1151–1161. doi: 10.1038/nbt1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Small J, Call DR, Brockman FJ, Straub TM, Chandler DP. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol. 2001;67:4708–4716. doi: 10.1128/AEM.67.10.4708-4716.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  159. Smyth GK, Speed T. Normalization of cDNA microarray data. Methods. 2003;31:265–273. doi: 10.1016/S1046-2023(03)00155-5. [DOI] [PubMed] [Google Scholar]
  160. Sohail M, Akhtar S, Southern EM. The folding of large RNAs studied by hybridization to arrays of complementary oligonucleotides. RNA. 1999;5:646–655. doi: 10.1017/S1355838299982195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Southern EM. Analysing polynucleotide sequences. Patent: 19891100 GB Ref Type; 1989. [Google Scholar]
  162. Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975;98:503–517. doi: 10.1016/S0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  163. Southern EM, Case-Green SC, Elder JK, Johnson M, Mir KU, Wang L, Williams JC. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 1994;22:1368–1373. doi: 10.1093/nar/22.8.1368. [DOI] [PMC free article] [PubMed] [Google Scholar]
  164. Southern EM, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet. 1999;21:5–9. doi: 10.1038/4429. [DOI] [PubMed] [Google Scholar]
  165. Stenger DA, Andreadis JD, Vora GJ, Pancrazio JJ. Potential applications of DNA microarrays in biodefense-related diagnostics. Curr Opin Biotechnol. 2002;13:208–212. doi: 10.1016/S0958-1669(02)00321-X. [DOI] [PubMed] [Google Scholar]
  166. Stimpson DI, Cooley PW, Knepper SM, Wallace DB. Parallel production of oligonucleotide arrays using membranes and reagent jet printing. Biotechniques. 1998;25:886–890. doi: 10.2144/98255rr03. [DOI] [PubMed] [Google Scholar]
  167. Stowe-Evans EL, Ford J, Kehoe DM. Genomic DNA microarray analysis: identification of new genes regulated by light color in the cyanobacterium Fremyella diplosiphon. J Bacteriol. 2004;186:4338–4349. doi: 10.1128/JB.186.13.4338-4349.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Straub TM, Chandler DP. Towards a unified system for detecting waterborne pathogens. J Microbiol Methods. 2003;53:185–197. doi: 10.1016/S0167-7012(03)00023-X. [DOI] [PubMed] [Google Scholar]
  169. Strezoska Z, Paunesku T, Radosavljevic D, Labat I, Drmanac R, Crkvenjakov R. DNA sequencing by hybridization: bases read by a non-gel-based method. Proc Natl Acad Sci U S A. 1991;88:10089–10093. doi: 10.1073/pnas.88.22.10089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  170. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999;96:2907–2912. doi: 10.1073/pnas.96.6.2907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  171. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol. 2003;69:1159–1171. doi: 10.1128/AEM.69.2.1159-1171.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  172. Taylor S, Smith S, Windle B, Guiseppi-Elie A. Impact of surface chemistry and blocking strategies on DNA microarrays. Nucleic Acids Res. 2003;31:e87. doi: 10.1093/nar/gng086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  173. Thiyagarajan S, Karhanek M, Akhras M, Davis RW, Pourmand N. PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens. BMC Bioinformatics. 2006;7:500. doi: 10.1186/1471-2105-7-500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  174. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques. 2004;36:664–665. doi: 10.2144/04364RR02. [DOI] [PubMed] [Google Scholar]
  175. Treimo J, Vegarud G, Langsrud T, Marki S, Rudi K. Total bacterial and species-specific 16S rDNA micro-array quantification of complex samples. J Appl Microbiol. 2006;100:985–998. doi: 10.1111/j.1365-2672.2006.02805.x. [DOI] [PubMed] [Google Scholar]
  176. Troesch A, Nguyen H, Miyada CG, Desvarenne S, Gingeras TR, Kaplan PM, Cros P, Mabilat C. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J Clin Microbiol. 1999;37:49–55. doi: 10.1128/jcm.37.1.49-55.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  177. Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 2001;29:2549–2557. doi: 10.1093/nar/29.12.2549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. 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. doi: 10.1128/AEM.69.5.2848-2856.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  179. 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. doi: 10.1128/AEM.68.1.235-244.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  180. Vainrub A, Pettitt BM. Coulomb blockage of hybridization in two-dimensional DNA arrays. Phys Rev E Stat Nonlin Soft Matter Phys. 2002;66:041905. doi: 10.1103/PhysRevE.66.041905. [DOI] [PubMed] [Google Scholar]
  181. van Bakel H, Holstege FC. In control: systematic assessment of microarray performance. EMBO Rep. 2004;5:964–969. doi: 10.1038/sj.embor.7400253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  182. van Leeuwen WB, Jay C, Snijders S, Durin N, Lacroix B, Verbrugh HA, Enright MC, Troesch A, Van Belkum A. Multilocus sequence typing of Staphylococcus aureus with DNA array technology. J Clin Microbiol. 2003;41:3323–3326. doi: 10.1128/JCM.41.7.3323-3326.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. Volokhov D, Rasooly A, Chumakov K, Chizhikov V. Identification of listeria species by microarray-based assay. J Clin Microbiol. 2002;40:4720–4728. doi: 10.1128/JCM.40.12.4720-4728.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  184. Voordouw G, Voordouw JK, Karkhoff-Schweizer RR, Fedorak PM, Westlake DW. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl Environ Microbiol. 1991;57:3070–3078. doi: 10.1128/aem.57.11.3070-3078.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  185. Vora GJ, Meador CE, Stenger DA, Andreadis JD. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol. 2004;70:3047–3054. doi: 10.1128/AEM.70.5.3047-3054.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  186. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002;99:15687–15692. doi: 10.1073/pnas.242579699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  187. Wang RF, Beggs ML, Erickson BD, Cerniglia CE. DNA microarray analysis of predominant human intestinal bacteria in fecal samples. Mol Cell Probes. 2004;18:223–234. doi: 10.1016/j.mcp.2004.03.002. [DOI] [PubMed] [Google Scholar]
  188. Wilson CL, Pepper SD, Hey Y, Miller CJ. Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques. 2004;36:498–506. doi: 10.2144/04363RN05. [DOI] [PubMed] [Google Scholar]
  189. Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL. High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol. 2002;68:2535–2541. doi: 10.1128/AEM.68.5.2535-2541.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  190. Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res. 2004;14:398–405. doi: 10.1101/gr.2141004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  191. Wu L, Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol. 2001;67:5780–5790. doi: 10.1128/AEM.67.12.5780-5790.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  192. de Kievit Y, Wu P, Vahlkamp L, Pijnenburg D, Smit M, Dankers M, Melchers D, Stax M, Boender PJ, Ingham C, Bastiaensen N, de Wijn R, van Alewijk D, van Damme H, Raap AK, van Beuningen R, Chan AB. Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles. Nucleic Acids Res. 2004;32:e123. doi: 10.1093/nar/gnh118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  193. Xiang CC, Chen M, Ma L, Phan QN, Inman JM, Kozhich OA, Brownstein MJ. A new strategy to amplify degraded RNA from small tissue samples for microarray studies. Nucleic Acids Res. 2003;31:e53. doi: 10.1093/nar/gng053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  194. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 2002;30:e15. doi: 10.1093/nar/30.4.e15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  195. Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet. 2002;3:579–588. doi: 10.1038/nrg863. [DOI] [PubMed] [Google Scholar]
  196. Ye RW, Wang T, Bedzyk L, Croker KM. Applications of DNA microarrays in microbial systems. J Microbiol Methods. 2001;47:257–272. doi: 10.1016/S0167-7012(01)00308-6. [DOI] [PubMed] [Google Scholar]
  197. Yershov G, Barsky V, Belgovskiy A, Kirillov E, Kreindlin E, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S, Mirzabekov A. DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci U S A. 1996;93:4913–4918. doi: 10.1073/pnas.93.10.4913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  198. Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R. An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 2001;29:E41. doi: 10.1093/nar/29.8.e41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  199. Zaigler A, Schuster SC, Soppa J. Construction and usage of a onefold-coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol Microbiol. 2003;48:1089–1105. doi: 10.1046/j.1365-2958.2003.03497.x. [DOI] [PubMed] [Google Scholar]
  200. Zammatteo N, Jeanmart L, Hamels S, Courtois S, Louette P, Hevesi L, Remacle J. Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal Biochem. 2000;280:143–150. doi: 10.1006/abio.2000.4515. [DOI] [PubMed] [Google Scholar]
  201. Zhang L, Hurek T, Reinhold-Hurek B (2006) A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms. Microb Ecol [DOI] [PubMed]
  202. Zhou J, Thompson DK. Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol. 2002;13:204–207. doi: 10.1016/S0958-1669(02)00319-1. [DOI] [PubMed] [Google Scholar]
  203. Zwick ME, Mcafee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A. Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol. 2005;6:R10. doi: 10.1186/gb-2004-6-1-r10. [DOI] [PMC free article] [PubMed] [Google Scholar]

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