Introduction to microarray technology

Microarray Technology Through Applications

Volumn , Issue , 2007, Pages 1-52

  Hobman, Jon L ^a   Jones, Antony ^a   Constantinidou, Chrystala ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 48349118804     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (190)

1. Adams EW, Ratner DM, Bokesch HR, McMahon JB, O'Keefe BR, Seeberger PH (2004) Oligosaccharide and glycoprotein microarrays as tools in HIV glycobiology: Glycan-dependent gp120/protein interactions. Chem Biol 11: 875-881.
2. Adams R, Bishof L (1994) Seeded region growing. IEEE Trans Pattern Anal Machine Intel 16: 641-647.
3. Affymetrix (2004) Gene expression analysis technical manual (http://www. affymetrix.com/support/technical/manual/expression_manual.affx).
4. Ahmed AA, Vias M, Iyer NG, Caldas C, Brenton JD (2004) Microarray segmentation methods significantly influence data precision. Nucleic Acids Res 32: e50.
5. Albert TJ, Norton J, Ott M, Richmond T, Nuwaysir K, Nuwaysir EF, Stengele KP, Green RD (2003) Light-directed 5'3' synthesis of complex oligonucleotide microarrays. Nucleic Acids Res 31: e35.
6. Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo W-L, Gray JW, Pinkel D (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25: 144-146.
7. Anderson MLM (1999) Types of hybridization and uses of each method. In: Nucleic Acid Hybridization Bios Scientific Publishers, Oxford, pp. 11-16.
8. Axon Instruments Inc. (1999) GenePix 4000: A User's Guide. Axon Instruments Inc., Union City, CA (Taken over by Molecular Devices Corporation, Sunnyvale, CA).
9. Ball CA, Sherlock G, Parkinson H, et al. (2002) Microarray Gene Expression Data (MGED) Society standards for microarray data. Science 298: 539.
10. Barry R, Soloviev M (2004) Quantitative protein profiling using antibody arrays. Proteomics 4: 3717-3726.
11. Beare R, Buckley M (2004) Spot: cDNA Microarray Image Analysis-User's Guide. CSIRO Mathematical and Information Sciences (http://www.cmis.csiro.au/IAP/ Spot/doc/Spot.pdf).
12. Behr MA, Wilson MA, Gill WP, Salamon H, Schoolniik GK, Rane S, Small M (1999) Comparative genomics of BCG vaccine by whole-genome DNA microarray. Science 284: 1520-1523.
13. Bengtsson A, Bengtsson H (2006) Microarray image analysis: background estimation using quantile and morphological filters. BMC Bioinformatics 7: 96.
14. Bengtsson H, Jonsson G, Vallon-Christersson J (2004) Calibration and assessment of channel-specific biases in microarray data with extended dynamical range. BMC Bioinformatics 5: 177.
15. Blixt O, Head S, Mondala T, et al. (2004) Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci USA 101: 17033-17038.
16. Boutell JM, Hart DJ, Godber BL, Kozlowski RZ, Blackburn JM (2004) Functional protein microarrays for parallel characterisation of p53 mutants. Proteomics 4: 1950-1958.
17. Bowtell D, Sambrook J (eds) (2003) DNA Microarrays: A Molecular Cloning Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
18. Brasch MA, Hartley JL, Vidal M (2004) ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res 14: 2001-2009.
19. Brazma A, Hingamp P, Quackenbush J, et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29: 365-371.
20. Buck MJ, Lieb JD (2004) ChIP-chip: considerations for the design, analysis, and applications of genome-wide chromatin immunoprecipitation experiments. Genomics 83: 349-360.
21. Buckley MJ (2002) The Spot User's Guide. CSIRO Mathematical and Information Sciences (http://www.cmis.csiro.au/IAP/Spot/spotmanual.htm).
22. Buhler J, Ideker T, Haynor D (2000) Dapple: Improved Techniques for Finding Spots on DNA Microarrays. Technical report UWTR 2000-08-05. University of Washington.
23. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 17: 573-577.
24. Call DR (2005) Challenges and opportunities for pathogen detection using DNA microarrays. Crit Rev Microbiol 31: 91-99.
25. Call DR, Borucki MK, Loge FK (2003) Detection of bacterial pathogens in environmental samples using DNA microarrays. J Microbiol Methods 53: 235-243.
26. Cao M, Kobel PA, Morshedi MM, Wu MF, Paddon C, Helmann JD (2002) Defining the Bacillus subtilis sW regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches. J Mol Biol 316: 443-457.
27. Case-Green S, Pritchard C, Southern EM (1999) Use of oligonucleotide arrays in enzymatic assays: assay optimization. In: DNA Microarrays-A Practical Approach (ed. M. Schena). Oxford University Press, Oxford, pp. 61-76.
28. Castellino AM (1997) When the chips are down. Genome Res 7: 943-946.
29. Chen Y, Dougherty ER, Bittner ML (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J Biomed Optics 2: 364-374.
30. Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32: 490-495.
31. Cortese JD (2001) Microarray readers: Pushing the envelope. Scientist 15: 36.
32. Cosma MP, Tanaka T, Nasmyth K (1999) Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell 97: 299-311.
33. Cutler P (2003) Protein arrays: The current state-of-the-art. Proteomics 3: 3-18.
34. DeRisi JL, Iyer WR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
35. De Wildt RM, Mundy CR, Gorick BD, Tomlinson IM (2000) Antibody arrays for highthroughput screening of antibody-antigen interactions. Nat Biotechnol 18: 989-994.
36. Diks SH, Kok K, O'Toole T, Hommes DW, van Dijken P, Joore J, Peppelenbosch MP (2004) Kinoem profiling for studying lipopolysaccharide signal transduction in human peripheral blood mononuclear cells. J Biol Chem 279: 49206-49213.
37. Disney MD, Seeberger PH (2004) The use of carbohydrate microarrays to study carbohydrate- cell interactions and to detect pathogens. Chem Biol 11: 1701-1707.
38. Dobbin K, Shih JH, Simon R (2003) Questions and answers on design of dual-label microarrays for identifying differentially expressed genes. J Natl Cancer Inst 95: 1362-1369.
39. Dombkowski AA, Thibodeau BJ, Starcevic SL, Novak RF (2004) Gene-specific dye bias in microarray reference designs. FEBS Lett 560: 120-124.
40. Drickamer K, Taylor ME (2002) Glycan arrays for functional genomics [Review]. Genome Biol 3: 1034.1-1034.4.
41. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rowenzweig F, Botstein D, et al. (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99: 16144-16149.
42. Edman CF, Raymond DE, Wu DJ, Tu E, Sosnowski RG, Butler WF, Nerenberg M, Heller MJ (1997) Electric field directed nucleic acid hybridization on microchips. Nucleic Acids Res 25: 4907-4914.
43. Eisen MB, Brown PO (1999) ScanAlyze, (available at http://rana/Stanford.Edu/ software).
44. Ekins R, Chu FW (1999) Microarrays: their origins and applications. Trends Biotechnol 17: 217-218.
45. Ekins RP, Chu F, Biggart E (1989a) Development of microspot multi-analyte ratiometric immunoassay using dual fluorescent-labelled antibodies. Anal Chim Acta 227: 73-96.
46. Ekins RP, Chu F, Micallef J (1989b) High specific activity chemiluminescent and fluorescent markers: their potential application to high sensitivity and 'multi analyte' immunoassays. J Biolumin Chemilumin 4: 59-78.
47. Ekins RP, Chu F, Biggart E (1990) Multispot, multianalyte, immunoassay. Ann Biol Clin 48: 655-666.
48. Emili AQ, Cagney G (2000) Large-scale functional analysis using peptide or protein arrays. Nat Biotechnol 18: 293-397.
49. Fan J-B, Chen X, Halushka MK, Lipshutz RJ, Lockhart DJ, Chakravarti A (2000) Parallel genotyping of SNPs using generic high-density oligonucleotide tag arrays. Genome Res 10: 853-860.
50. Feizi T, Fazio F, Chai W, Wong C-H (2003) Carbohydrate microarrays-a new set of technologies at the frontiers of glycomics. Curr Opin Struct Biol 13: 637-645.
51. Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767-773.
52. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL (1993) Multiplexed biochemical assays with biological chips. Nature 364: 555-556.
53. Frank R (2002) The SPOT-synthesis technique-Synthetic peptide arrays on membrane supports-principles and applications. J Immunol Methods 267: 13-26.
54. Freeman WM, Robertson DJ, Vrana KE (2000) Fundamentals of DNA hybridization arrays for gene expression analysis. Biotechniques 29: 1042-1055.
55. Fukui S, Feizi T, Galustian C, Lawson AM, Chai W (2002) Oligosaccharide microarrays for high-throughput detection and specificity assignments of carbohydrate- protein interactions. Nat Biotechnol 20: 1011-1017.
56. Gao X, LeProust E, Zhang H, Srivannavit O, Gulari E, Yu P, Mishiguchi C, Xiang Q, Zhou X (2001) A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res 29: 4744-4750.
57. Gao X, Zhou X, Gulari E (2003) Light directed massively parallel on-chip synthesis of peptide arrays with t-Boc chemistry. Proteomics 3: 2135-2141.
58. Gold L, Brown D, He Y-Y, Shtatland T, Singer BS, Wu Y (1997) From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops. Proc Natl Acad Sci USA 94: 59-64.
59. Grainger DC, Overton TW, Hobman JL, Constantinidou C, Tamai E, Wade JT, Struhl K, Reppas N, Church G, Busby SJW (2004). Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol 186: 6938-6943.
60. Grunstein M, Hogness DS (1975) Colony hybridization: A method for the isolation of cloned cDNAs that contain a specific gene. Proc Natl Acad Sci USA 72: 3961-3965.
61. Guo Y, Feinberg H, Conroy E, Mitchell DA, Alvarez R, Blixt O, Taylor ME, Weis WI, Drickamer K (2004) Structural basis of distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR. Nat Struct Mol Biol 11: 591-597.
62. Haab BB, Dunham MJ, Brown PO (2001) Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions [Research]. Genome Biol 2: 0004.1-0004.13.
63. Hacia JG (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 21: 42-47.
64. Harding MA, Arden KC, Gildea JW, Gildea JJ, Perlman EJ, Viars C, Theodorescu D (2002) Functional genomic comparison of lineage-related human bladder cancer cell lines with differing tumorigenic and metastatic potentials by spectral karyotyping, comparative genomic hybridization, and a novel method of positional expression profiling. Cancer Res 62: 6981-6989.
65. Harrington CA, Rosenow C, Retief J (2000) Monitoring gene expression using DNA arrays. Curr Opin Microbiol 3: 285-291.
66. Heller MJ, Tu E, Holmsen A, Sosnowski RG, O'Connell J (1999) Active microelectronic arrays for DNA hybridization analysis. In: DNA Microarrays-A Practical Approach (ed. M. Schena). Oxford University Press, Oxford, pp. 167-185.
67. Heller MJ, Forster AH, Tu E (2000) Active microeletronic chip devices which utilize controlled electrophoretic fields for multiplex DNA hybridization and other genomic applications. Electrophoresis 21: 157-164.
68. Heller RA, Schena M, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 94: 2150-2155.
69. Hepburne-Scott H, Herick K (2005) Protein function arrays vs. protein expression arrays-An introduction. Origins 18: 4-6 (www.sigmaaldrich.com).
70. Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BØ (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol 187: 6166-6174.
71. Hirschhorn JN, Sklar P, Lindblad-Toh K, Lim Y-M, Ruiz-Gutierrez M, Bolk S, Langhorst B, Schaffner S, Winchester E, Lander ES (2000) SBE-TAGS: An array based method for efficient single-nucleotide polymorphism genotyping. Proc Natl Acad Sci USA 97: 12164-12169.
72. Hitt E (2004) Advances in Microarray Readers. Scientist 18: 42.
73. Holloway AJ, van Laar RK, Tothill RW, Bowtell DDR (2002) Options available-from start to finish-for obtaining data from DNA microarrays II. Nat Genet 32: 481-489.
74. Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M (2002) GATA-1 binding sites mapped in the beta-globin locus by using mammalian chip-chip analysis. Proc Natl Acad Sci USA 99: 2924-2929.
75. Houseman BT, Mrksich M (2002) Carbohydrate arrays for the evaluation of protein binding and enzymatic modification. Chem Biol 9: 443-454.
76. Houseman BT, Huh JH, Kron SJ, Mrksich M (2002) Peptide chips for the quantitative evaluation of protein kinase activity. Nat Biotechnol 20: 270-274.
77. Huber M, Losert D, Hiller R, Harwanegg C, Mueller MW, Schmidt WM (2001) Detection of single base alterations in genomic DNA by solid phase polymerase chain reaction on oligonucleotide microarrays. Anal Biochem 299: 24-30.
78. Hughes JD, Estep PW, Tavazoie S, Church GW (2000) Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296: 1205-1214.
79. Hughes TR, Mao M, Jones AR, et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342-347.
80. Imbeaud S, Auffray C (2005) 'The 39 steps' in gene expression profiling, critical issues and proposed best practices for microarray experiments. Drug Discovery today 10: 1175-1182.
81. Ishkanian AS, Malloff CA, Watson SK, et al. (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36: 299-303.
82. Iyer VR, Horak CE, Scarfe CS, Botstein D, Snyder M, Brown PO (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF, and MBF. Nature 409: 533-538.
83. Jain AN, Tokuyasu TA, Snjiders AM, Segraves R, Albertson DG, Pinkel D (2002) Fully automatic quantification of microarray image data. Genome Res 12: 325-332.
84. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992). Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818-821.
85. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296: 916-919.
86. Karsten SL, Van Deerlin VMD, Sabatti C, Gill LH, Geschwind DH (2002) An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 30: e4.
87. Kennedy GC, Matsuzaki H, Dong S, et al. (2003) Large-scale genotyping of complex DNA. Nat Biotechnol 21: 1233-1237.
88. Kerr MK, Churchill GA (2001) Statistical design and the analysis of gene expression microarray data. Genet Res 77: 123-128.
89. Khrapko KR, Lysov YuP, Khorlyn AA, Shick VV, Florentiev VL, Mirazabekov AD (1989) An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett 256: 118-122.
90. Kiessling LL, Cairo CW (2002) Hitting the sweet spot. Nat Biotechnol 20: 234-235.
91. Korczak B, Frey J, Schrenzel J, Pluschke G, Pfister R, Ehricht R, Kuhnert P (2005) Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J Clin Microbiol 43: 1024-1031.
92. Krebs JE, Kuo M-H, Allis CD, Peterson CL (1999) Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev 13: 1412-1421.
93. Kuo M-H, Allis CD (1999) in vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods 19: 425-433.
94. Lander ES (1999) Array of hope. Nat Genet 21(Suppl): 3-4.
95. Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison J, Hood L, Lasky SR (2004) POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol 5: R58.
96. Lazebnik Y (2002) Can a biologist fix a radio?-Or, what I learned while studying apoptosis. Cancer Cell 2: 179-182.
97. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334.
98. Lindroos K, Sigurdsson S, Johansson K, Rönnblom L, Syvänen A-C (2002) Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res 30: 14 e70.
99. Lipshutz RF, Fodor SPA (1994) Advanced DNA sequencing technologies. Curr Opin Struct Biol 4: 376-380.
100. Lockhart DJ, Dong H, Byrne MC, et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680.
101. Lueking A, Horn M, Eickhoff H, Büssow K, Lehrach H, Walter G (1999) Protein microarrays for gene expression and antibody screening. Anal Biochem 270: 103-111.
102. Luo Z, Geschwind DH (2001) Microarray applications in neuroscience. Neurobiol Disease 8:183-193.
103. Lyng H, Badiee A, Svendsrud DH, Hovig E, Myklebost O, Stokke T (2004) Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction BMC. Genomics 5: 10.
104. MacBeath G (2002) Protein microarrays and proteomics. Nat Genet 32: 526-532.
105. MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289: 1760-1763.
106. Mahal LK (2004) Catching bacteria with sugar. Chem Biol 11: 1602-1604.
107. Manduchi E, Scearce LM, Brestelli JE, Grant GR, Kaestner KH, Stoeckert CJ (2002) Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol Genomics 10: 169-179.
108. Mann M, Jensen ON (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21: 255-261.
109. Matsuzaki H, Loi H, Dong S, et al. (2004) Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high density oligonucleotide array. Genome Res 14: 414-425.
110. Medigue C, Rechenmann F, Danchin A, Viari A (1999) Imagene: an integrated computer environment for sequence annotation and analysis. Bioinformatics 15: 2-15.
111. Microarray Gene Expression Data (MGED) (2002) A guide to microarray experiments - an open letter to the scientific journals. Lancet 360: 1019.
112. Mitchell P (2002) A perspective on protein microarrays. Nat Biotechnol 20: 225-229.
113. Mockler TC, Ecker JR (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics 85: 1-15.
114. Nagy PL, Cleary ML, Brown PO, Lieb JB (2003) Genomewide demarcation of RNA polymeraser II transcription units revealed by physical fractionation of chromatin. Proc Natl Acad Sci USA 100: 6364-6369.
115. Nallur G, Luo C, Fang L, Cooley S, Dave V, Lambert J, Kukanskis K, Kingsmore S, Lasken R, Schweitzer B (2001) Signal amplification by rolling circle amplification on DNA microarrays. Nucleic Acids Res 29: e118.
116. Ngundi MM, Taitt CR, McMurray SA, Kahne D, Ligler FS (2005) Detection of bacterial toxins with monosaccharide arrays. Biosens Bioelectron 22: 124-130.
117. Nuwaysir EF, Huang W, Albert TJ, et al. (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12: 1749-1755.
118. Ofir K, Berdichevsky Y, Benhar I, Azriel-Rosenfeld R, Lamed R, Barak Y, Bayer EA, Morag E (2005) Versatile protein microarray based on carbohydrate-binding modules. Proteomics 5: 1806-1814.
119. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SPA (1994) Lightdirected oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 91: 5022-5026.
120. Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA (2003) Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 31: e142.
121. Phillips J, Eberwine JH (1996) Antisense RNA amplification: A linear amplification method for analyzing the mRNA population from single living cells. Methods 10: 283-288.
122. Phimister B (1999) Going global. Nat Genet 21(suppl 1-1).
123. Pinkel D, Segraves R, Sudar D, et al. (1998). High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20: 207-211.
124. Poetz O, Ostendorp R, Brocks B, Schwenk JM, Stoll D, Joos TO, Templin MF (2005) Protein microarrays for antibody profiling: specificity and affinity determination on a chip. Proteomics 5: 2402-2411.
125. Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis RW, Esposito RE (2000) The core meiotic transcriptome in budding yeasts. Nat Genet 26: 415-423.
126. Ramdas L, Wang J, Hu L, Cogdell D, Taylor E, Zhang W (2001) Comparative evaluation of laser-based microarray scanners. Biotechniques 31: 546-550.
127. Reimer U, Reineke U, Schneider-Mergener J (2002) Peptide arrays: from macro to micro. Curr Opin Biotechnol 13: 315-320.
128. Reineke U, Volkmer-Engert R, Schneider-Mergener J (2001) Applications of peptide arrays prepared by SPOT-technology. Curr Opin Biotechnol 12: 59-64.
129. Ren B, Robert F, Wyrick JJ, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
130. Sakanyan V (2005) High-throughput and multiplexed protein array technology: protein-DNA and protein-protein interactions. J Chromatogr B 815: 77-95.
131. Salma N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S (2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci USA 97: 14668-14673.
132. Schadt EE, Li C, Ellis B, Wong WH (1999) Feature Extraction And Normalization Algorithms for High-density Oligonucleotide Gene Expression Array Data. Technical Report 303. Department of Statistics UCLA.
133. Schena M (2000) Microarray Biochip Technology. Eaton Publishing, Natick, MA.
134. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
135. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 93: 10614-10619.
136. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW (1998) Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 16: 301-306.
137. Scherer A, Krause A, Walker JR, Sutton SE, Seron D, Raulf F, Cooke MP (2003) Optimized protocol for linear RNA amplification and application to gene expression profiling of human renal biopsies. Biotechniques 34: 546-550, 552-554, 556.
138. Schmid M, Uhlenhaut NH, Godard F, Demar M, Bressan R, Weigel D, Lohmann JU (2003) Dissection of floral induction pathways using global expression analysis. Development 130: 6001-6012.
139. Schoolnik GK (2002) Functional and comparative genomics of pathogenic bacteria. Curr Opin Microbiol 5: 20-26.
140. Schwartz M, Spector L, Gargir A, Shtevi A, Gortler M, Alstock RT, Dukler AA, Dotan N (2003) A new kind of carbohydrate array, its use for profiling antiglycan antibodies, and the discovery of a novel human cellulose-binding antibody. Glycobiology 13: 749-754.
141. Schweitzer B, Predki P, Snyder M (2003) Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 3: 2190-2199.
142. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FS, Lockhart DJ, Church GM (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18: 1262-1268.
143. Shao W, Zhou Z, Laroche I, Lu H, Zong Q, Patel DD, Kingsmore S, Piccoli S (2003) Optimization of rolling-circle amplified protein microarrays for multiplexed protein profiling. J Biomed Biotechnol 5: 299-307.
144. Shin I, Park S, Lee M-R (2005) Carbohydrate microarrays: An advanced technology for functional studies of glycans. Chem Eur J 11: 2894-2901.
145. Soille P (1999) Morphological Image Analysis: Principles and Applications. Springer, New York.
146. Sosnowski RG, Tu E, Butler WF, O'Connell JP, Heller MJ (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc Natl Acad Sci USA 94: 1119-1123.
147. Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98: 503-517.
148. Southern EM (1996) DNA chips: analyzing sequence by hybridization to oligonucleotides on a large scale. Trends Genet 12: 110-115.
149. Southern EM, Maskos U, Elder JK (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13: 1008-1017.
150. Speiss AN, Mueller N, Ivell R (2003) Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 4: 44.
151. Spellman PT, Miller M, Stewart J, et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML) [Research]. Genome Biol 3: 0046.
152. Spring DR (2005) Chemical genetics to chemical genomics: small molecules offer big insights. Chem Soc Rev 34: 472-482.
153. Stears RL, Getts RC, Gullans SR (2000) A novel, sensitive detection system for highdensity microarrays using dendrimer technology. Physio Genomics 3: 93-99.
154. Stears RL, Martinsky T, Schena M (2003) Trends in microarray analysis. Nat Med 9: 140-145.
155. Steinfath M, Wruck W, Seidel H, Lehrach H, Radelof U, O'Brien J (2001) Automated image analysis for array hybridization experiments. Bioinformatics 17: 634-641.
156. Stekel D (2003a) Microarrays: Making them and using them. In: Microarray Bioinformatics. Cambridge University Press, Cambridge, pp. 1-18.
157. Stekel D (2003b) Experimental design. In: Microarray Bioinformatics. Cambridge University Press, Cambridge, pp. 211-230.
158. Stormo GD (2000) DNA binding sites, representation and discovery. Bioinformatics 16: 16-23.
159. Stoughton RB (2005) Applications of DNA microarrays in biology. Annu Rev Biochem 74: 53-82.
160. Syvänen A-C (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2: 930-942.
161. Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo GD (2001) A comparative genomics approach to prediction of new members of regulons. Genome Res 11: 566-584.
162. Templin MF, Stoll D, Schrenk M, Traub PC, Vöhringer CF, Joos TO (2002). Protein microarray technology. Trends Biotechnol 20: 160-166.
163. Theriault TP, Winder SC, Gamble RC (1999) Application of ink-jet printing technology to the manufacture of molecular arrays. In: DNA Microarrays-A Practical Approach (ed. M. Schena). Oxford University Press, Oxford, pp. 101-120.
164. Thirumalapura NR, Morton RJ, Ramachandran A, Malayer JR (2005) Lipopolysaccharide microarrays for the detection of antibodies. J Immunol Methods 298: 73-81.
165. Twyman RM (2004a) From genomics to proteomics. In: Principles of Proteomics. BIOS Scientific Publishers, Oxford, pp.1-22.
166. Twyman RM (2004b) Protein chips and functional proteomics. In: Principles of Proteomics. BIOS Scientific Publishers, Oxford, pp. 193-215.
167. Vahey M, Nau ME, Barrick S, et al. (1999) Performance of the Affymetrix GeneChip HIV PRT 440 platform for antiretroviral drug resistance genotyping of human immunodeficiency virus type 1 clades and viral isolates with length polymorphisms. J Clin Microbiol 37: 2533-2537.
168. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87: 1663-1667.
169. Van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31: 3593-3596.
170. Van Helden J, André B, Collado-Vides J (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281: 827-842.
171. Venkatasubbarao S (2004) Microarrays-status and prospects. Trends Biotechnol 22: 630-637.
172. Walter G, Büssow K, Cahill D, Lueking A, Lehrach H (2000) Protein arrays for gene expression and molecular interaction screening. Curr Opin Microbiol 3: 298-302.
173. Wang D (2003) Carbohydrate microarrays. Proteomics 3: 2167-2175.
174. Wang D, Liu S, Trummer BJ, Deng C, Wang A (2002) Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells. Nat Biotechnol 20: 275-281.
175. Wang DG, Fan JB, Siao CJ, et al. (1998). Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280: 1077-1082.
176. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 15: 1637-1651.
177. Werz DB, Seeberger PH (2005) Carbohydrates as the next frontier in pharmaceutical research. Chem Eur J 11: 3195-3206.
178. Whetzel PL, Parkinson H, Causton HC, et al. (2006) MGED ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22: 866-873.
179. Willats WG, Rasmussen SE, Kristensen T, Mikkelson JD (2002) Sugar-coated microarrays: a novel slide surface for the high-throughput analysis of glycans. Proteomics 2: 1666-1671.
180. Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD (2004) Tracking the evolution of the SARS coronavirus using highthroughput, high-density resequencing arrays. Genome Res 14: 398-405.
181. Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev Genet 3: 579-588.
182. Yang YH, Buckley MJ, Dudoit S, Speed T (2000) Comparison of Methods for Image Analysis on cDNA Microarray Data. Technical report #584. University of California, Berkeley.
183. Yang YH, Buckley MJ, Dudoit S, Speed T (2002) Comparison of methods for image analysis on cDNA microarray data. J Comput Graph Stat 11: 108-136.
184. Young BD, Anderson MLM (1985) Quantitative analysis of solution hybridization. In: Nucleic Acid Hybridization-A Practical Approach (eds B.D. Hames and S.J. Higgins). IRL Press, Oxford, pp. 47-71.
185. Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50: 1111-1124.
186. Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 32: 5874-5893.
187. Zheng T, Peelen D, Smith LM (2005) Lectin arrays for profiling cell surface carbohydrate expression. J Am Chem Soc 127: 9982-9983.
188. Zhu H, Snyder M (2001) Protein arrays and microarrays. Curr Opin Chem Biol 5: 40-45.
189. Zhu H, Bilgin M, Bangham R, et al. (2001) Global analysis of protein activities using proteome chips. Science 293: 2101-2105.
190. Zwick ME, McAffee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A (2004) Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol 6: R10.