Protein arrays, an excellent tool in biomedical research

Frontiers in Bioscience

Volumn 8, Issue , 2003, Pages

  Huang, Ruo Pan ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Antibody; Antibody Arrays; Biochip; Capture Molecules; Diagnosis; Expression; Modification; Protein Arrays; Protein DNA Interaction; Protein Protein Interaction; Proteomics; Review

Indexed keywords

REAGENT;

ANALYTIC METHOD; ANTIBODY DETECTION; CARBOHYDRATE ANALYSIS; CELL TYPE; DEVICE; GENOME ANALYSIS; MEDICAL RESEARCH; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; HUMAN; METHODOLOGY;

BIOMEDICAL RESEARCH; HUMANS; PROTEIN ARRAY ANALYSIS;

EID: 0346423698     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/1017     Document Type: Review

References (140)

1. Venter, J. C., M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural, G. G. Sutton, H. O. Smith, M. Yandell, C. A. Evans, R. A. Holt, J. D. Gocayne, P. Amanatides, R. M. Ballew, D. H. Huson, J. R. Wortman, Q. Zhang, C. D. Kodira, X. H. Zheng, L. Chen, M. Skupski, G. Subramanian, P. D. Thomas, J. Zhang, G. L. Gabor Miklos, C. Nelson, S. Broder, A. G. Clark, J. Nadeau, V. A. McKusick, N. Zinder, A. J. Levine, R. J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, F. Di, V, P. Dunn, K. Eilbeck, C. Evangelista, A. E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T. J. Heiman, M. E. Higgins, R. R. Ji, Z. Ke, K. A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G. V. Merkulov, N. Milshina, H. M. Moore, A. K. Naik, V. A. Narayan, B. Neelam, D. Nusskern, D. B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M. L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y. H. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N. N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J. F. Abril, R. Guigo, M. J. Campbell, K. V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania and others: The sequence of the human genome. Science 291, 1304-1351 (2001)
2. Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J. P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J. C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R. H. Waterston, R. K. Wilson, L. W. Hillier, J. D. McPherson, M. A. Marra, E. R. Mardis, L. A. Fulton, A. T. Chinwalla, K. H. Pepin, W. R. Gish, S. L. Chissoe, M. C. Wendl, K. D. Delehaunty, T. L. Miner, A. Delehaunty, J. B. Kramer, L. L. Cook, R. S. Fulton, D. L. Johnson, P. J. Minx, S. W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J. F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R. A. Gibbs, D. M. Muzny, S. E. Scherer, J. B. Bouck, E. J. Sodergren, K. C. Worley, C. M. Rives, J. H. Gorrell, M. L. Metzker, S. L. Naylor, R. S. Kucherlapati, D. L. Nelson, G. M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D. R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H. M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R. W. Davis, N. A. Federspiel, A. P. Abola, M. J. Proctor, R. M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D. R. Cox, M. V. Olson, R. Kaul, C. Raymond, N. Shimizu, K. Kawasaki, S. Minoshima, G. A. Evans, M. Athanasiou, R. Schultz, B. A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W. R. McCombie, B. M. de la, N. Dedhia, H. Blocker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J. A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D. G. Brown, C. B. Burge, L. Cerutti, H. C. Chen, D. Church, M. Clamp, R. R. Copley, T. Doerks, S. R. Eddy, E. E. Eichler, T. S. Furey and others: Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001)
3. Eisen, J. A., K. E. Nelson, I. T. Paulsen, J. F. Heidelberg, M. Wu, R. J. Dodson, R. Deboy, M. L. Gwinn, W. C. Nelson, D. H. Haft, E. K. Hickey, J. D. Peterson, A. S. Durkin, J. L. Kolonay, F. Yang, I. Holt, L. A. Umayam, T. Mason, M. Brenner, T. P. Shea, D. Parksey, W. C. Nierman, T. V. Feldblyum, C. L. Hansen, M. B. Craven, D. Radune, J. Vamathevan, H. Khouri, O. White, T. M. Gruber, K. A. Ketchum, J. C. Venter, H. Tettelin, D. A. Bryant, and C. M. Fraser: The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A 99, 9509-9514 (2002)
4. Hoffman, S. L., G. M. Subramanian, F. H. Collins, and J. C. Venter: Plasmodium, human and Anopheles genomics and malaria. Nature 415, 702-709 (2002)
5. Tettelin, H., K. E. Nelson, I. T. Paulsen, J. A. Eisen, T. D. Read, S. Peterson, J. Heidelberg, R. T. DeBoy, D. H. Haft, R. J. Dodson, A. S. Durkin, M. Gwinn, J. F. Kolonay, W. C. Nelson, J. D. Peterson, L. A. Umayam, O. White, S. L. Salzberg, M. R. Lewis, D. Radune, E. Holtzapple, H. Khouri, A. M. Wolf, T. R. Utterback, C. L. Hansen, L. A. McDonald, T. V. Feldblyum, S. Angiuoli, T. Dickinson, E. K. Hickey, I. E. Holt, B. J. Loftus, F. Yang, H. O. Smith, J. C. Venter, B. A. Dougherty, D. A. Morrison, S. K. Hollingshead, and C. M. Fraser: Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293, 498-506 (2001)
6. Nierman, W. C., T. V. Feldblyum, M. T. Laub, I. T. Paulsen, K. E. Nelson, J. A. Eisen, J. F. Heidelberg, M. R. Alley, N. Ohta, J. R. Maddock, I. Potocka, W. C. Nelson, A. Newton, C. Stephens, N. D. Phadke, B. Ely, R. T. DeBoy, R. J. Dodson, A. S. Durkin, M. L. Gwinn, D. H. Haft, J. F. Kolonay, J. Smit, M. B. Craven, H. Khouri, J. Shetty, K. Berry, T. Utterback, K. Tran, A. Wolf, J. Vamathevan, M. Ermolaeva, O. White, S. L. Salzberg, J. C. Venter, L. Shapiro, C. M. Fraser, and J. Eisen: Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci U S A 98, 4136-4141 (2001)
7. Gregory, S. G., M. Sekhon, J. Schein, S. Zhao, K. Osoegawa, C. E. Scott, R. S. Evans, P. W. Burridge, T. V. Cox, C. A. Fox, R. D. Hutton, I. R. Mullenger, K. J. Phillips, J. Smith, J. Stalker, G. J. Threadgold, E. Birney, K. Wylie, A. Chinwalla, J. Wallis, L. Hillier, J. Carter, T. Gaige, S. Jaeger, C. Kremitzki, D. Layman, J. Maas, R. McGrane, K. Mead, R. Walker, S. Jones, M. Smith, J. Asano, I. Bosdet, S. Chan, S. Chittaranjan, R. Chiu, C. Fjell, D. Fuhrmann, N. Girn, C. Gray, R. Guin, L. Hsiao, M. Krzywinski, R. Kutsche, S. S. Lee, C. Mathewson, C. McLeavy, S. Messervier, S. Ness, P. Pandoh, A. L. Prabhu, P. Saeedi, D. Smailus, L. Spence, J. Stott, S. Taylor, W. Terpstra, M. Tsai, J. Vardy, N. Wye, G. Yang, S. Shatsman, B. Ayodeji, K. Geer, G. Tsegaye, A. Shvartsbeyn, E. Gebregeorgis, M. Krol, D. Russell, L. Overton, J. A. Malek, M. Holmes, M. Heaney, J. Shetty, T. Feldblyum, W. C. Nierman, J. J. Catanese, T. Hubbard, R. H. Waterston, J. Rogers, P. J. De Jong, C. M. Fraser, M. Marra, J. D. McPherson, and D. R. Bentley: A physical map of the mouse genome. Nature 418, 743-750 (2002)
8. Mohr, S., G. D. Leikauf, G. Keith, and B. H. Rihn: Microarrays as cancer keys: an array of possibilities. J Clin Oncol 20, 3165-3175 (2002)
9. Warner, E. E. and B. K. Dieckgraefe: Application of genome-wide gene expression profiling by high-density DNA arrays to the treatment and study of inflammatory bowel disease. Inflamm Bowel Dis 8, 140-157 (2002)
10. Leikauf, G. D., S. A. McDowell, C. J. Bachurski, B. J. Aronow, K. Gammon, S. C. Wesselkamper, W. Hardie, J. S. Wiest, J. E. Leikauf, T. R. Korfhagen, and D. R. Prows: Functional genomics of oxidant-induced lung injury. Adv Exp Med Biol 500, 479-487 (2001)
11. Ekins, R. and F. Chu: Multianalyte microspot immunoassay. The microanalytical 'compact disk' of the future. Ann Biol Clin (Paris) 50, 337-353 (1992)
12. Ekins, R. and F. Chu: Immunoassay and other ligand assays: present status and future trends. J Int Fed Clin Chem 9, 100-109 (1997)
13. Ekins, R. P.: Ligand assays: from electrophoresis to miniaturized microarrays. Clin Chem 44, 2015-2030 (1998)
14. Silzel, J. W., B. Cercek, C. Dodson, T. Tsay, and R. J. Obremski: Mass-sensing, multianalyte microarray immunoassay with imaging detection. Clin Chem 44, 2036-2043 (1998)
15. Mendoza, L. G., P. McQuary, A. Mongan, R. Gangadharan, S. Brignac, and M. Eggers: High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques 27, 778-6, 788 (1999)
16. Young, R. A.: Biomedical discovery with DNA arrays. Cell 102, 9-15 (2000)
17. Carulli, J. P., M. Artinger, P. M. Swain, C. D. Root, L. Chee, C. Tulig, J. Guerin, M. Osborne, G. Stein, J. Lian, and P. T. Lomedico: High throughput analysis of differential gene expression. J Cell Biochem Suppl 30-31, 286-296 (1998)
18. Lockhart, D. J. and E. A. Winzeler: Genomics, gene expression and DNA arrays. Nature 405, 827-836 (2000)
19. Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold: Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19, 1720-1730 (1999)
20. Anderson, L. and J. Seilhamer: A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18, 533-537 (1997)
21. Yanagida, M.: Functional proteomics; current achievements. J Chromatogr B Analyt Technol Biomed Life Sci 771, 89-106 (2002)
22. Srinivas, P. R., M. Verma, Y. Zhao, and S. Srivastava: Proteomics for cancer biomarker discovery. Clin Chem 48, 1160-1169 (2002)
23. Fountoulakis, M.: Proteomics: current technologies and applications in neurological disorders and toxicology. Amino Acids 21, 363-381 (2001)
24. Strosberg, A. D.: Functional proteomics to exploit genome sequences. Cell Mol Biol (Noisy -le-grand) 47, 1295-1299 (2001)
25. Hanash, S. M.: Global profiling of gene expression in cancer using genomics and proteomics. Curr Opin Mol Ther 3, 538-545 (2001)
26. Merchant, M. and S. R. Weinberger: Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 21, 1164-1177 (2000)
27. Li, J., Z. Zhang, J. Rosenzweig, Y. Y. Wang, and D. W. Chan: Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 48, 1296-1304 (2002)
28. Ardekani, A. M., L. A. Liotta, and E. F. Petricoin, III: Clinical potential of proteomics in the diagnosis of ovarian cancer. Expert Rev Mol Diagn 2, 312-320 (2002)
29. Rosty, C., L. Christa, S. Kuzdzal, W. M. Baldwin, M. L. Zahurak, F. Carnot, D. W. Chan, M. Canto, K. D. Lillemoe, J. L. Cameron, C. J. Yeo, R. H. Hruban, and M. Goggins: Identification of hepatocarcinoma-intestine-pancreas/ pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res 62, 1868-1875 (2002)
30. Verma, M., G. L. Wright, Jr., S. M. Hanash, R. Gopal-Srivastava, and S. Srivastava: Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers. Ann N Y Acad Sci 945, 103-115 (2001)
31. Petricoin, E. F., A. M. Ardekani, B. A. Hitt, P. J. Levine, V. A. Fusaro, S. M. Steinberg, G. B. Mills, C. Simone, D. A. Fishman, E. C. Kohn, and L. A. Liotta: Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572-577 (2002)
32. Hearn, M. T.: High-performance liquid chromatography and its application to protein chemistry. Adv Chromatogr 20, 1-82 (1982)
33. Hancock, W. S., C. A. Bishop, R. L. Prestidge, D. R. Harding, and M. T. Hearn: Reversed-phase, high-pressure liquid chromatography of peptides and proteins with ion-pairing reagents. Science 200, 1168-1170 (1978)
34. Dolnik, V. and K. M. Hutterer: Capillary electrophoresis of proteins 1999-2001. Electrophoresis 22, 4163-4178 (2001)
35. Carson, R. T. and D. A. Vignali: Simultaneous quantitation of 15 cytokines using a multiplexed flow cytometric assay. J Immunol Methods 227, 41-52 (1999)
36. Cook, E. B., J. L. Stahl, L. Lowe, R. Chen, E. Morgan, J. Wilson, R. Varro, A. Chan, F. M. Graziano, and N. P. Barney: Simultaneous measurement of six cytokines in a single sample of human tears using microparticle-based flow cytometry: allergies vs. non-allergies. J Immunol Methods 254, 109-118 (2001)
37. Kettman, J. R., T. Davies, D. Chandler, K. G. Oliver, and R. J. Fulton: Classification and properties of 64 multiplexed microsphere sets. Cytometry 33, 234-243 (1998)
38. Bellisario, R., R. J. Colinas, and K. A. Pass: Simultaneous measurement of antibodies to three HIV-1 antigens in newborn dried blood-spot specimens using a multiplexed microsphere-based immunoassay. Early Hum Dev 64, 21-25 (2001)
39. MacBeath, G. and S. L. Schreiber: Printing proteins as microarrays for high-throughput function determination [see comments]. Science 289, 1760-1763 (2000)
40. Huang, R., Y. Lin, C. C. Wang, J. Gano, B. Lin, Q. Shi, A. Boynton, J. Burke, and R. P. Huang: Connexin 43 suppresses human glioblastoma cell growth by down-regulation of monocyte chemotactic protein 1, as discovered using protein array technology. Cancer Res 62, 2806-2812 (2002)
41. Wang, C. C., R.-P. Huang, M. Sommer, H. Lisoukov, R. Huang, Y. Lin, and J. Burke: Array-based multiplexed screening and quantitation of human cytokines and chemokines. J. Proteome Res. 1:337-343 (2002
42. Huang, R. P.: Simultaneous detection of multiple proteins with an array-based enzyme-linked immunosorbent assay (ELISA) and enhanced chemiluminescence (ECL). Clin Chem Lab Med 39, 209-214 (2001)
43. Huang, R. P.: Detection of multiple proteins in an antibody-based protein microarray system. J Immunol Methods 255, 1-13 (2001)
44. Huang, R. P., R. Huang, Y. Fan, and Y. Lin: Simultaneous detection of multiple cytokines from conditioned media and patient's sera by an antibody-based protein array system. Anal Biochem 294, 55-62 (2001)
45. Fang, Y., A. G. Frutos, and J. Lahiri: Membrane protein microarrays. J Am Chem Soc 124, 2394-2395 (2002)
46. Wiese, R., Y. Belosludtsev, T. Powdrill, P. Thompson, and M. Hogan: Simultaneous multianalyte ELISA performed on a microarray platform. Clin Chem 47, 1451-1457 (2001)
47. Dontha, N., W. B. Nowall, and W. G. Kuhr: Generation of biotin/avidin/enzyme nanostructures with maskless photolithography. Anal Chem 69, 2619-2625 (1997)
48. Nowall, W. B., N. Dontha, and W. G. Kuhr: Electron transfer kinetics at a biotin/avidin patterned glassy carbon electrode. Biosens Bioelectron 13, 1237-1244 (1998)
49. Lesaicherre, M. L., R. Y. Lue, G. Y. Chen, Q. Zhu, and S. Q. Yao: Intein-mediated biotinylation of proteins and its application in a protein microarray. J Am Chem Soc 124, 8768-8769 (2002)
50. Pritchard, D. J., H. Morgan, and J. M. Cooper: Patterning and regeneration of surfaces with antibodies. Anal Chem 67, 3605-3607 (1995)
51. Zhu, H., M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Snyder: Global analysis of protein activities using proteome chips. Science 293, 2101-2105 (2001)
52. Li, M.: Applications of display technology in protein analysis. Nat Biotechnol 18, 1251-1256 (2000)
53. Mao, S., C. Gao, C. H. Lo, P. Wirsching, C. H. Wong, and K. D. Janda: Phage-display library selection of high-affinity human single-chain antibodies to tumor-associated carbohydrate antigens sialyl Lewisx and Lewisx. Proc Natl Acad Sci U S A 96, 6953-6958 (1999)
54. Gao, C., S. Mao, C. H. Lo, P. Wirsching, R. A. Lerner, and K. D. Janda: Making artificial antibodies: a format for phage display of combinatorial heterodimeric arrays. Proc Natl Acad Sci U S A 96, 6025-6030 (1999)
55. Knappik, A., L. Ge, A. Honegger, P. Pack, M. Fischer, G. Wellnhofer, A. Hoess, J. Wolle, A. Pluckthun, and B. Virnekas: Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J Mol Biol 296, 57-86 (2000)
56. Johnston, S. A. and M. A. Barry: Genetic to genomic vaccination. Vaccine 15, 808-809 (1997)
57. Barry, M. A. and S. A. Johnston: Biological features of genetic immunization. Vaccine 15, 788-791 (1997)
58. Sykes, K. F. and S. A. Johnston: Linear expression elements: a rapid, in vivo, method to screen for gene functions. Nat Biotechnol 17, 355-359 (1999)
59. Barry, M. A., M. E. Barry, and S. A. Johnston: Production of monoclonal antibodies by genetic immunization. Biotechniques 16, 616-8, 620 (1994)
60. Brody, E. N., M. C. Willis, J. D. Smith, S. Jayasena, D. Zichi, and L. Gold: The use of aptamers in large arrays for molecular diagnostics. Mol Diagn 4, 381-388 (1999)
61. Brody, E. N. and L. Gold: Aptamers as therapeutic and diagnostic agents. J Biotechnol 74, 5-13 (2000)
62. Lee, M. and D. R. Walt: A fiber-optic microarray biosensor using aptamers as receptors. Anal Biochem 282, 142-146 (2000)
63. Smith, G. P. and V. A. Petrenko: Phage Display. Chem Rev 97, 391-410 (1997)
64. Soth, M. J. and J. S. Nowick: Unnatural oligomers and unnatural oligomer libraries. Curr Opin Chem Biol 1, 120-129 (1997)
65. Figliozzi, G. M., R. Goldsmith, S. C. Ng, S. C. Banville, and R. N. Zuckermann: Synthesis of N-substituted glycine peptoid libraries. Methods Enzymol 267, 437-447 (1996)
66. Oliver, S. F. and C. Abell: Combinatorial synthetic design. Curr Opin Chem Biol 3, 299-306 (1999)
67. Nuttall, S. D., M. J. Rousch, R. A. Irving, S. E. Hufton, H. R. Hoogenboom, and P. J. Hudson: Design and expression of soluble CTLA-4 variable domain as a scaffold for the display of functional polypeptides. Proteins 36, 217-227 (1999)
68. Skerra, A.: 'Anticalins': a new class of engineered ligand-binding proteins with antibody-like properties. J Biotechnol 74, 257-275 (2001)
69. Zhang, Z., W. Zhu, and T. Kodadek: Selection and application of peptide-binding peptides. Nat Biotechnol 18, 71-74 (2000)
70. Visintin, M., E. Tse, H. Axelson, T. H. Rabbitts, and A. Cattaneo: Selection of antibodies for intracellular function using a two-hybrid in vivo system. Proc Natl Acad Sci U S A 96, 11723-11728 (1999)
71. Kodadek, T.: Protein microarrays: prospects and problems. Chem Biol 8, 105-115 (2001)
72. Nord, K., E. Gunneriusson, m. M. Uhl inverted question, and P. A. Nygren: Ligands selected from combinatorial libraries of protein A for use in affinity capture of apolipoprotein A-1M and taq DNA polymerase. J Biotechnol 80, 45-54 (2000)
73. He, M. and M. J. Taussig: Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res 29, E73-E73 (2001)
74. Hanash, S. M., J. Madoz-Gurpide, and D. E. Misek: Identification of novel targets for cancer therapy using expression proteomics. Leukemia 16, 478-485 (2002)
75. Bussow, K., D. Cahill, W. Nietfeld, D. Bancroft, E. Scherzinger, H. Lehrach, and G. Walter: A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Res 26, 5007-5008 (1998)
76. Joos, T. O., M. Schrenk, P. Hopfl, K. Kroger, U. Chowdhury, D. Stoll, D. Schorner, M. Durr, K. Herick, S. Rupp, K. Sohn, and H. Hammerle: A microarray enzyme-linked immunosorbent assay for autoimmune diagnostics. Electrophoresis 21, 2641-2650 (2000)
77. Arenkov, P., A. Kukhtin, A. Gemmell, S. Voloshchuk, V. Chupeeva, and A. Mirzabekov: Protein microchips: use for immunoassay and enzymatic reactions. Anal Biochem 278, 123-131 (2000)
78. Haab, B. B., M. J. Dunham, and P. O. Brown: Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2, RESEARCH0004-(2001)
79. Schweitzer, B., S. Roberts, B. Grimwade, W. Shao, M. Wang, Q. Fu, Q. Shu, I. Laroche, Z. Zhou, V. T. Tchernev, J. Christiansen, M. Velleca, and S. F. Kingsmore: Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol 20, 359-365 (2002)
80. Ge, H.: UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions. Nucleic Acids Res 28, e3-(2000)
81. Zhu, H., J. F. Klemic, S. Chang, P. Bertone, A. Casamayor, K. G. Klemic, D. Smith, M. Gerstein, M. A. Reed, and M. Snyder: Analysis of yeast protein kinases using protein chips. Nat Genet 26, 283-289 (2000)
82. Nelson, B. P., T. E. Grimsrud, M. R. Liles, R. M. Goodman, and R. M. Corn: Surface plasmon resonance imaging measurements of DNA and RNA hybridization adsorption onto DNA microarrays. Anal Chem 73, 1-7 (2001)
83. Pawlak, M., E. Schick, M. A. Bopp, M. J. Schneider, P. Oroszlan, and M. Ehrat: Zeptosens' protein microarrays: a novel high performance microarray platform for low abundance protein analysis. Proteomics 2, 383-393 (2002)
84. Pei, R., Z. Cheng, E. Wang, and X. Yang: Amplification of antigen-antibody interactions based on biotin labeled protein-streptavidin network complex using impedance spectroscopy. Biosens Bioelectron 16, 355-361 (2001)
85. Rickert, J., A. Brecht, and W. Gopel: Quartz crystal microbalances for quantitative biosensing and characterizing protein multilayers. Biosens Bioelectron 12, 567-575 (1997)
86. Renken, J., R. Dahint, M. Grunze, and F. Josse: Multifrequency evaluation of different immunosorbents on acoustic plate mode sensors. Anal Chem 68, 176-182 (1996)
87. Nakanishi, K., K. Ikebukuro, and I. Karube: Determination of cyanide using a microbial sensor. Appl Biochem Biotechnol 60, 97-106 (1996)
88. Wu, G., H. Ji, K. Hansen, T. Thundat, R. Datar, R. Cote, M. F. Hagan, A. K. Chakraborty, and A. Majumdar: Origin of nanomechanical cantilever motion generated from biomolecular interactions. Proc Natl Acad Sci USA 98, 1560-1564 (2001)
89. Wu, G., R. H. Datar, K. M. Hansen, T. Thundat, R. J. Cote, and A. Majumdar: Bioassay of prostate-specific antigen (PSA) using microcantilevers. Nat Biotechnol 19, 856-860 (2001)
90. Guschin, D., G. Yershov, A. Zaslavsky, A. Gemmell, V. Shick, D. Proudnikov, P. Arenkov, and A. Mirzabekov: Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal Biochem 250, 203-211 (1997)
91. Roda, A., M. Guardigli, C. Russo, P. Pasini, and M. Baraldini: Protein microdeposition using a conventional ink-jet printer. Biotechniques 28, 492-496 (2000)
92. Fodor, S. P., J. L. Read, M. C. Pirrung, L. Stryer, A. T. Lu, and D. Solas: Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767-773 (1991)
93. Frank, R.: The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports-principles and applications. J Immunol Methods 267, 13-26 (2002)
94. Morozov, V. N., A. V. Gavryushkin, and A. A. Deev: Direct detection of isotopically labeled metabolites bound to a protein microarray using a charge-coupled device. J Biochem Biophys Methods 51, 57-67 (2002)
95. Avseenko, N. V., T. Y. Morozova, F. I. Ataullakhanov, and V. N. Morozov: Immunoassay with multicomponent protein microarrays fabricated by electrospray deposition. Anal Chem 74, 927-933 (2002)
96. Wadu-Mesthrige, K., N. A. Amro, and G. Y. Liu: Immobilization of proteins on self-assembled monolayers. Scanning 22, 380-388 (2000)
97. Wadu-Mesthrige, K., N. A. Amro, J. C. Garno, S. Xu, and G. Liu: Fabrication of nanometer-sized protein patterns using atomic force microscopy and selective immobilization. Biophys J 80, 1891-1899 (2001)
98. Unger, M. A., H. P. Chou, T. Thorsen, A. Scherer, and S. R. Quake: Monolithic microfabricated valves and pumps by multilayer soft lithography. Science 288, 113-116 (2000)
99. Deng, T., H. Wu, S. T. Brittain, and G. M. Whitesides: Prototyping of masks, masters, and stamps/molds for soft lithography using an office printer and photographic reduction. Anal Chem 72, 3176-3180 (2000)
100. Shieh, J., C. To, J. Carramao, N. Nishimura, Y. Maruta, Y. Hashimoto, D. Wright, H. C. Wu, and A. Azarani: High-throughput array production using precision glass syringes. Biotechniques 32, 1360-1365 (2002)
101. Jellis, C. L., T. J. Cradick, P. Rennert, P. Salinas, J. Boyd, T. Amirault, and G. S. Gray: Defining critical residues in the epitope for a HIV-neutralizing monoclonal antibody using phage display and peptide array technologies. Gene 137, 63-68 (1993)
102. Lesaicherre, M. L., M. Uttamchandani, G. Y. Chen, and S. Q. Yao: Antibody-Based fluorescence detection of kinase activity on a peptide array. Bioorg Med Chem Lett 12, 2085-2088 (2002)
103. Hoff, K. G., D. T. Ta, T. L. Tapley, J. J. Silberg, and L. E. Vickery: Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU. J Biol Chem 277, 27353-27359 (2002)
104. Ducruet, A. P., R. L. Rice, K. Tamura, F. Yokokawa, S. Yokokawa, P. Wipf, and J. S. Lazo: Identification of new Cdc25 dual specificity phosphatase inhibitors in a targeted small molecule array. Bioorg Med Chem 8, 1451-1466 (2000)
105. Kuruvilla, F. G., A. F. Shamji, S. M. Sternson, P. J. Hergenrother, and S. L. Schreiber: Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653-657 (2002)
106. Robinson, W. H., C. DiGennaro, W. Hueber, B. B. Haab, M. Kamachi, E. J. Dean, S. Fournel, D. Fong, M. C. Genovese, H. E. de Vegvar, K. Skriner, D. L. Hirschberg, R. I. Morris, S. Muller, G. J. Pruijn, W. J. van Venrooij, J. S. Smolen, P. O. Brown, L. Steinman, and P. J. Utz: Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med 8, 295-301 (2002)
107. Paweletz, C. P., L. Charboneau, V. E. Bichsel, N. L. Simone, T. Chen, J. W. Gillespie, M. R. Emmert-Buck, M. J. Roth, E. F. Petricoin III, and L. A. Liotta: Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981-1989 (2001)
108. Tam, S. W., R. Wiese, S. Lee, J. Gilmore, and K. D. Kumble: Simultaneous analysis of eight human Thl/Th2 cytokines using microarrays. J Immunol Methods 261, 157-165 (2002)
109. Lin, Y., R. Huang, N. Santanam, Y.-G. Liu, S. Parthasarathy and R.-P. Huang. Profiling of human cytokines in healthy individuals with vitamin E supplementation by antibody arrays. Cancer letter. 187: 17-24 (2002).
110. Sreekumar, A., M. K. Nyati, S. Varambally, T. R. Barrette, D. Ghosh, T. S. Lawrence, and A. M. Chinnaiyan: Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res 61, 7585-7593 (2001)
111. Knezevic, V., C. Leethanakul, V. E. Bichsel, J. M. Worth, V. V. Prabhu, J. S. Gutkind, L. A. Liotta, P. J. Munson, E. F. Petricoin, III, and D. B. Krizman: Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics 1, 1271-1278 (2001)
112. Li, J., Z. Zhang, J. Rosenzweig, Y. Y. Wang, and D. W. Chan: Proteomics and bioinformatics approaches for identification of serum biomarkers to detect breast cancer. Clin Chem 48, 1296-1304 (2002)
113. Ardekani, A. M., L. A. Liotta, and E. F. Petricoin, III: Clinical potential of proteomics in the diagnosis of ovarian cancer. Expert Rev Mol Diagn 2, 312-320 (2002)
114. Rosty, C., L. Christa, S. Kuzdzal, W. M. Baldwin, M. L. Zahurak, F. Carnot, D. W. Chan, M. Canto, K. D. Lillemoe, J. L. Cameron, C. J. Yeo, R. H. Hruban, and M. Goggins: Identification of hepatocarcinoma-intestine-pancreas/ pancreatitis-associated protein I as a biomarker for pancreatic ductal adenocarcinoma by protein biochip technology. Cancer Res 62, 1868-1875 (2002)
115. Verma, M., G. L. Wright, Jr., S. M. Hanash, R. Gopal-Srivastava, and S. Srivastava: Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers. Ann N Y Acad Sci 945, 103-115 (2001)
116. Alberts, B.: The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (1998)
117. Kukar, T., S. Eckenrode, Y. Gu, W. Lian, M. Megginson, J. X. She, and D. Wu: Protein microarrays to detect protein-protein interactions using red and green fluorescent proteins. Anal Biochem 306, 50-54 (2002)
118. Wang, Y., T. R. Wu, S. Cai, T. Weite, and Y. E. Chin: Statl as a component of tumor necrosis factor alpha receptor 1-TRADD signaling complex to inhibit NF-kappaB activation. Mol Cell Biol 20, 4505-4512 (2000)
119. Espejo, A., J. Cote, A. Bednarek, S. Richard, and M. T. Bedford: A protein-domain microarray identifies novel protein-protein interactions. Biochem J Pt, (2002)
120. Zhu, H., J. F. Klemic, S. Chang, P. Bertone, A. Casamayor, K. G. Klemic, D. Smith, M. Gerstein, M. A. Reed, and M. Snyder: Analysis of yeast protein kinases using protein chips. Nat Genet 26, 283-289 (2000)
121. Houseman, B. T., J. H. Huh, S. J. Kron, and M. Mrksich: Peptide chips for the quantitative evaluation of protein kinase activity. Nat Biotechnol 20, 270-274 (2002)
122. Bulyk, M. L., E. Gentalen, D. J. Lockhart, and G. M. Church: Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 17, 573-577 (1999)
123. de Wildt, R. M., C. R. Mundy, B. D. Gorick, and I. M. Tomlinson: Antibody arrays for high-throughput screening of antibody-antigen interactions. Nat Biotechnol 18, 989-994 (2000)
124. Holt, L. J., K. Bussow, G. Walter, and I. M. Tomlinson: By-passing selection: direct screening for antibody-antigen interactions using protein arrays. Nucleic Acids Res 28, E72-(2000)
125. Houseman, B. T. and M. Mrksich: Carbohydrate arrays for the evaluation of protein binding and enzymatic modification. Chem Biol 9, 443-454 (2002)
126. Bidlingmaier, S. and M. Snyder: Carbohydrate analysis prepares to enter the "Omics" era. Chem Biol 9, 400-401 (2002)
127. Pietropaolo, M. and G. S. Eisenbarth: Autoantibodies in human diabetes. Curr Dir Autoimmun 4, 252-282 (2001)
128. Craft, J. and S. Fatenejad: Self antigens and epitope spreading in systemic autoimmunity. Arthritis Rheum 40, 1374-1382 (1997)
129. James, J. A. and J. B. Harley: B-cell epitope spreading in autoimmunity. Immunol Rev 164, 185-200 (1998)
130. Rowe, C. A., L. M. Tender, M. J. Feldstein, J. P. Golden, S. B. Scruggs, B. D. MacCraith, J. J. Cras, and F. S. Ligler: Array biosensor for simultaneous identification of bacterial, viral, and protein analytes. Anal Chem 71, 3846-3852 (1999)
131. Mezzasoma, L., T. Bacarese-Hamilton, M. Di Cristina, R. Rossi, F. Bistoni, and A. Crisanti: Antigen microarrays for serodiagnosis of infectious diseases. Clin Chem 48, 121-130 (2002)
132. Hiller, R., S. Laffer, C. Harwanegg, M. Huber, W. M. Schmidt, A. Twardosz, B. Barletta, W. M. Becker, K. Blaser, H. Breiteneder, M. Chapman, R. Crameri, M. Duchene, F. Ferreira, H. Fiebig, K. Hoffmann-Sommergruber, T. P. King, T. Kleber-Janke, V. P. Kurup, S. B. Lehrer, J. Lidholm, U. Muller, C. Pini, G. Reese, O. Scheiner, A. Scheynius, H. D. Shen, S. Spitzauer, R. Suck, I. Swoboda, W. Thomas, R. Tinghino, M. Hage-Hamsten, T. Virtanen, D. Kraft, M. W. Muller, and R. Valenta: Microarrayed allergen molecules: diagnostic gatekeepers for allergy treatment. FASEB J 16, 414-416 (2002)
133. Belov, L., I. de, V, C. G. dos Remedios, S. P. Mulligan, and R. I. Christopherson: Immunophenotyping of leukemias using a cluster of differentiation antibody microarray. Cancer Res 61, 4483-4489 (2001)
134. Madoz-Gurpide, J., H. Wang, D. E. Misek, F. Brichory, and S. M. Hanash: Protein based microarrays: a tool for probing the proteome of cancer cells and tissues. Proteomics 1, 1279-1287 (2001)
135. Levsky, J. M., S. M. Shenoy, R. C. Pezo, and R. H. Singer: Single-cell gene expression profiling. Science 297, 836-840 (2002)
136. Jain, K. K.: Post-genomic applications of lab-on-a-chip and microarrays. Trends Biotechnol 20, 184-185 (2002)
137. Meldrum, D. R. and M. R. Holl: MICROFLUIDICS: Microscale Bioanalytical Systems. Science 297, 1197-1198 (2002)
138. Chovan, T. and A. Guttman: Microfabricated devices in biotechnology and biochemical processing. Trends Biotechnol 20, 116-122 (2002)
139. Kasianowicz, J. J., E. Brandin, D. Branton, and D. W. Deamer: Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93, 13770-13773 (1996)
140. Vercoutere, W., S. Winters-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson: Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol 19, 248-252 (2001)