Diagnostics and high throughput screening

Biomedical Nanotechnology

Volumn , Issue , 2005, Pages 75-112

  del Campo, Aránzazu ^a   Bruce, Ian J ^b  

^a MAX PLANCK INSTITUTE FOR INTELLIGENT SYSTEMS   (Germany)

^b UNIVERSITY OF KENT   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 38749123655     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (150)

1. MC Roco. Nanotechnology: convergence with modern biology and medicine. Curr Opin Biotechnol 14: 337–346, 2003.
2. DF Emerich and CG Thanos. Nanotechnology and medicine. Expert Opin Biol Th 3: 655–663, 2003.
3. J Letowski, R Brousseau, and L Masson. DNA microarray applications in environmental microbiology. Anal Lett 36: 3165–3184, 2003.
4. KS Lam and M Renil. From combinatorial chemistry to chemical microarray. Curr Opin Chem Biol 6: 353–358, 2002.
5. J Khandurina and A Guttman. Microchip-based high throughput screening analysis of combinatorial libraries. Curr Opin Chem Biol 6: 359–366, 2002.
6. JL West and NJ Halas. Engineered nanomaterials for biophotonics applications: improving sensing, imaging, and therapeutics. Annu Rev Biomed Eng 5: 285–292, 2003.
7. T Vo-Dinh. Nanobiosensors: probing the sanctuary of individual living cells. J Cell Biochem 87: 154–161, 2002.
8. C Tilstone. Vital statistics. Nature 424: 610–612, 2003.
9. D Michalovich, J Overington, and R Fagan. Protein sequence analysis in silico: application of structure-based bioinformatics to genomic initiatives. Curr Opin Pharmacol 2: 574–580, 2002.
10. RJ Carroll. Variances are not always nuisance parameters. Biometrics 59: 211–220, 2003.
11. AD Weston and L Hood. Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res 3: 179–196, 2004.
12. G Walter, K Bussow, D Cahill, A Lueking, and H Lehrach. Protein arrays for gene expression and molecular interaction screening. Curr Opin Microbiol 3: 298–302, 2000.
13. RA Young. Biomedical discovery with DNA arrays. Cell 102: 9–15, 2000.
14. ZP Weng and C DeLisi. Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol 20: 29–35, 2002.
15. ME Chicurel and DD Dalma-Weiszhausz. Microarrays in pharmacogenomics: advances and future promise. Pharmacogenomics 3: 589–601, 2002.
16. OE Beske and S Goldbard. High-throughput cell analysis using multiplexed array technologies. Drug Discov Today 7: S131–S135, 2002.
17. A Schulze and J Downward. Navigating gene expression using microarrays: a technology review. Nat Cell Biol 3: E190–E195, 2001.
18. M Gabig and G Wegrzyn. An introduction to DNA chips: principles, technology, applications and analysis. Acta Biochim Pol 48: 615–622, 2001.
19. M Arcellana-Panlilio and SM Robbins. Cutting-edge technology. I. Global gene expression profiling using DNA microarrays. Am J Physiol Gastr 282: G397–G402, 2002.
20. MJ Heller. DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 4: 129–153, 2002.
21. CM Roth and ML Yarmush. Nucleic acid biotechnology. Annu Rev Biomed Eng 1: 265–297, 1999.
22. WM Freeman, DJ Robertson, and KE Vrana. Fundamentals of DNA hybridization arrays for gene expression analysis. Biotechniques 29: 1042–1045, 2000.
23. JD Pollock. Gene expression profiling: methodological challenges, results, and prospects for addiction research. Chem Phys Lipids 121: 241–256, 2002.
24. F Gros. From the messenger RNA saga to the transcriptome era. Cr Biol 326: 893–900, 2003.
25. H Zhu and M Snyder. “Omic” approaches for unraveling signaling networks. Curr Opin Cell Biol 14: 173–179, 2002.
26. DD Shoemaker and PS Linsley. Recent developments in DNA microarrays. Curr Opin Microbiol 5: 334–337, 2002.
27. HP Saluz, J Iqbal, GV Limmon, A Ruryk, and ZH Wu. Fundamentals of DNA chip/array technology for comparative gene expression analysis. Curr Sci India 83: 829–833, 2002.
28. L Smith and A Greenfield. DNA microarrays and development. Hum Mol Genet 12: R1–R8, 2003.
29. CM Ding and CR Cantor. Quantitative analysis of nucleic acids: the last few years of progress. J Biochem Mol Biol 37: 1–10, 2004.
30. D Vetter. Chemical microarrays, fragment diversity, label-free imaging by plasmon resonance: a chemical genomics approach. J Cell Biochem 87: 79–84, 2002.
31. BJ Battersby and M Trau. Novel miniaturized systems in high-throughput screening. Trends Biotechnol 20: 167–173, 2002.
32. A Bauer, B Beckmann, C Busold, O Brandt, W Kusnezow, J Pullat, V Aign, K Fellenberg, R Fleischer, A Jacob, M Frohme, and JD Hoheisel. Use of complex DNA and antibody microarrays as tools in functional analyses. Comp Funct Genom 4: 520–524, 2003.
33. MC Pirrung. How to make a DNA chip. Angew Chem Int Edit 41: 1277, 2002.
34. DV Nguyen, AB Arpat, NY Wang, and RJ Carroll. DNA microarray experiments: biological and technological aspects. Biometrics 58: 701–717, 2002.
35. M Glazer, J Fidanza, G McGall, and C Frank. Colloidal silica films for high-capacity DNA probe arrays. Chem Mater 13: 4773–4782, 2001.
36. MJ Buck and JD Lieb. ChIP chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83: 349–360, 2004.
37. L Joos, E Eryuksel, and MH Brutsche. Functional genomics and gene microarrays: use in research and clinical medicine. Swiss Med Wkly 133: 31–38, 2003.
38. FL Kiechle and XB Zhang. The postgenomic era: implications for the clinical laboratory. Arch Pathol Lab Med 126: 255–262, 2002.
39. FL Kiechle and CA Holland-Staley. Genomics, transcriptomics, proteomics, and numbers. Arch Pathol Lab Med 127: 1089–1097, 2003.
40. RC McGlennen. Miniaturization technologies for molecular diagnostics. Clin Chem 47: 393–402, 2001.
41. P Cutler. Protein arrays: current state of the art. Proteomics 3: 3–18, 2003.
42. MF Templin, D Stoll, JM Schwenk, O Potz, S Kramer, and TO Joos. Protein microarrays: promising tools for proteomic research. Proteomics 3: 2155–2166, 2003.
43. C Huels, S Muellner, HE Meyer, and DJ Cahill. The impact of protein biochips and microarrays on the drug development process. Drug Discov Today 7: S119–S124, 2002.
44. JM Nam, SW Han, KB Lee, XG Liu, MA Ratner, and CA Mirkin. Bioactive protein nanoarrays on nickel oxide surfaces formed by dip-pen nanolithography. Angew Chem Int Edit 43: 1246–1249, 2004.
45. KB Lee, SJ Park, CA Mirkin, JC Smith, and M Mrksich. Protein nanoarrays generated by dip-pen nanolithography. Science 295: 1702–1705, 2002.
46. G Walter, K Bussow, A Lueking, and J Glokler. High-throughput protein arrays: prospects for molecular diagnostics. Trends Mol Med 8: 250–253, 2002.
47. XL Gao, XC Zhou, and E Gulari. Light directed massively parallel on-chip synthesis of peptide arrays with t-Boc chemistry. Proteomics 3: 2135–2141, 2003.
48. R Frank. The SPOT synthesis technique: synthetic peptide arrays on membrane supports: principles and applications. J Immunol Methods 267: 13–26, 2002.
49. YS Lee and M Mrksich. Protein chips: from concept to practice. Trends Biotechnol 20: S14–S18, 2002.
50. Y Fang, J Lahiri, and L Picard. G protein-coupled receptor microarrays for drug discovery. Drug Discov Today 8: 755–761, 2003.
51. SP Lal, RI Christopherson, and CG dos Remedios. Antibody arrays: an embryonic but rapidly growing technology. Drug Discov Today 7: S143–S149, 2002.
52. G Elia, M Silacci, S Scheurer, J Scheuermann, and D Neri. Affinity-capture reagents for protein arrays. Trends Biotechnol 20: S19–S22, 2002.
53. DN Wang. Carbohydrate microarrays. Proteomics 3: 2167–2175, 2003.
54. KR Love and PH Seeberger. Carbohydrate arrays as tools for glycomics. Angew Chem Int Edit 41: 3583–3586, 2002.
55. J Hirabayashi. Oligosaccharide microarrays for glycomics. Trends Biotechnol 21: 141–143, 2003.
56. PA Johnston. Cellular platforms for HTS: three case studies. Drug Discov Today 7: 353–363, 2002.
57. SN Bailey, RZ Wu, and DM Sabatini. Applications of transfected cell microarrays in high-throughput drug discovery. Drug Discov Today 7: S113–S118, 2002.
58. G Sauter, R Simon, and K Hillan. Tissue microarrays in drug discovery. Nat Rev Drug Discov 2: 962–972, 2003.
59. DL Rimm, RL Camp, LA Charette, J Costa, DA Olsen, and M Reiss. Tissue microarray: new technology for amplification of tissue resources. Cancer J 7: 24–31, 2001.
60. H Moch, J Kononen, OP Kallioniemi, and G Sauter. Tissue microarrays: what will they bring to molecular and anatomic pathology? Adv Anat Pathol 8: 14–20, 2001.
61. JR Epstein, APK Leung, KH Lee, and DR Walt. High-density, microsphere-based fiber optic DNA microarrays. Biosens Bioelectron 18: 541–546, 2003.
62. JR Epstein and DR Walt. Fluorescence-based fibre optic arrays: a universal platform for sensing. Chem Soc Rev 32: 203–214, 2003.
63. DR Walt. Molecular biology: bead-based fiber-optic arrays. Science 287: 451–452, 2000.
64. AD Sheehan, J Quinn, S Daly, P Dillon, and R O’Kennedy. The development of novel miniaturized immuno-sensing devices: review of a small technology with a large future. Anal Lett 36: 511–537, 2003.
65. SJ Lee and SY Lee. Micro total analysis system (mu-TAS) in biotechnology. Appl Microbiol Biot 64: 289–299, 2004.
66. J Khandurina and A Guttman. Bioanalysis in microfluidic devices. J Chromatogr A 943: 159–183, 2002.
67. J Khandurina and A Guttman. Microscale separation and analysis. Curr Opin Chem Biol 7: 595–602, 2003.
68. LJ Kricka and P Wilding. Microchip PCR. Anal Bioanal Chem 377: 820–825, 2003.
69. P Gascoyne, J Satayavivad, and M Ruchirawat. Microfluidic approaches to malaria detection. Acta Trop 89: 357–369, 2004.
70. TH Park and ML Shuler. Integration of cell culture and microfabrication technology. Biotechnol Progr 19: 243–253, 2003.
71. JK Jaiswal, H Mattoussi, JM Mauro, and SM Simon. Long-term multiple color imaging of live cells using quantum dot bioconjugates. Nat Biotechnol 21: 47–51, 2003.
72. LA Bottomley. Scanning probe microscopy. Anal Chem 70: 425–475, 1998.
73. P Dutta, CA Tipple, NV Lavrik, PG Datskos, H Hofstetter, O Hofstetter, and MJ Sepaniak. Enantioselective sensors based on antibody-mediated nanomechanics. Anal Chem 75: 2342–2348, 2003.
74. JH Pei, F Tian, and T Thundat. Glucose biosensor based on the microcantilever. Anal Chem 76: 292–297, 2004.
75. M Su, SU Li, and VP Dravid. Microcantilever resonance-based DNA detection with nanoparticle probes. Appl Phys Lett 82: 3562–3564, 2003.
76. B Daviss. A springboard to easier bioassays. Scientist 18: 40–44, 2004.
77. J Tamames, D Clark, J Herrero, J Dopazo, C Blaschke, JM Fernandez, JC Oliveros, and A Valencia. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J Biotechnol 98: 269–283, 2002.
78. TG Dewey. From microarrays to networks: mining expression time series. Drug Discov Today 7: S170–S175, 2002.
79. M Carella, S Volinia, and P Gasparini. Nanotechnologies and microchips in genetic diseases. J Nephrol 16: 597–602, 2003.
80. PA Clarke, RT Poele, R Wooster, and P Workman. Gene expression microarray analysis in cancer biology, pharmacology, and drug development: progress and potential. Biochem Pharmacol 62: 1311–1336, 2001.
81. V Reinke and KP White. Developmental genomic approaches in model organisms. Annu Rev Genom Hum G 3: 153–178, 2002.
82. G Colebatch, B Trevaskis, and M Udvardi. Functional genomics: tools of the trade. New Phytol 153: 27–36, 2002.
83. RO Elferink. One step further toward real high-throughput functional genomics. Trends Biotechnol 21: 146–147, 2003.
84. F Michiels, H van Es, and P Tomme. One step further toward real high throughput functional genomics. Trends Biotechnol 21: 147–148, 2003.
85. S Steer and AJ MacGregor. Genetic epidemiology: disease susceptibility and severity. Curr Opin Rheumatol 15: 116–121, 2003.
86. K Susztak, K Sharma, M Schiffer, P McCue, E Ciccone, and EP Bottinger. Genomic strategies for diabetic nephropathy. J Am Soc Nephrol 14: S271–S278, 2003.
87. P Devarajan, J Mishra, S Supavekin, LT Patterson, and SS Potter. Gene expression in early ischemic renal injury: clues toward pathogenesis, biomarker discovery, and novel therapeutics. Mol Genet Metab 80: 365–376, 2003.
88. PS Hayden, A El-Meanawy, JR Schelling, and JR Sedor. DNA expression analysis: serial analysis of gene expression, microarrays and kidney disease. Curr Opin Nephrol Hy 12: 407–414, 2003.
89. EP Bottinger, WJ Ju, and J Zavadil. Applications for microarrays in renal biology and medicine. Exp Nephrol 10: 93–101, 2002.
90. NA Shackel, MD Gorrell, and GW McCaughan. Gene array analysis and the liver. Hepatology 36: 1313–1325, 2002.
91. F Eertmans, W Dhooge, S Stuyvaert, and F Comhaire. Endocrine disruptors: effects on male fertility and screening tools for their assessment. Toxicol in Vitro 17: 515–524, 2003.
92. KD Hirschi, JA Kreps, and KK Hirschi. Molecular approaches to studying nutrient metabolism and function: an array of possibilities. J Nutr 131: 1605s–1609s, 2001.
93. GP Page, JW Edwards, S Barnes, R Weindruch, and DB Allison. A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindedness. Nutrition 19: 997–1000, 2003.
94. E Bernal-Mizrachi, C Cras-Meneur, M Ohsugi, and MA Permutt. Gene expression profiling in islet biology and diabetes research. Diabetes Metab Res 19: 32–42, 2003.
95. S Welle. Gene transcript profiling in aging research. Exp Gerontol 37: 583–590, 2002.
96. SA Cook and A Rosenzweig. DNA microarrays: implications for cardiovascular medicine. Circ Res 91: 559–564, 2002.
97. WP Kuo, ME Whipple, ST Sonis, L Ohno-Machado, and TK Jenssen. Gene expression profiling by DNA microarrays and its application to dental research. Oral Oncol 38: 650–656, 2002.
98. WP Kuo, ME Whipple, TK Jenssen, R Todd, JB Epstein, L Ohno-Machado, ST Sonis, and PJ Park. Microarrays and clinical dentistry. J Am Dent Assoc 134: 456–462, 2003.
99. ME Whipple and WP Kuo. DNA microarrays in otolaryngology: head and neck surgery. Otolaryng Head Neck 127: 196–204, 2002.
100. EP Hoffman, KJ Brown, and E Eccleston. New molecular research technologies in the study of muscle disease. Curr Opin Rheumatol 15: 698–707, 2003.
101. JN Haslett and LM Kunkel. Microarray analysis of normal and dystrophic skeletal muscle. Int J Dev Neurosci 20: 359–365, 2002.
102. AY Gracey and AR Cossins. Application of microarray technology in environmental and comparative physiology. Annu Rev Physiol 65: 231–259, 2003.
103. B van Steensel and S Henikoff. Epigenomic profiling using microarrays. Biotechniques 35: 346, 2003.
104. Z Luo and DH Geschwind. Microarray applications in neuroscience. Neurobiol Dis 8: 183–193, 2001.
105. TJ Sendera, D Dorris, R Ramakrishnan, A Nguyen, D Trakas, and A Mazumder. Expression profiling with oligonucleotide arrays: technologies and applications for neurobiology. Neurochem Res 27: 1005–1026, 2002.
106. SJ Watson, F Meng, RC Thompson, and H Akil. The “chip” as a specific genetic tool. Biol Psychiatr 48: 1147–1156, 2000.
107. TA Prolla. DNA microarray analysis of the aging brain. Chem Senses 27: 299–306, 2002.
108. FM Bareyre and ME Schwab. Inflammation, degeneration and regeneration in the injured spinal cord: insights from DNA microarrays. Trends Neurosci 26: 555–563, 2003.
109. KE Vrana, WM Freeman, and M Aschner. Use of microarray technologies in toxicology research. Neurotoxicology 24: 321–332, 2003.
110. ER Marcotte, LK Srivastava, and R Quirion. cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer’s disease. Pharmacol Therap 100: 63–74, 2003.
111. JC Weeks. Thinking globally, acting locally: steroid hormone regulation of the dendritic architecture, synaptic connectivity and death of an individual neuron. Progr Neurobiol 70: 421–442, 2003.
112. WE Bunney, BG Bunney, MP Vawter, H Tomita, J Li, SJ Evans, PV Choudary, RM Myers, EG Jones, SJ Watson, and H Akil. Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders. Am J Psychiatr 160: 657–666, 2003.
113. DG Albertson. Profiling breast cancer by array CGH. Breast Cancer Res Tr 78: 289–298, 2003.
114. S Mohr, GD Leikauf, G Keith, and BH Rihn. Microarrays as cancer keys: an array of possibilities. J Clin Oncol 20: 3165–3175, 2002.
115. S Ramaswamy and TR Golub. DNA microarrays in clinical oncology. J Clin Oncol 20: 1932–1941, 2002.
116. JK Nagpal and BR Das. Oral cancer: reviewing the present understanding of its molecular mechanism and exploring the future directions for its effective management. Oral Oncol 39: 213–221, 2003.
117. CA Bandera, B Ye, and SC Mok. New technologies for the identification of markers for early detection of ovarian cancer. Curr Opin Obstet Gyn 15: 51–55, 2003.
118. I Haviv and IG Campbell. DNA microarrays for assessing ovarian cancer gene expression. Mol Cell Endocrinol 191: 121–126, 2002.
119. W Wu, W Hu, and JJ Kavanagh. Proteomics in cancer research. Int J Gynecol Cancer 12: 409–423, 2002.
120. F Bertucci, P Viens, P Hingamp, V Nasser, R Houlgatte, and D Birnbaum. Breast cancer revisited using DNA array-based gene expression profiling. Int J Cancer 103: 565–571, 2003.
121. TR Golub. Genomic approaches to the pathogenesis of hematologic malignancy. Curr Opin Hematol 8: 252–261, 2001.
122. C Schwaenen, S Wessendorf, HA Kestler, H Dohner, P Lichter, and M Bentz. DNA microarray analysis in malignant lymphomas. Ann Hematol 82: 323–332, 2003.
123. M van de Rijn and CB Gilks. Applications of microarrays to histopathology. Histopathology 44: 97–108, 2004.
124. AE Frolov, AK Godwin, and OO Favorova. Differential gene expression analysis by DNA microarray technology and its application in molecular oncology. Mol Biol 37: 486–494, 2003.
125. JKC Chan. The new World Health Organization classification of lymphomas: the past, the present and the future (reprinted from Int. Med 86, 434–443, 2000). Hematol Oncol 19: 129–150, 2001.
126. JE Celis and P Gromov. Proteomics in translational cancer research: toward an integrated approach. Cancer Cell 3: 9–15, 2003.
127. BB Haab. Methods and applications of antibody microarrays in cancer research. Proteomics 3: 2116–2122, 2003.
128. DD Dalma-Weiszhausz, ME Chicurel, and TR Gingeras. Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field. Genet Epidemiol 23: 4–20, 2002.
129. A Boussioutas and I Haviv. Current and potential uses for DNA microarrays in transplantation medicine: lessons from other disciplines. Tissue Antigens 62: 93–103, 2003.
130. P Kellam. Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions. Rev Med Virol 11: 313–329, 2001.
131. JP Clewley. A role for arrays in clinical virology: fact or fiction? J Clin Virol 29: 2–12, 2004.
132. PA Bryant, D Venter, R Robins-Browne, and N Curtis. Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 4: 100–111, 2004.
133. D Ivnitski, DJ O’Neil, A Gattuso, R Schlicht, M Calidonna, and R Fisher. Nucleic acid approaches for detection and identification of biological warfare and infectious disease agents. Biotechniques 35: 862–869, 2003.
134. FX Berthet, T Coche, and C Vinals. Applied genome research in the field of human vaccines. J Biotechnol 85: 213–226, 2001.
135. JC Boothroyd, I Blader, M Cleary, and U Singh. DNA microarrays in parasitology: strengths and limitations. Trends Parasitol 19: 470–476, 2003.
136. PK Rathod, K Ganesan, RE Hayward, Z Bozdech, and JL DeRisi. DNA microarrays for malaria. Trends Parasitol 18: 39–45, 2002.
137. GK Schoolnik. Functional and comparative genomics of pathogenic bacteria. Curr Opin Microbiol 5: 20–26, 2002.
138. M Kato-Maeda, Q Gao, and PM Small. Microarray analysis of pathogens and their interaction with hosts. Cell Microbiol 3: 713–719, 2001.
139. DN Howbrook, AM van der Valk, MC O’Shaughnessy, DK Sarker, SC Baker, and AW Lloyd. Developments in microarray technologies. Drug Discov Today 8: 642–651, 2003.
140. D Brunner, E Nestler, and E Leahy. In need of high throughput behavioral systems. Drug Discov Today 7: S107–S112, 2002.
141. TW Gant. Application of toxicogenomics in drug development. Drug News Perspect 16: 217–221, 2003.
142. AS Verkman. Drug discovery in academia. Am J Physiol Cell Ph 286: C465–C474, 2004.
143. EH Ohlstein, RR Ruffolo, and JD Elliott. Drug discovery in the next millennium. Annu Rev Pharmacol 40: 177–191, 2000.
144. KV Chin and ANT Kong. Application of DNA Microarrays in pharmacogenomics and toxicogenomics. Pharmaceut Res 19: 1773–1778, 2002.
145. G Orphanides. Toxicogenomics: challenges and opportunities. Toxicol Lett 140: 145–148, 2003.
146. H Loferer. Mining bacterial genomes for antimicrobial targets. Mol Med Today 6: 470–474, 2000.
147. M Basik, S Mousses, and J Trent. Integration of genomic technologies for accelerated cancer drug development. Biotechniques 35: 580, 2003.
148. KD Kumble. Protein microarrays: new tools for pharmaceutical development. Anal Bioanal Chem 377: 812–819, 2003.
149. TW Snell, SE Brogdon, and MB Morgan. Gene expression profiling in ecotoxicology. Ecotoxicology 12: 475–483, 2003.
150. JI Glass, AE Belanger, and GT Robertson. Streptococcus pneumoniae as a genomics platform for broad-spectrum antibiotic discovery. Curr Opin Microbiol 5: 338–342, 2002.