| This Publication is Supported by COST |
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| Preface |
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Introduction to Microarray-Based Detection Methods |
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1 | (34) |
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Introduction to Microarray Technology |
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1 | (1) |
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Technical Aspects of Microarray Technology |
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2 | (15) |
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2 | (1) |
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3 | (1) |
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3 | (1) |
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3 | (3) |
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6 | (3) |
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Slides with Poly-L-lysine Coating |
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9 | (1) |
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Slides with Amino Silane Coating |
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9 | (1) |
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Slides with Aldehyde Coating |
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9 | (1) |
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Slides with Epoxy Coating |
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9 | (1) |
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Proprietary Surface Chemistries |
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9 | (1) |
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9 | (1) |
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Targets for Microarray Analysis |
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10 | (1) |
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Target Amplifications and Sensitivity Issues |
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10 | (1) |
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11 | (1) |
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Hybridization and Wash Conditions |
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11 | (1) |
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Classical Commercially Available Microarray Formats |
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12 | (1) |
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12 | (1) |
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12 | (2) |
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Alternative Methods for Improving Microarray-Based Detection Sensitivity |
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14 | (1) |
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Resonance-Light Scattering (RLS) |
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14 | (1) |
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Planar-Waveguide Technology (PWT) |
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14 | (1) |
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15 | (1) |
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Three-Dimensional Microarray Formats |
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15 | (1) |
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Marker Genes Used on MDMs |
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16 | (1) |
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Analysis and Quality Control Aspects |
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17 | (1) |
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Applications of Microarray Technology in Microbial Diagnostics |
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18 | (4) |
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18 | (1) |
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Comparative Genomic Hybridization (CGH) |
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18 | (1) |
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Generic or Universal Microarrays |
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19 | (1) |
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Microarrays for Sequence Analysis |
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20 | (1) |
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Microbial Diagnostic Microarrays (MDMs) |
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21 | (1) |
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Further Developments and New Perspectives Regarding Array Sensitivity and Specificity |
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22 | (1) |
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22 | (13) |
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22 | (13) |
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35 | (70) |
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Long Oligonucleotide Microarray-Based Microbial Detection |
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37 | (10) |
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37 | (1) |
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38 | (6) |
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38 | (1) |
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38 | (1) |
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Klenow Amplification/Labeling |
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39 | (1) |
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Probe and Slide Preparation |
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40 | (1) |
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Slide Processing Protocol (for Amino Surfaces) |
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41 | (1) |
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Hybridization and Slide Washing |
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42 | (2) |
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44 | (1) |
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Our Test System and Results |
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44 | (1) |
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44 | (3) |
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46 | (1) |
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Sequence-Specific End-Labeling of Oligonucleotides |
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47 | (12) |
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47 | (3) |
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50 | (1) |
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Slide Preparation (Spotting) |
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51 | (1) |
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Slide Processing Protocol (for Aldehyde Surfaces) |
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52 | (1) |
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DNA Extraction and PCR Amplification of the Targeted Gene |
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52 | (1) |
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Shrimp Alkaline Phosphatase Treatment |
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53 | (1) |
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53 | (1) |
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Hybridization and Slide Washing |
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54 | (1) |
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55 | (1) |
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55 | (1) |
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Microarray for Detection of Pathogenic Bacteria |
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55 | (4) |
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56 | (3) |
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Non-Cognate Approaches for Pathogen Detection on Microarrays |
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59 | (8) |
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59 | (1) |
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Non-Cognate Hybridization System |
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60 | (4) |
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60 | (1) |
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Definition of the Optimal Probe Length |
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60 | (1) |
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Virtual Assessment of Array Performances (in Silico Experiments) |
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61 | (2) |
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Array Manufacturing and Hybridization (Wet-Lab Experiments) |
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63 | (1) |
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64 | (1) |
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64 | (3) |
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64 | (3) |
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Patterning Techniques for Array Platforms |
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67 | (18) |
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67 | (1) |
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68 | (2) |
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70 | (1) |
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71 | (3) |
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71 | (1) |
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72 | (2) |
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74 | (6) |
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Dip-Pen Lithography with AFM |
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75 | (1) |
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76 | (1) |
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Nanoshaving and Nanografting |
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77 | (3) |
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80 | (5) |
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81 | (4) |
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Probe Immobilization Techniques in Array Technologies |
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85 | (20) |
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85 | (1) |
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86 | (8) |
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86 | (4) |
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90 | (1) |
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90 | (1) |
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91 | (1) |
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91 | (3) |
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94 | (11) |
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99 | (6) |
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105 | (28) |
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Low-Cost and Low-Density Microarrays -- A Novel Technique for Identification and Typing of Microorganisms |
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107 | (6) |
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107 | (1) |
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Chip Design/Array Description |
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107 | (1) |
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Protocol for a LCD Array Experiment |
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108 | (3) |
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108 | (1) |
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Short Protocol for Hybridization and Labeling |
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109 | (2) |
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111 | (1) |
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111 | (2) |
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DNA Microarray Technique for Detection and Identification of Viruses Causing Encephalitis and Hemorrhagic Fever |
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113 | (12) |
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113 | (1) |
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Principle of Applying Microarray Technology for Virus Detection and Identification |
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113 | (2) |
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Viruses and the Importance of Rapid Diagnostics |
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115 | (1) |
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Advantages and Drawbacks of Using the Microarray Technique |
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115 | (1) |
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Key Factors for Development of a Microarray-Based Test |
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116 | (1) |
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117 | (1) |
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117 | (4) |
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Hemorrhagic Fever Viruses |
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121 | (2) |
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123 | (2) |
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123 | (2) |
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Microarrays for Genomotyping of Pathogens |
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125 | (8) |
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125 | (1) |
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125 | (3) |
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128 | (2) |
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130 | (3) |
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131 | (2) |
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133 | (20) |
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Single Nucleotide Polymorphisms as Targets for DNA-Based Identification and Typing of Biosafety Level 3 Bacteria |
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135 | (12) |
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135 | (1) |
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Real-Time Polymerase Chain Reaction: More Than a Simple Polymerase Chain Reaction |
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135 | (1) |
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Results of Different SNP Typing Methods |
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136 | (8) |
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Locked Nucleic Acid-containing TaqMan probes as SNP Typing Tools |
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136 | (1) |
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Use of TaqMan LNA Probes for the Typing of Brucella suis Subspecies |
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136 | (3) |
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Typing SNPs with Molecular Beacons |
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139 | (1) |
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Use of Molecular Beacons for Typing Burkholderia pseudomallei Subspecies |
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139 | (1) |
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Typing Large Number of SNPs by Ligation Detection Reaction |
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139 | (3) |
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Use of LDR Probes and Low-Density Microarrays for the Multiplex Diagnostic of BSL3 Bacteria |
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142 | (2) |
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144 | (3) |
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145 | (2) |
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Use of a Microchip to Detect Antibiotic Resistance Genes in Bacillus anthracis |
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147 | (6) |
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147 | (1) |
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Conjugal Transfer of Antibiotic Resistance Genes Between Enterococcus Species and Avirulent Strains of B. anthracis |
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148 | (1) |
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Determination of the MICs of Different Antibiotics for the B. anthracis Transconjugants |
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148 | (1) |
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Detection of Antibiotic Resistance Genes in B. anthracis by Microchip-Based Hybridization System (ArrayTube) |
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149 | (1) |
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150 | (3) |
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151 | (2) |
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153 | (16) |
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Progress Towards Development of Microarrays for Routine Diagnostic Use |
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155 | (14) |
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155 | (2) |
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157 | (3) |
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Bacterial Strains, Culture and Nucleic Acid Purification |
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157 | (1) |
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Design and Printing of Oligonucleotide Probes |
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157 | (2) |
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Random Amplification and Cy3-labeling of Nucleic Acid |
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159 | (1) |
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Hybridization of Labeled Targets and Data Processing |
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159 | (1) |
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160 | (5) |
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Random Amplification and Hybridization of Cy3-labeled Pathogen DNA Targets |
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160 | (1) |
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Quality Assessment of Intra- and Inter-Operator Variation |
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161 | (1) |
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Sources of Intra-Operator Experimental Variation |
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162 | (2) |
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Sources of Inter-Operator Experimental Variation |
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164 | (1) |
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165 | (4) |
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165 | (4) |
| Index |
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169 | |
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