Course Overview
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Course Synopsis
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It is an introductory course where students get a basic knowledge on genomics and proteomics
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Course Learning Outcomes
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After complection of this course students will be able to
- learn how genomics and proteomics application in biological research can benefit in solving the complex biological and biochemical processes regardless of the type of organism which is the model for the research.
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Course Calendar
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Week 01
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2
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Genomics, Proteomics and metabolomics
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6
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6_Introduction to Genomics
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7
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Anatomy and organization of genome
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9
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9_Prokaryotic gene and eukarytic gene
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10
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10_Prokaryotic and eukaryotic gene expression_Difference
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11
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11_Gene families and Gene clusters
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Week 02
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12
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12_Types of Proteins and Families
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16
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Epichromosomal elements (EEs)
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18
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Transposable Elements (TEs)
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19
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Eukaryotic Gene Structure
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Week 03
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23
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23_Concepts of comparative genomics
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26
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26_Why Sequence Genomes
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27
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27_Genome characteriazation - Techniques used
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28
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28_Genome Analysis Steps
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29
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29_Benefits of genome analysis
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30
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30_Size of Genomes - Genes
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Week 04
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34
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34_Mitochondrial genome
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35
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35_Genomes comparisons
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36
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36_Comparing distantly and closely related species
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38
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38_Genetic mapping of Genomes
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39
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39_Physical mapping of genomes
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40
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40_Cytogenetic mapping
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42
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42_Restriction mapping of genomes
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43
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43_Radiation hybrid mapping of genomes
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44
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44_Clone contigs mapping of genomes
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Week 05
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45
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45_Generating sequence of genomes
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46
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46_Human genome project
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47
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47_Human genome project - Hierarchical shotgun sequencing
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48
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48_Human genome project - whole genome shotgun sequencing
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49
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49_Characteristics of our genome (A)
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50
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50_Characteristics_human genome (B)
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51
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51_Genome browsers_UCSC
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52
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52_ Genome browser_Ensembl
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53
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53_HGP_ethical and legal issues
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55
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55_Genome annotations - transcription factors
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54
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54_Genome annotations - protein coding genes
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Week 06
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58
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58_ Comparison of human and Mouse genome
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59
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59_Mapping of Disease Genes
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61
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61_Types of microarray
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62
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62_Microarrays Formats_some errors
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63
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63_Microarray - procedure
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65
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65_Microarray applications
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66
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66_Types of RNA and RNomics
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Week 07
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70
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70_Biogenesis of miRNA
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72
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72_Mode of action miRNA
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73
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73_Non coding RNA and X chromosome Silencing
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74
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74_RNA Induced Silencing Complex
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78
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78_Applications of siRNA
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Week 08
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80
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80_Sequencing Techniques
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81
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81_Automated Sequencing
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82
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82_Shot Gun Sequencing
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83
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83_Next Generation Sequencing
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86
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86_Illumina sequencing
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Week 09
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92
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92_Comparison of NGS Methods
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96
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96_Genes Predictions in prokaryotes
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97
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97_Genes Predictions in Eukaryotes
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98
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98_GO functional analysis
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103
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103_Splice sites Prediction
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Week 10
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106
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106_Genome Assembly Overview
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107
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107_Genome Assembly Planning
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108
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108_Effect of repeats
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109
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109_Related Species Assembled
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110
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110_Greedy Graph Algo
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112
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112_Lander Waterman Curve
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Week 11
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113
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113_Assembly Pipeline1
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114
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114_Assembly Pipeline2
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115
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115_Quality of Assembled Genome
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121
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121 Introduction to Proteomics
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122
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122 Comparative Proteomics
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123
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123 Between Proteome Comparison
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124
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124_Proteomics Types and Techniques
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Week 12
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125
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125_Characteristics of human proteome
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127
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127 Importance of Proteins
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128
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128 Chemical composition of proteins
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129
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129 Primary structure of proteins
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130
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130 Secondary structure of proteins
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132
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132 ß- Pleated Sheets
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133
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133 Tertiary Structure of Proteins
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134
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134 Quaternary Structure of Proteins
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135
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135_ Life and death of a protein
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136
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136 Proteins as Modular Structures
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Week 13
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137
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137_Proteins and Families
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138
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138 over view of analytical proteomics
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139
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139 Extracting Proteins from Biological Samples
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140
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140 Protein Separations Before Digestion
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141
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141. One-Dimensional SDS-PAGE
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142
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142 Two-Dimensional SDS-PAGE
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143
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143 Problems of 2D SDS-PAGE
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144
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144 Isoelectric Focusing
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145
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145 High-Performance Liquid Chromatography
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146
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146 Protein Separations After Digestion
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147
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147 Tandem LC Approaches for Peptide Analysis
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148
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148 Capillary Electrophoresis (CE)
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