| Preface |
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iv | |
| Abbreviations |
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xv | |
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A Glance at Evolution through the Genomic Window |
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1 | (30) |
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1 | (1) |
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2 | (1) |
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Towards the Understanding of ``The Mechanisms That Bring about Evolutionary Changes'' |
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2 | (12) |
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Genome Structures and New Concepts of Evolution |
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14 | (7) |
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How Could Transposable Elements Contribute to Evolution? |
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21 | (4) |
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Concluding Remarks: What about Genes That Make Us Humans? |
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25 | (6) |
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Complex Genome Comparisons: Problems and Approaches |
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31 | (20) |
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31 | (1) |
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Introduction: Complex Genomes---The Ocean of Cryptic Information |
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31 | (1) |
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Classification of Comparative Techniques |
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32 | (2) |
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Information Content and Resolution Power of Different Methods for Complex Genome Comparisons |
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34 | (1) |
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Random Displays: From Fingerprinting to Flowthrough-Based Assays |
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35 | (3) |
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Display Methods Targeted at the Flanks of Interspersed Repetitive Elements |
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38 | (2) |
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DNA Microarrays As a New Tool to Display Genomic Differences |
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40 | (2) |
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Genomic Subtractive Hybridization |
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42 | (3) |
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45 | (6) |
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A Brief Introduction to Primate Evolution |
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51 | (17) |
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51 | (1) |
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51 | (1) |
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The Problem of Primate Definition |
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52 | (1) |
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Linking Primates to Other Eutherian Orders |
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53 | (3) |
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The Major Groups of Primates |
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56 | (8) |
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Evolution of Anatomically Modern Humans |
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64 | (1) |
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65 | (3) |
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How Different Is the Human Genome from the Genomes of the Great Apes? |
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68 | (25) |
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68 | (1) |
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68 | (3) |
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First Human---Chimpanzee Molecular Comparisons: Changes in Regulatory Systems Are Most Important for Speciation |
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71 | (1) |
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General Characteristics of Interspecies Divergence and Intraspecies Polymorphisms in Hominoids |
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72 | (6) |
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Differences between Particular Elements of the Hominoid Genomes |
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78 | (6) |
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Conclusion: A Supercomplex Disease---To Be a Human |
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84 | (9) |
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Retroviruses, Their Domesticated Relatives and Other Retroinvaders: Potential Genetic and Epigenetic Mediators of Phenotypic Variation |
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93 | (11) |
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93 | (1) |
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Introduction: Continuum of The Retroworld |
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93 | (1) |
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94 | (1) |
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95 | (2) |
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97 | (1) |
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98 | (1) |
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Endogenization of Exogenous Retroviruses |
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98 | (1) |
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Army of Retroelements in the Human Genome |
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99 | (1) |
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Some Traditionally Discussed Functional Potentials of Retroelements |
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100 | (1) |
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Stochastic Drivers of Organismal Epigenetic Mosaicism. All of Us Are Probably Complex Epigenetic Mosaics, and What? |
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101 | (1) |
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102 | (2) |
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Genomic Distributions of Human Retroelements |
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104 | (19) |
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104 | (1) |
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104 | (1) |
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Types of Human Retroelements |
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104 | (2) |
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Effects of Transposable Elements on Genomes |
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106 | (1) |
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Integration Patterns of Exogenous Retroviruses |
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106 | (1) |
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Impact of Genetic Drift and Selection |
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107 | (1) |
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Insights from Other Species |
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107 | (2) |
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Experimental Determinations of Distributions |
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109 | (1) |
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Large Scale Analysis of Retroelement Distributions |
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110 | (3) |
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Retroelement Distributions Relative to Genes |
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113 | (3) |
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Retroelements and the Y Chromosome |
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116 | (2) |
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Genomic Clearance of Retroelements |
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118 | (1) |
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118 | (5) |
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Influence of Human Endogenous Retroviruses on Cellular Gene Expression |
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123 | (21) |
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123 | (1) |
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123 | (1) |
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Variations in LTR Structure and Activity of Different HERV Families |
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123 | (6) |
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Endogenous and Exogenous Factors Influencing HERV Expression |
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129 | (1) |
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Modulation of Cellular Gene Expression |
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130 | (9) |
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139 | (5) |
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Genome-Wide Search for Human Specific Retroelements |
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144 | (18) |
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144 | (1) |
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Introduction: Hypotheses Are Indispensable on the Way towards Understanding the Genetic Basis of Humankind Evolution |
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144 | (1) |
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Retroelement Families and Subfamilies in the Homo Sapiens Genome |
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145 | (1) |
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What Makes REs Possible Candidates for Evolutionary Pacemakers? |
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146 | (2) |
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Strategies and Approaches to the Genome-Wide Identification of Human-Specific RE Integrations |
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148 | (8) |
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156 | (6) |
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Genome-Wide Analysis of Human Gene Expression: Application to the Expression of Human Endogenous Retroviruses |
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162 | (24) |
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162 | (1) |
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Introduction: What Is the Function of a Genomic Constituent? |
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162 | (1) |
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Detection of Gene Expression and Comparative Analysis of the Expression Using Cross-Hybridization of the Samples Under Comparison |
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163 | (8) |
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Methods of Detection and Comparison of Transcripts Avoiding Denaturation-Renaturation Steps |
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171 | (11) |
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182 | (4) |
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Phylogeny of Human Endogenous and Exogenous Retroviruses |
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186 | (18) |
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186 | (1) |
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186 | (2) |
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Identification and Phylogenetic Reconstruction of Endogenous Retroviruses in the Human Genome |
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188 | (1) |
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HERV Lineages within Retroviral Phylogeny |
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189 | (5) |
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Characterization of New Families |
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194 | (2) |
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Further Characterization of Previously Reported Families |
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196 | (1) |
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Relationships between HERVs and Exogenous Retroviruses |
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196 | (2) |
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Ancient and Modern HERV Families |
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198 | (2) |
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Concluding Remarks: Prospects for HERV Phylogenetics |
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200 | (4) |
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Evolutionary Aspects of Human Endogenous Retroviral Sequences (HERVs) and Disease |
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204 | (35) |
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204 | (1) |
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204 | (1) |
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205 | (1) |
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Events following Endogenization of a Retrovirus |
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206 | (3) |
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Active HERVs, Expressed As Particles or As Proteins |
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209 | (6) |
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Diseases Where a Connection with HERVs Has Been Implicated |
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215 | (13) |
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What Can Be Done to Demonstrate a HERV-Disease Connection? |
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228 | (1) |
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229 | (10) |
| Index |
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239 | |
