Genomics

  1. Comparative and Evolutionary Genomics
    1. Principles of Comparative Genomics
      1. Genome Comparison Strategies
        1. Whole-Genome Alignments
          1. Synteny Analysis
            1. Orthology and Paralogy Detection
            2. Sequence Conservation Analysis
              1. Conserved Non-Coding Elements
                1. Ultra-Conserved Elements
                  1. Phylogenetic Footprinting
                  2. Functional Element Prediction
                    1. Comparative Gene Prediction
                      1. Regulatory Element Identification
                        1. Non-Coding RNA Prediction
                      2. Phylogenomics and Molecular Evolution
                        1. Molecular Clock Analysis
                          1. Molecular Clock Hypothesis
                            1. Rate Variation Among Lineages
                              1. Calibration Methods
                              2. Phylogenetic Tree Construction
                                1. Distance-Based Methods
                                  1. Character-Based Methods
                                    1. Bayesian Phylogenetics
                                      1. Species Tree vs. Gene Tree
                                      2. Genome Evolution Mechanisms
                                        1. Point Mutations
                                          1. Insertions and Deletions
                                            1. Gene Duplications
                                              1. Chromosomal Rearrangements
                                                1. Horizontal Gene Transfer
                                                  1. Mechanisms of Transfer
                                                    1. Detection Methods
                                                      1. Evolutionary Impact
                                                  2. Comparative Genomics Applications
                                                    1. Model Organism Comparisons
                                                      1. Vertebrate Genome Comparisons
                                                        1. Plant Genome Comparisons
                                                          1. Microbial Genome Comparisons
                                                          2. Human Evolutionary Genomics
                                                            1. Human-Primate Comparisons
                                                              1. Ancient DNA Analysis
                                                                1. Neanderthal Genome
                                                                  1. Denisovan Genome
                                                                    1. Archaic Introgression
                                                                    2. Human Population Genomics
                                                                      1. Population Structure
                                                                        1. Migration Patterns
                                                                          1. Adaptive Evolution
                                                                        2. Domestication Genomics
                                                                          1. Crop Domestication
                                                                            1. Animal Domestication
                                                                              1. Genomic Signatures of Selection

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                                                                          4. Structural and Functional Genomics

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                                                                          6. Applications of Genomics