Genomics

  1. Structural and Functional Genomics
    1. Structural Genomics
      1. Genome Mapping Approaches
        1. Genetic Mapping
          1. Linkage Analysis
            1. Recombination Mapping
              1. Quantitative Trait Loci (QTL) Mapping
              2. Physical Mapping
                1. Restriction Mapping
                  1. Fluorescence In Situ Hybridization (FISH)
                    1. Sequence Tagged Sites (STS)
                      1. Bacterial Artificial Chromosome (BAC) Mapping
                    2. Structural Variation Analysis
                      1. Types of Structural Variants
                        1. Copy Number Variations (CNVs)
                          1. Insertions and Deletions (Indels)
                            1. Inversions
                              1. Translocations
                                1. Complex Rearrangements
                                2. Detection Methods
                                  1. Array-Based Methods
                                    1. Sequencing-Based Methods
                                      1. Optical Mapping
                                      2. Population Genetics of Structural Variation
                                        1. Disease Associations
                                        2. Three-Dimensional Genome Organization
                                          1. Chromosome Territories
                                            1. Topologically Associating Domains (TADs)
                                              1. Chromatin Loops
                                                1. Nuclear Lamina Interactions
                                              2. Functional Genomics
                                                1. Gene Function Analysis
                                                  1. Forward Genetics Approaches
                                                    1. Reverse Genetics Approaches
                                                      1. High-Throughput Functional Screens
                                                        1. RNA Interference (RNAi) Screens
                                                          1. CRISPR Screens
                                                            1. Chemical Genetic Screens
                                                          2. Transcriptomics
                                                            1. RNA Sequencing (RNA-Seq)
                                                              1. Experimental Design Principles
                                                                1. Library Preparation Methods
                                                                  1. Single-End vs. Paired-End Sequencing
                                                                    1. Data Analysis Pipeline
                                                                      1. Read Alignment
                                                                        1. Transcript Assembly
                                                                          1. Quantification Methods
                                                                        2. Differential Gene Expression Analysis
                                                                          1. Statistical Methods
                                                                            1. Multiple Testing Correction
                                                                              1. Functional Enrichment Analysis
                                                                                1. Pathway Analysis
                                                                                2. Alternative Splicing Analysis
                                                                                  1. Isoform Detection
                                                                                    1. Splicing Event Classification
                                                                                      1. Regulatory Mechanisms
                                                                                      2. Single-Cell RNA Sequencing
                                                                                        1. Technical Considerations
                                                                                          1. Cell Type Identification
                                                                                            1. Trajectory Analysis
                                                                                          2. Proteomics
                                                                                            1. Mass Spectrometry-Based Proteomics
                                                                                              1. Protein Identification
                                                                                                1. Quantitative Proteomics
                                                                                                  1. Label-Free Quantification
                                                                                                    1. Isotope Labeling Methods
                                                                                                    2. Post-Translational Modification Analysis
                                                                                                    3. Protein-Protein Interaction Networks
                                                                                                      1. Experimental Methods
                                                                                                        1. Yeast Two-Hybrid
                                                                                                          1. Affinity Purification-Mass Spectrometry
                                                                                                            1. Cross-Linking Mass Spectrometry
                                                                                                            2. Network Analysis
                                                                                                              1. Functional Modules
                                                                                                            3. Epigenomics
                                                                                                              1. DNA Methylation Analysis
                                                                                                                1. Bisulfite Sequencing Methods
                                                                                                                  1. Methylation Arrays
                                                                                                                    1. Single-Cell Methylation Analysis
                                                                                                                    2. Histone Modification Profiling
                                                                                                                      1. ChIP-Seq Analysis
                                                                                                                        1. Histone Code Interpretation
                                                                                                                          1. Chromatin States
                                                                                                                          2. Chromatin Accessibility
                                                                                                                            1. ATAC-Seq Analysis
                                                                                                                              1. DNase-Seq Analysis
                                                                                                                                1. Nucleosome Positioning
                                                                                                                                2. Three-Dimensional Chromatin Structure
                                                                                                                                  1. Hi-C Data Analysis
                                                                                                                                    1. Chromatin Interaction Networks
                                                                                                                                      1. Enhancer-Promoter Interactions

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                                                                                                                                3. Bioinformatics and Computational Genomics

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                                                                                                                                5. Comparative and Evolutionary Genomics