Genomics

  1. Genomic Technologies and Methodologies
    1. DNA Sequencing Technologies
      1. First-Generation Sequencing
        1. Sanger Sequencing (Chain Termination Method)
          1. Principle and Chemistry
            1. Workflow and Protocol
              1. Applications and Limitations
                1. Capillary Electrophoresis
              2. Next-Generation Sequencing (NGS)
                1. Core Principles of NGS
                  1. Massively Parallel Sequencing
                    1. Clonal Amplification
                      1. Sequencing by Synthesis
                      2. Library Preparation
                        1. DNA Fragmentation Methods
                          1. Adapter Ligation
                            1. Size Selection
                              1. Amplification Methods
                                1. Quality Control
                                2. Major Sequencing Platforms
                                  1. Illumina Sequencing
                                    1. Bridge Amplification
                                      1. Sequencing Chemistry
                                        1. Paired-End Sequencing
                                          1. Strengths and Limitations
                                          2. Ion Torrent Sequencing
                                            1. Semiconductor Technology
                                              1. pH Detection
                                                1. Workflow and Applications
                                                2. Roche 454 Sequencing
                                                  1. Pyrosequencing Chemistry
                                                    1. Emulsion PCR
                                                      1. Historical Significance
                                                  2. Third-Generation Sequencing
                                                    1. Pacific Biosciences (PacBio)
                                                      1. Single-Molecule Real-Time (SMRT) Sequencing
                                                        1. Long-Read Capabilities
                                                          1. Error Profiles and Correction
                                                          2. Oxford Nanopore Technologies
                                                            1. Nanopore Sequencing Principle
                                                              1. Real-Time Sequencing
                                                                1. Portability and MinION
                                                                  1. Ultra-Long Reads
                                                                2. Emerging Sequencing Technologies
                                                                  1. Single-Cell Sequencing
                                                                    1. Spatial Sequencing
                                                                      1. Direct RNA Sequencing
                                                                    2. Genome Assembly and Analysis
                                                                      1. Principles of Genome Assembly
                                                                        1. De Novo Assembly
                                                                          1. Overlap-Layout-Consensus (OLC) Approach
                                                                            1. De Bruijn Graph Approach
                                                                              1. String Graph Approach
                                                                              2. Reference-Based Assembly
                                                                                1. Read Mapping and Alignment
                                                                                  1. Variant Calling
                                                                                    1. Structural Variation Detection
                                                                                  2. Assembly Algorithms and Tools
                                                                                    1. Short-Read Assemblers
                                                                                      1. Long-Read Assemblers
                                                                                        1. Hybrid Assembly Approaches
                                                                                        2. Challenges in Assembly
                                                                                          1. Repetitive Regions
                                                                                            1. Genome Size and Complexity
                                                                                              1. Sequencing Errors and Bias
                                                                                                1. Heterozygosity
                                                                                                2. Assembly Quality Assessment
                                                                                                  1. Contiguity Metrics
                                                                                                    1. N50 and N90 Statistics
                                                                                                      1. Scaffold Statistics
                                                                                                      2. Completeness Assessment
                                                                                                        1. BUSCO Analysis
                                                                                                          1. Core Gene Sets
                                                                                                          2. Error Detection and Correction
                                                                                                        2. Specialized Genomic Technologies
                                                                                                          1. Microarray Technologies
                                                                                                            1. Gene Expression Arrays
                                                                                                              1. Principle and Design
                                                                                                                1. Hybridization Chemistry
                                                                                                                  1. Data Analysis Workflow
                                                                                                                  2. Genotyping Arrays
                                                                                                                    1. SNP Chip Technology
                                                                                                                      1. Copy Number Arrays
                                                                                                                        1. Applications in GWAS
                                                                                                                      2. Chromosome Conformation Technologies
                                                                                                                        1. 3C (Chromosome Conformation Capture)
                                                                                                                          1. Principle and Protocol
                                                                                                                          2. 4C (Circularized Chromosome Conformation Capture)
                                                                                                                            1. 5C (Carbon Copy Chromosome Conformation Capture)
                                                                                                                              1. Hi-C (High-Throughput Chromosome Conformation Capture)
                                                                                                                                1. Genome-Wide Interaction Mapping
                                                                                                                                  1. Topologically Associating Domains
                                                                                                                                2. Epigenomic Technologies
                                                                                                                                  1. Bisulfite Sequencing
                                                                                                                                    1. Whole-Genome Bisulfite Sequencing
                                                                                                                                      1. Reduced Representation Bisulfite Sequencing
                                                                                                                                      2. Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
                                                                                                                                        1. Histone Modification Mapping
                                                                                                                                          1. Transcription Factor Binding
                                                                                                                                          2. Chromatin Accessibility Assays
                                                                                                                                            1. ATAC-Seq
                                                                                                                                              1. FAIRE-Seq
                                                                                                                                                1. DNase-Seq

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                                                                                                                                          1. Foundations of Genomics

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                                                                                                                                          3. Bioinformatics and Computational Genomics