Bacterial Genetics and Genomics

  1. Bacterial Genomics and Bioinformatics
    1. Introduction to Genomics
      1. Genome Concepts
        1. Genome Definition
          1. Genome Size Variation
            1. Gene Content Variation
              1. Coding Density
              2. Transcriptome Analysis
                1. mRNA Populations
                  1. Expression Profiling
                    1. Condition-Specific Expression
                    2. Proteome Studies
                      1. Protein Expression
                        1. Post-Translational Modifications
                          1. Protein-Protein Interactions
                          2. Systems Biology Approaches
                            1. Multi-Omics Integration
                              1. Network Analysis
                                1. Pathway Reconstruction
                              2. DNA Sequencing Technologies
                                1. First-Generation Sequencing
                                  1. Sanger Method
                                    1. Chain Termination Principle
                                      1. Dideoxynucleotides
                                        1. Capillary Electrophoresis
                                          1. Read Length and Accuracy
                                        2. Second-Generation Sequencing
                                          1. Illumina Platform
                                            1. Library Preparation
                                              1. Cluster Generation
                                                1. Sequencing-by-Synthesis
                                                  1. Base Calling
                                                  2. Ion Torrent Platform
                                                    1. Semiconductor Detection
                                                      1. pH Change Measurement
                                                        1. Homopolymer Challenges
                                                        2. 454 Pyrosequencing
                                                          1. Pyrophosphate Detection
                                                            1. Emulsion PCR
                                                          2. Third-Generation Sequencing
                                                            1. PacBio Platform
                                                              1. Single-Molecule Real-Time
                                                                1. Zero-Mode Waveguides
                                                                  1. Long Read Advantages
                                                                    1. Error Profiles
                                                                    2. Oxford Nanopore
                                                                      1. Nanopore Technology
                                                                        1. Real-Time Sequencing
                                                                          1. Portable Devices
                                                                            1. Direct RNA Sequencing
                                                                        2. Genome Assembly and Annotation
                                                                          1. Genome Assembly Strategies
                                                                            1. De Novo Assembly
                                                                              1. Overlap-Layout-Consensus
                                                                                1. String Graph Approach
                                                                                  1. De Bruijn Graph Method
                                                                                    1. Assembly Quality Metrics
                                                                                    2. Reference-Based Assembly
                                                                                      1. Read Mapping
                                                                                        1. Variant Calling
                                                                                          1. Structural Variation Detection
                                                                                          2. Hybrid Assembly Approaches
                                                                                            1. Long and Short Read Integration
                                                                                              1. Error Correction Strategies
                                                                                            2. Genome Annotation
                                                                                              1. Gene Prediction
                                                                                                1. Open Reading Frame Identification
                                                                                                  1. Start Codon Prediction
                                                                                                    1. Gene Boundary Determination
                                                                                                      1. Pseudogene Detection
                                                                                                      2. Functional Annotation
                                                                                                        1. Homology-Based Annotation
                                                                                                          1. Domain-Based Annotation
                                                                                                            1. Pathway Assignment
                                                                                                              1. GO Term Assignment
                                                                                                              2. Non-Coding Element Annotation
                                                                                                                1. tRNA Gene Prediction
                                                                                                                  1. rRNA Gene Identification
                                                                                                                    1. Regulatory Element Prediction
                                                                                                                      1. Small RNA Identification
                                                                                                                    2. Quality Assessment
                                                                                                                      1. Assembly Statistics
                                                                                                                        1. Annotation Completeness
                                                                                                                          1. Contamination Detection
                                                                                                                            1. Genome Validation
                                                                                                                          2. Comparative Genomics
                                                                                                                            1. Homology Relationships
                                                                                                                              1. Ortholog Identification
                                                                                                                                1. Paralog Detection
                                                                                                                                  1. Homolog Clustering
                                                                                                                                    1. Evolutionary Relationships
                                                                                                                                    2. Genome Content Analysis
                                                                                                                                      1. Core Genome Determination
                                                                                                                                        1. Accessory Genome Analysis
                                                                                                                                          1. Pan-Genome Construction
                                                                                                                                            1. Gene Gain and Loss
                                                                                                                                            2. Synteny Analysis
                                                                                                                                              1. Gene Order Conservation
                                                                                                                                                1. Syntenic Block Identification
                                                                                                                                                  1. Chromosomal Rearrangements
                                                                                                                                                    1. Inversion Detection
                                                                                                                                                    2. Phylogenomic Analysis
                                                                                                                                                      1. Whole-Genome Phylogenies
                                                                                                                                                        1. Concatenated Gene Trees
                                                                                                                                                          1. Species Tree Construction
                                                                                                                                                            1. Horizontal Transfer Detection
                                                                                                                                                          2. Functional Genomics
                                                                                                                                                            1. Transcriptomics
                                                                                                                                                              1. RNA-Seq Technology
                                                                                                                                                                1. Library Preparation Methods
                                                                                                                                                                  1. Sequencing Strategies
                                                                                                                                                                    1. Data Processing Pipelines
                                                                                                                                                                      1. Differential Expression Analysis
                                                                                                                                                                      2. Microarray Analysis
                                                                                                                                                                        1. Probe Design
                                                                                                                                                                          1. Hybridization Principles
                                                                                                                                                                            1. Data Normalization
                                                                                                                                                                              1. Statistical Analysis
                                                                                                                                                                              2. Single-Cell RNA-Seq
                                                                                                                                                                                1. Cell Isolation Methods
                                                                                                                                                                                  1. Amplification Strategies
                                                                                                                                                                                    1. Heterogeneity Analysis
                                                                                                                                                                                  2. Proteomics
                                                                                                                                                                                    1. Mass Spectrometry
                                                                                                                                                                                      1. Protein Identification
                                                                                                                                                                                        1. Quantitative Proteomics
                                                                                                                                                                                          1. Post-Translational Modifications
                                                                                                                                                                                          2. Protein-Protein Interactions
                                                                                                                                                                                            1. Two-Hybrid Systems
                                                                                                                                                                                              1. Co-Immunoprecipitation
                                                                                                                                                                                                1. Cross-Linking Mass Spectrometry
                                                                                                                                                                                              2. Metabolomics
                                                                                                                                                                                                1. Metabolite Extraction
                                                                                                                                                                                                  1. Analytical Platforms
                                                                                                                                                                                                    1. GC-MS Analysis
                                                                                                                                                                                                      1. LC-MS Analysis
                                                                                                                                                                                                        1. NMR Spectroscopy
                                                                                                                                                                                                        2. Data Analysis
                                                                                                                                                                                                          1. Peak Identification
                                                                                                                                                                                                            1. Pathway Mapping
                                                                                                                                                                                                              1. Statistical Analysis

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                                                                                                                                                                                                        3. Mechanisms of Genetic Variation and Adaptation

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                                                                                                                                                                                                        5. Applications and Advanced Topics