Systems Biology

  1. High-Throughput Experimental Technologies
    1. Genomics
      1. DNA Sequencing Technologies
        1. Sanger Sequencing
          1. Next-Generation Sequencing
            1. Illumina Sequencing
              1. Oxford Nanopore
                1. PacBio Sequencing
                2. Third-Generation Sequencing
                3. Genome Assembly and Annotation
                  1. De Novo Assembly
                    1. Reference-Based Assembly
                      1. Gene Prediction
                        1. Functional Annotation
                        2. Genomic Variation Analysis
                          1. Single Nucleotide Polymorphisms
                            1. Copy Number Variations
                              1. Structural Variants
                                1. Genome-Wide Association Studies
                                2. Comparative Genomics
                                  1. Cross-Species Comparisons
                                    1. Evolutionary Genomics
                                      1. Phylogenetic Analysis
                                    2. Transcriptomics
                                      1. RNA Sequencing Technologies
                                        1. Bulk RNA-Seq
                                          1. Library Preparation
                                            1. Sequencing Protocols
                                              1. Data Quality Assessment
                                              2. Single-Cell RNA-Seq
                                                1. Cell Isolation Methods
                                                  1. Droplet-Based Methods
                                                    1. Plate-Based Methods
                                                    2. Spatial Transcriptomics
                                                      1. Tissue Section Analysis
                                                        1. In Situ Sequencing
                                                      2. Gene Expression Analysis
                                                        1. Differential Expression Analysis
                                                          1. Time-Course Expression Studies
                                                            1. Co-Expression Analysis
                                                            2. Alternative Splicing Analysis
                                                              1. Splice Variant Detection
                                                                1. Isoform Quantification
                                                                2. Non-Coding RNA Analysis
                                                                  1. microRNA Profiling
                                                                    1. Long Non-Coding RNA Discovery
                                                                      1. Circular RNA Detection
                                                                    2. Proteomics
                                                                      1. Mass Spectrometry Approaches
                                                                        1. Sample Preparation Methods
                                                                          1. Ionization Techniques
                                                                            1. Mass Analyzers
                                                                              1. Data Acquisition Strategies
                                                                              2. Protein Identification and Quantification
                                                                                1. Database Searching
                                                                                  1. Label-Free Quantification
                                                                                    1. Isotope Labeling Methods
                                                                                      1. SILAC
                                                                                        1. iTRAQ
                                                                                          1. TMT
                                                                                        2. Post-Translational Modification Analysis
                                                                                          1. Phosphoproteomics
                                                                                            1. Ubiquitinomics
                                                                                              1. Glycoproteomics
                                                                                                1. Acetylomics
                                                                                                2. Protein-Protein Interaction Studies
                                                                                                  1. Affinity Purification Mass Spectrometry
                                                                                                    1. Cross-Linking Mass Spectrometry
                                                                                                      1. Proximity Labeling
                                                                                                    2. Metabolomics
                                                                                                      1. Analytical Platforms
                                                                                                        1. Mass Spectrometry
                                                                                                          1. GC-MS
                                                                                                            1. LC-MS
                                                                                                              1. Direct Infusion MS
                                                                                                              2. Nuclear Magnetic Resonance
                                                                                                                1. 1D NMR
                                                                                                                  1. 2D NMR
                                                                                                                    1. High-Resolution Magic Angle Spinning
                                                                                                                  2. Metabolite Identification and Quantification
                                                                                                                    1. Database Matching
                                                                                                                      1. Spectral Libraries
                                                                                                                        1. De Novo Structure Elucidation
                                                                                                                        2. Metabolic Flux Analysis
                                                                                                                          1. Stable Isotope Labeling
                                                                                                                            1. Flux Balance Analysis
                                                                                                                              1. Dynamic Flux Analysis
                                                                                                                              2. Lipidomics
                                                                                                                                1. Lipid Extraction Methods
                                                                                                                                  1. Lipid Classification
                                                                                                                                    1. Membrane Dynamics
                                                                                                                                  2. Epigenomics
                                                                                                                                    1. DNA Methylation Analysis
                                                                                                                                      1. Bisulfite Sequencing
                                                                                                                                        1. Methylation Arrays
                                                                                                                                          1. Reduced Representation Bisulfite Sequencing
                                                                                                                                          2. Histone Modification Profiling
                                                                                                                                            1. Chromatin Immunoprecipitation Sequencing
                                                                                                                                              1. CUT&RUN
                                                                                                                                                1. CUT&Tag
                                                                                                                                                2. Chromatin Accessibility
                                                                                                                                                  1. ATAC-Seq
                                                                                                                                                    1. FAIRE-Seq
                                                                                                                                                      1. DNase-Seq
                                                                                                                                                      2. Chromosome Conformation
                                                                                                                                                        1. Hi-C
                                                                                                                                                          1. ChIA-PET
                                                                                                                                                            1. Capture-C

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