Bioinformatics

1. Genomics
   1. Sequencing Technologies
      1. Sanger Sequencing
         1. Historical significance and discoveries
         2. Use in small-scale experiments
         3. Strengths and limitations
      2. Next-Generation Sequencing (NGS)
         1. Illumina Sequencing
            1. Core principles and mechanisms
            2. Applications in large-scale genomic studies
            3. Cost-effectiveness and efficiency
         2. Pyrosequencing
            1. How it works and typical use cases
            2. Comparison with Illumina
            3. Limitations and potential troubleshooting
         3. Other NGS Technologies
            1. Ion Torrent sequencing basics
            2. Single-molecule real-time (SMRT) sequencing
            3. Nanopore sequencing innovations
         4. Data analysis challenges and solutions
            1. Error correction methods
            2. Signal processing and base calling
   2. Genome Assembly
      1. De novo Assembly
         1. Algorithms and methodologies
         2. Challenges in assembling complex genomes
         3. Applications and case studies
      2. Reference-Guided Assembly
         1. Advantages and limitations
         2. Use in population genomics
         3. Handling genetic variations and structural variants
   3. Functional Genomics
      1. Gene Expression Analysis
         1. Technologies and methods such as RNA-Seq
         2. Computational analysis of expression data
         3. Interpretation of expression patterns
      2. Transcriptomics
         1. Study of transcriptomes and applications
         2. Challenges in transcriptome data interpretation
         3. Integration with proteomics and metabolomics
      3. Epigenomics
         1. Study of chemical modifications on DNA and histones
         2. Techniques such as ChIP-sequencing
         3. Implications in disease and developmental biology
      4. Non-coding RNA
         1. Types and functions
         2. Impact on gene regulation
   4. Comparative Genomics
      1. Comparative analysis techniques
      2. Evolutionary conservation and divergence
      3. Applications in functional annotation
      4. Role in understanding human disease
   5. Human Genomics
      1. The Human Genome Project insights
      2. HapMap and population-specific studies
      3. Genome-wide association studies (GWAS)
         1. Methodology and implications
         2. Case studies in common diseases
   6. Metagenomics
      1. Techniques for studying microbial communities
      2. Applications in ecology and human health
      3. Bioinformatics approaches to metagenomic data
      4. Future prospects in environmental genomics
   7. Pharmacogenomics
      1. Role in personalized medicine
      2. Drug response and genomic variants
      3. Challenges in clinical implementation
   8. Structural Genomics
      1. Study of 3D structures of genome segments
      2. Computational tools and predictions
      3. Insights into genome organization and function
   9. Ethical, Legal, and Social Issues in Genomics
      1. Privacy concerns in genomic data sharing
      2. Consent in genomic research participation
      3. Impact of genomics on healthcare and society