Bioinformatics and Computational Biology

  1. Foundational Concepts and Skills
    1. Essential Molecular Biology
      1. Nucleic Acid Structure and Function
        1. DNA Structure
          1. Nucleotide Composition
            1. Double Helix Architecture
              1. Base Pairing Rules
                1. Structural Variations
                2. RNA Structure and Types
                  1. RNA Nucleotides
                    1. Secondary Structures
                      1. Messenger RNA
                        1. Transfer RNA
                          1. Ribosomal RNA
                            1. Non-coding RNAs
                          2. Protein Structure and Function
                            1. Amino Acid Properties
                              1. Chemical Classification
                                1. Hydrophobicity and Charge
                                  1. Special Properties
                                  2. Protein Structure Levels
                                    1. Primary Structure
                                      1. Secondary Structure
                                        1. Tertiary Structure
                                          1. Quaternary Structure
                                          2. Protein Folding Principles
                                            1. Enzyme Function and Kinetics
                                            2. Gene Structure and Organization
                                              1. Prokaryotic Gene Structure
                                                1. Promoters and Operators
                                                  1. Coding Sequences
                                                    1. Terminators
                                                    2. Eukaryotic Gene Structure
                                                      1. Promoters and Enhancers
                                                        1. Exons and Introns
                                                          1. Splice Sites
                                                            1. Regulatory Elements
                                                            2. Gene Regulation Mechanisms
                                                              1. Transcriptional Control
                                                                1. Post-transcriptional Control
                                                                  1. Epigenetic Regulation
                                                                2. Genome Organization
                                                                  1. Genome Size and Complexity
                                                                    1. Chromosome Structure
                                                                      1. Repetitive Elements
                                                                        1. Genome Evolution
                                                                        2. Transcriptome Characteristics
                                                                          1. Alternative Splicing
                                                                            1. Transcript Variants
                                                                              1. Expression Patterns
                                                                              2. Proteome Diversity
                                                                                1. Protein Modifications
                                                                                  1. Protein Complexes
                                                                                    1. Functional Diversity
                                                                                  2. Core Computer Science Principles
                                                                                    1. Algorithm Design and Analysis
                                                                                      1. Time Complexity
                                                                                        1. Big O Notation
                                                                                          1. Best, Average, and Worst Cases
                                                                                          2. Space Complexity
                                                                                            1. Memory Usage Analysis
                                                                                            2. Algorithmic Paradigms
                                                                                              1. Greedy Algorithms
                                                                                                1. Dynamic Programming
                                                                                                  1. Divide and Conquer
                                                                                                    1. Backtracking
                                                                                                  2. Data Structures
                                                                                                    1. Linear Data Structures
                                                                                                      1. Arrays
                                                                                                        1. Linked Lists
                                                                                                          1. Stacks
                                                                                                            1. Queues
                                                                                                            2. Tree Structures
                                                                                                              1. Binary Trees
                                                                                                                1. Search Trees
                                                                                                                  1. Balanced Trees
                                                                                                                  2. Graph Structures
                                                                                                                    1. Directed and Undirected Graphs
                                                                                                                      1. Graph Representations
                                                                                                                        1. Graph Traversal
                                                                                                                        2. Hash Tables
                                                                                                                          1. Hash Functions
                                                                                                                            1. Collision Resolution
                                                                                                                          2. Database Systems
                                                                                                                            1. Relational Database Concepts
                                                                                                                              1. Tables and Relationships
                                                                                                                                1. Normalization
                                                                                                                                  1. Indexing Strategies
                                                                                                                                  2. SQL Fundamentals
                                                                                                                                    1. Data Definition Language
                                                                                                                                      1. Data Manipulation Language
                                                                                                                                        1. Query Optimization
                                                                                                                                        2. NoSQL Databases
                                                                                                                                          1. Document Stores
                                                                                                                                            1. Graph Databases
                                                                                                                                              1. Key-Value Stores
                                                                                                                                            2. Machine Learning Foundations
                                                                                                                                              1. Supervised Learning
                                                                                                                                                1. Classification Algorithms
                                                                                                                                                  1. Regression Algorithms
                                                                                                                                                    1. Model Training and Validation
                                                                                                                                                    2. Unsupervised Learning
                                                                                                                                                      1. Clustering Algorithms
                                                                                                                                                        1. Dimensionality Reduction
                                                                                                                                                          1. Association Rules
                                                                                                                                                          2. Feature Engineering
                                                                                                                                                            1. Feature Selection
                                                                                                                                                              1. Feature Extraction
                                                                                                                                                                1. Feature Scaling
                                                                                                                                                                2. Model Evaluation
                                                                                                                                                                  1. Cross-Validation
                                                                                                                                                                    1. Performance Metrics
                                                                                                                                                                      1. Overfitting and Underfitting
                                                                                                                                                                  2. Statistical Foundations
                                                                                                                                                                    1. Probability Theory
                                                                                                                                                                      1. Basic Probability Concepts
                                                                                                                                                                        1. Conditional Probability
                                                                                                                                                                          1. Bayes' Theorem
                                                                                                                                                                            1. Random Variables
                                                                                                                                                                            2. Probability Distributions
                                                                                                                                                                              1. Discrete Distributions
                                                                                                                                                                                1. Binomial Distribution
                                                                                                                                                                                  1. Poisson Distribution
                                                                                                                                                                                    1. Geometric Distribution
                                                                                                                                                                                    2. Continuous Distributions
                                                                                                                                                                                      1. Normal Distribution
                                                                                                                                                                                        1. Exponential Distribution
                                                                                                                                                                                          1. Gamma Distribution
                                                                                                                                                                                        2. Statistical Inference
                                                                                                                                                                                          1. Hypothesis Testing
                                                                                                                                                                                            1. Null and Alternative Hypotheses
                                                                                                                                                                                              1. Type I and Type II Errors
                                                                                                                                                                                                1. p-values and Significance Levels
                                                                                                                                                                                                  1. Power Analysis
                                                                                                                                                                                                  2. Confidence Intervals
                                                                                                                                                                                                    1. Construction and Interpretation
                                                                                                                                                                                                      1. Bootstrap Methods
                                                                                                                                                                                                    2. Bayesian vs Frequentist Statistics
                                                                                                                                                                                                      1. Bayesian Inference
                                                                                                                                                                                                        1. Prior and Posterior Distributions
                                                                                                                                                                                                          1. Bayesian Updating
                                                                                                                                                                                                            1. Markov Chain Monte Carlo
                                                                                                                                                                                                            2. Frequentist Inference
                                                                                                                                                                                                              1. Maximum Likelihood Estimation
                                                                                                                                                                                                                1. Classical Hypothesis Testing
                                                                                                                                                                                                              2. Statistical Modeling
                                                                                                                                                                                                                1. Linear Regression
                                                                                                                                                                                                                  1. Simple Linear Regression
                                                                                                                                                                                                                    1. Multiple Linear Regression
                                                                                                                                                                                                                      1. Model Assumptions
                                                                                                                                                                                                                      2. Logistic Regression
                                                                                                                                                                                                                        1. Binary Classification
                                                                                                                                                                                                                          1. Multinomial Classification
                                                                                                                                                                                                                          2. Model Selection
                                                                                                                                                                                                                            1. Information Criteria
                                                                                                                                                                                                                              1. Cross-Validation
                                                                                                                                                                                                                                1. Regularization Methods
                                                                                                                                                                                                                              2. Multiple Testing Correction
                                                                                                                                                                                                                                1. Family-wise Error Rate
                                                                                                                                                                                                                                  1. False Discovery Rate
                                                                                                                                                                                                                                    1. Bonferroni Correction
                                                                                                                                                                                                                                      1. Benjamini-Hochberg Procedure
                                                                                                                                                                                                                                    2. Computational Environment and Tools
                                                                                                                                                                                                                                      1. Command Line Interface
                                                                                                                                                                                                                                        1. Unix/Linux Fundamentals
                                                                                                                                                                                                                                          1. File System Navigation
                                                                                                                                                                                                                                            1. File Operations
                                                                                                                                                                                                                                              1. Text Processing Tools
                                                                                                                                                                                                                                                1. Process Management
                                                                                                                                                                                                                                                2. Shell Scripting
                                                                                                                                                                                                                                                  1. Bash Scripting Basics
                                                                                                                                                                                                                                                    1. Variables and Control Structures
                                                                                                                                                                                                                                                      1. Regular Expressions
                                                                                                                                                                                                                                                        1. Automation Techniques
                                                                                                                                                                                                                                                      2. Programming Languages
                                                                                                                                                                                                                                                        1. Python for Bioinformatics
                                                                                                                                                                                                                                                          1. Basic Python Syntax
                                                                                                                                                                                                                                                            1. Data Structures
                                                                                                                                                                                                                                                              1. Object-Oriented Programming
                                                                                                                                                                                                                                                                1. Error Handling
                                                                                                                                                                                                                                                                  1. File Input/Output
                                                                                                                                                                                                                                                                    1. Data Manipulation Libraries
                                                                                                                                                                                                                                                                      1. NumPy
                                                                                                                                                                                                                                                                        1. pandas
                                                                                                                                                                                                                                                                          1. matplotlib
                                                                                                                                                                                                                                                                          2. Bioinformatics Libraries
                                                                                                                                                                                                                                                                            1. Biopython
                                                                                                                                                                                                                                                                              1. scikit-bio
                                                                                                                                                                                                                                                                                1. pysam
                                                                                                                                                                                                                                                                              2. R for Statistical Computing
                                                                                                                                                                                                                                                                                1. R Syntax and Data Types
                                                                                                                                                                                                                                                                                  1. Data Manipulation
                                                                                                                                                                                                                                                                                    1. Statistical Analysis
                                                                                                                                                                                                                                                                                      1. Data Visualization
                                                                                                                                                                                                                                                                                        1. Bioconductor Ecosystem
                                                                                                                                                                                                                                                                                          1. Core Packages
                                                                                                                                                                                                                                                                                            1. Genomic Data Structures
                                                                                                                                                                                                                                                                                              1. Analysis Workflows
                                                                                                                                                                                                                                                                                          2. Version Control Systems
                                                                                                                                                                                                                                                                                            1. Git Fundamentals
                                                                                                                                                                                                                                                                                              1. Repository Initialization
                                                                                                                                                                                                                                                                                                1. Staging and Committing
                                                                                                                                                                                                                                                                                                  1. Branching and Merging
                                                                                                                                                                                                                                                                                                    1. Remote Repositories
                                                                                                                                                                                                                                                                                                    2. Collaboration Workflows
                                                                                                                                                                                                                                                                                                      1. Pull Requests
                                                                                                                                                                                                                                                                                                        1. Code Review
                                                                                                                                                                                                                                                                                                          1. Conflict Resolution
                                                                                                                                                                                                                                                                                                        2. High-Performance Computing
                                                                                                                                                                                                                                                                                                          1. Parallel Computing Concepts
                                                                                                                                                                                                                                                                                                            1. Cluster Computing
                                                                                                                                                                                                                                                                                                              1. Cloud Computing Platforms
                                                                                                                                                                                                                                                                                                                1. Job Scheduling Systems

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                                                                                                                                                                                                                                                                                                            1. Introduction to Bioinformatics and Computational Biology

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                                                                                                                                                                                                                                                                                                            3. Biological Databases and Data Management