Molecular Biology

1. Molecular Systems Biology
   1. Overview of Molecular Systems Biology
      1. Definition and scope
      2. Historical development and significant milestones
      3. Interdisciplinary nature and integration of biology, technology, and computation
   2. Systems of Cellular Regulation
      1. Signaling Pathways
         1. Components of signaling pathways
            1. Receptors
            2. Second messengers
            3. Kinases and phosphatases
         2. Types of signaling pathways
            1. Endocrine, paracrine, autocrine, and juxtacrine signaling
         3. Pathway dynamics and feedback mechanisms
            1. Positive and negative feedback loops
            2. Crosstalk between pathways
      2. Metabolic Networks
         1. Key metabolic pathways
            1. Glycolysis and gluconeogenesis
            2. Citric acid cycle
            3. Oxidative phosphorylation
         2. Interaction between catabolic and anabolic pathways
         3. Regulation of metabolism
            1. Allosteric regulation
            2. Enzymatic control
            3. Hormonal regulation
         4. Metabolic flux analysis
            1. Techniques to measure rates of metabolism
            2. Flux balance analysis
   3. Computational Molecular Biology
      1. Bioinformatics Tools
         1. Sequence alignment and analysis
            1. Algorithms for sequence comparison
            2. Databases for sequence data
         2. Functional genomics
            1. Gene ontology and function prediction
            2. Pathway mapping and enrichment analysis
         3. Data integration and management
            1. Handling large-scale datasets
            2. Integrating multi-omic data (genomics, proteomics, metabolomics)
      2. Structural Modeling
         1. Molecular dynamics simulations
            1. Principles of molecular dynamics
            2. Applications in protein folding and interactions
         2. Docking studies
            1. Protein-ligand docking
            2. Protein-protein interaction prediction
         3. Structural prediction methods
            1. Homology modeling
            2. Ab initio and threading methods
   4. Omics Technologies in Systems Biology
      1. Genomics
         1. Whole genome sequencing
         2. Comparative and functional genomics
      2. Transcriptomics
         1. RNA-seq and its applications
         2. Differential expression analysis
      3. Proteomics
         1. Mass spectrometry-based proteomics
         2. Quantitative proteomics
      4. Metabolomics
         1. Techniques for metabolome analysis
         2. Linking metabolomic data with phenotypic outcomes
   5. Modeling and Simulation in Systems Biology
      1. Mathematical models in systems biology
         1. Differential equations and their use in modeling
         2. Stochastic models and their applications
      2. Network modeling
         1. Construction of biological networks
         2. Analysis of network properties (connectivity, hubs, modularity)
      3. Systems dynamics and control
         1. Dynamic models and time-series analysis
         2. Control theory in biological systems
   6. Applications of Systems Biology
      1. Drug discovery and development
         1. Identifying new drug targets
         2. Predicting drug effects and interactions
      2. Personalized medicine
         1. Integrating systems biology data to tailor treatments
         2. Biomarker discovery for patient stratification
      3. Disease modeling
         1. Systems approaches to understanding complex diseases
         2. Use of models to predict disease progression and treatment responses