Modeling in Biology

  1. Applications Across Biological Scales
    1. Molecular and Cellular Biology
      1. Enzyme Kinetics
        1. Michaelis-Menten Kinetics
          1. Allosteric Regulation
            1. Cooperative Binding
              1. Inhibition Mechanisms
              2. Gene Regulatory Networks
                1. Transcriptional Switches
                  1. Oscillators and Clocks
                    1. Feedback Loops
                      1. Bistability
                      2. Metabolic Pathway Analysis
                        1. Flux Balance Analysis
                          1. Constraint-Based Modeling
                            1. Metabolic Control Analysis
                            2. Cell Signaling Cascades
                              1. Signal Transduction Pathways
                                1. Amplification and Attenuation
                                  1. Crosstalk Between Pathways
                                  2. Protein Structure and Folding
                                    1. Energy Landscapes
                                      1. Folding Pathways
                                        1. Misfolding and Aggregation
                                        2. Electrophysiology
                                          1. The Hodgkin-Huxley Model
                                            1. Action Potential Propagation
                                              1. Synaptic Transmission
                                              2. Cell Cycle Modeling
                                                1. Checkpoint Controls
                                                  1. Oscillatory Dynamics
                                                  2. DNA Replication and Repair
                                                    1. Replication Fork Dynamics
                                                      1. Error Correction Mechanisms
                                                    2. Developmental Biology
                                                      1. Morphogenesis
                                                        1. Tissue Patterning
                                                          1. Cell Migration
                                                            1. Mechanical Forces
                                                            2. Pattern Formation
                                                              1. Turing Patterns
                                                                1. Stripe and Spot Formation
                                                                  1. Gradient-Based Patterning
                                                                  2. Cell Fate Specification
                                                                    1. Lineage Tracing
                                                                      1. Regulatory Networks in Differentiation
                                                                        1. Stem Cell Dynamics
                                                                        2. Organ Development
                                                                          1. Limb Development
                                                                            1. Neural Development
                                                                              1. Vascular Development
                                                                            2. Physiology and Medicine
                                                                              1. Pharmacokinetics and Pharmacodynamics
                                                                                1. Drug Absorption
                                                                                  1. Distribution
                                                                                    1. Metabolism
                                                                                      1. Excretion
                                                                                        1. Dose-Response Relationships
                                                                                        2. Cardiovascular System Modeling
                                                                                          1. Heart Function Models
                                                                                            1. Blood Flow Dynamics
                                                                                              1. Cardiac Arrhythmias
                                                                                              2. Immune System Dynamics
                                                                                                1. Host-Pathogen Interactions
                                                                                                  1. Immune Response Modeling
                                                                                                    1. Autoimmune Diseases
                                                                                                    2. Tumor Growth and Angiogenesis
                                                                                                      1. Tumor-Host Interactions
                                                                                                        1. Vascular Network Formation
                                                                                                          1. Cancer Metastasis
                                                                                                          2. Respiratory System
                                                                                                            1. Gas Exchange Models
                                                                                                              1. Airway Dynamics
                                                                                                              2. Renal Function
                                                                                                                1. Kidney Filtration
                                                                                                                  1. Electrolyte Balance
                                                                                                                  2. Endocrine System
                                                                                                                    1. Hormone Regulation
                                                                                                                      1. Feedback Control
                                                                                                                    2. Ecology and Evolutionary Biology
                                                                                                                      1. Population Dynamics
                                                                                                                        1. Exponential Growth
                                                                                                                          1. Logistic Growth
                                                                                                                            1. Predator-Prey Models
                                                                                                                              1. Competition Models
                                                                                                                                1. Age-Structured Models
                                                                                                                                2. Metapopulation Dynamics
                                                                                                                                  1. Patch Occupancy Models
                                                                                                                                    1. Colonization and Extinction
                                                                                                                                      1. Spatial Connectivity
                                                                                                                                      2. Evolutionary Game Theory
                                                                                                                                        1. Payoff Matrices
                                                                                                                                          1. Evolutionarily Stable Strategies
                                                                                                                                            1. Cooperation and Altruism
                                                                                                                                            2. Phylogenetics and Evolutionary Trees
                                                                                                                                              1. Tree Construction Methods
                                                                                                                                                1. Molecular Clock Models
                                                                                                                                                  1. Species Divergence
                                                                                                                                                  2. Community Ecology
                                                                                                                                                    1. Food Web Dynamics
                                                                                                                                                      1. Species Interactions
                                                                                                                                                        1. Biodiversity Patterns
                                                                                                                                                        2. Conservation Biology
                                                                                                                                                          1. Population Viability Analysis
                                                                                                                                                            1. Habitat Fragmentation
                                                                                                                                                              1. Species Reintroduction
                                                                                                                                                            2. Epidemiology
                                                                                                                                                              1. Compartmental Models
                                                                                                                                                                1. SIR Model
                                                                                                                                                                  1. SEIR Model
                                                                                                                                                                    1. Extensions with Vital Dynamics
                                                                                                                                                                      1. Vaccination Strategies
                                                                                                                                                                        1. Vector-Borne Diseases
                                                                                                                                                                        2. Network-Based Disease Spread
                                                                                                                                                                          1. Contact Networks
                                                                                                                                                                            1. Superspreading Events
                                                                                                                                                                              1. Social Network Effects
                                                                                                                                                                              2. Agent-Based Epidemiological Simulations
                                                                                                                                                                                1. Individual-Level Disease Transmission
                                                                                                                                                                                  1. Behavioral Interventions
                                                                                                                                                                                    1. Spatial Disease Spread
                                                                                                                                                                                    2. Chronic Disease Modeling
                                                                                                                                                                                      1. Disease Progression
                                                                                                                                                                                        1. Risk Factor Analysis

                                                                                                                                                                                    Previous

                                                                                                                                                                                    4. Modeling Paradigms and Techniques

                                                                                                                                                                                    Go to top

                                                                                                                                                                                    Next

                                                                                                                                                                                    6. Model Implementation, Analysis, and Validation