Mathematical and Theoretical Epidemiology and Ecology Models

A computationally tractable birth-death model that combines phylogenetic and epidemiological data

The paper introduces a computationally efficient birth-death model that integrates phylogenetic and epidemiological data to estimate transmission dynamics and unreported infections.

Estimation of the probability of epidemic fade-out from multiple outbreak data

The paper estimates the probability of epidemic fade-out using Bayesian hierarchical modeling on synthetic outbreak data, showing improved accuracy compared to individual epidemic analysis.

The competition dynamics of resistant and sensitive infections

The paper develops a model to study antimicrobial resistance dynamics and competition, finding that competitive release has limited impact once resistance emerges, and effective treatment is key to mitigating spread.

Stochastic Simulation Algorithm for effective spreading dynamics on Time-evolving Adaptive NetworX (SSATAN-X)

This paper introduces SSATAN-X, a stochastic simulation algorithm for pathogen spreading on adaptive networks, achieving up to 100x speed-up over existing methods.

Cross immunity protection and antibody dependent enhancement: A distributed delay dynamic model

This paper develops a distributed delay dynamic model to study Dengue fever transmission dynamics, incorporating cross immunity and antibody dependent enhancement.

Transmission dynamics and control of Sporotrichosis in domestic felines

The paper develops a mathematical model to study Sporotrichosis transmission dynamics in domestic cats, finding that mass treatment combined with contact reduction strategies significantly reduces disease prevalence.

A hybrid PDE-ABM model for viral dynamics with application to SARS-CoV-2 and influenza

The paper introduces a hybrid PDE-ABM model to simulate viral dynamics in cell populations, showing it can predict SARS-CoV-2 and influenza infections and replicate experimental results.

Comparison between Lotka-Volterra and Multivariate Autoregressive models of ecological interaction systems

This study compares Lotka-Volterra and Multivariate Autoregressive models for ecological interaction systems, finding LV models generally superior for dynamic data with large deviations from steady states.

The Paradox of the Plankton: Coexistence of Structured Microbial Communities

The paper investigates biophysical models to resolve the Paradox of the Plankton by combining resource competition, metabolic trade-offs, and stochastic assembly, showing simulations align with empirical observations.

Inference and Validation of the Structure of Lotka-Volterra Models

The paper infers and validates interaction parameters in Lotka-Volterra models using two new strategies and assesses data compliance with LV structure.

Understanding the role of urban design in disease spreading

This paper develops a mathematical framework to model how urban design influences the spread of influenza-like diseases using census and pandemic data from Guadalajara.

Viral-structured models of dividing cells shows cell-virus coexistence via viral load partitioning between cell progeny

The paper develops a mathematical model showing that dividing cells and lytic viruses can coexist through viral load partitioning during cell division and growth.

Social networks with strong spatial embedding generate non-standard epidemic dynamics driven by higher-order clustering

The paper models socio-spatial networks with strong spatial embedding to show how they generate non-standard epidemic dynamics with sub-exponential growth and lower peak incidence.

Stochastic logistic models reproduce experimental time series of microbial communities

The paper shows stochastic logistic models can reproduce stochastic properties of microbial time series from plankton and the human microbiome.

Optimising Renewal Models for Real-Time Epidemic Prediction and Estimation

This paper optimizes the renewal model for real-time epidemic prediction by developing a principled method to select the optimal window length k using the accumulated prediction error metric.

Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models

This paper introduces a method to optimally select the number of parameters in epidemic renewal and phylogenetic skyline models using minimum description length to improve estimation accuracy.

Adaptive social contact rates induce complex dynamics during epidemics

This paper develops a model of adaptive social contact rates during epidemics, showing complex dynamics including oscillations and multiple peaks under parameter changes.

A macro-ecological approach to predators' functional response

This paper investigates whether predator functional response follows mass action at macro-ecological scales and finds it follows a power-law with square root dependence on predator-prey densities.

Control and simulation impact on nonlinear Hepatitis-B model by using Pade-approximation based Differential Evolution

This paper applies Pade-approximation based Differential Evolution to solve a nonlinear Hepatitis-B model, showing improved convergence and error performance compared to NSFD.

A sub-exponential branching process to study early epidemic dynamics with application to Ebola

The paper introduces a sub-exponential branching process model to study early epidemic dynamics, applied to Ebola data showing sub-exponential transmission.

Double asymmetric percolation drives a quadruple transition in sexual contact networks

This study models ZIKV transmission through sexual contact networks with double asymmetric percolation, revealing a quadruple epidemic transition.

Cooperation Enhances Robustness of Coexistence in Spatially Structured Consortia

This study shows cooperative interactions enhance robustness of coexistence in spatially structured microbial consortia, while competition leads to spatial heterogeneity and fragile coexistence.

Waterborne, abiotic and other indirectly transmitted (W.A.I.T.) infections are defined by the dynamics of free-living pathogens and environmental reservoirs

The paper develops a mathematical framework to model waterborne and indirectly transmitted infections and applies it to cholera and hepatitis C to show the importance of environmental reservoir dynamics.

Quantifying bacterial fitness in intracellular dynamics

The paper develops a mathematical model to quantify bacterial fitness dynamics in intracellular infection scenarios, identifying key parameters that influence infection outcomes.

Process noise distinguishes between indistinguishable population dynamics

The paper demonstrates that process noise can distinguish between indistinguishable stochastic population dynamics models using Bayesian methods and summary statistics.

Resolving outbreak dynamics using Approximate Bayesian Computation for stochastic birth-death models

This paper uses Approximate Bayesian Computation to improve parameter estimation in stochastic birth-death models for disease outbreaks, showing better identifiability of key parameters like R and infectious population size.

Epithelial stratification shapes infection dynamics

This paper develops a mathematical model to simulate infections in stratified epithelia, finding that infection outcomes depend on pathogen interactions with epithelial layers and cell responses.

Unifying mutualism diversity for interpretation and prediction

The paper develops a general rule for predicting mutualistic system outcomes and introduces a calibration method to apply it without full mechanistic understanding.

Mathematical Model For Plant-Insect Interaction With Dynamic Response To PAD4-BIK1 Interaction And Effect Of BIK1 Inhibition

The paper develops a mathematical model to study plant-insect interactions, focusing on the role of BIK-1 inhibition in enhancing plant immunity and biomass production.

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences

FAVITES simulates epidemic datasets for fast-evolving pathogens like HIV, enabling study of transmission networks and intervention impacts.