Populations & Evolution
Population dynamics, evolutionary biology, and epidemiological modeling.
q-bio.PE · 101 papersA modelling perspective on mosquito infectiousness: time-varying transmission competence in arbovirus vector
A new model reveals mosquito arbovirus transmission competence is often time-varying, not lifelong, improving epidemiological understanding.
Bayesian Rate Inference for Sequence Motif Dynamics in Systems of Reactive Nucleic Acids
This paper introduces a Bayesian inference framework to determine parameters for sequence motif dynamics in reactive nucleic acid systems, linking simulations to theory.
Equation Learning for multiscale models of infectious diseases
This paper introduces a gender-stratified multiscale modeling framework using equation learning to study tuberculosis dynamics and the impact of sex/gender.
Generative diffusion models for spatiotemporal influenza forecasting
Influpaint, a novel diffusion model, forecasts spatiotemporal influenza incidence by treating seasons as images, achieving competitive accuracy.
Fisher Information and Dynamical Sampling I
This paper calculates the bias of Fisher information for dynamical systems reconstructed from sampled data, showing clustering improves accuracy.
Polynomial-time completion of phylogenetic tree sets
This paper introduces a polynomial-time algorithm for completing phylogenetic tree sets with partial taxon overlap, preserving data lost by pruning.
Mean-Field and Pairwise Approaches for the SIRI Model on Poisson Networks
This paper shows when complex SIRI epidemic dynamics on Poisson networks can be accurately approximated by simpler mean-field equations.
Simple sign epistasis and evolutionary detours in fitness landscapes
Simple sign epistasis causes evolutionary detours, longer paths to fitness peaks, and is more common than reciprocal sign epistasis in weakly epistatic landscapes.
Stochastic reversal of deterministic selection in epidemic strain competition
Stochastic effects can reverse deterministic selection in epidemic strain competition, drastically reducing fixation times from years to days.
Global remote sensing reveals vegetation clustering as a physical footprint of shifting aridity trends in drylands
This paper uses remote sensing to show that vegetation clustering reveals whether dryland ecosystems are degrading due to increasing aridity or recovering.
Local growth laws determine global shape of molluscan shells
This paper shows that the diverse shapes of molluscan shells can be explained by a simple mathematical model based on local growth laws.
Integrating opportunities and parametrized signatures for improved mutational processes estimation in extended sequence contexts
This paper introduces a robust method for estimating mutational signatures by integrating opportunities and parametrized signatures in extended sequence contexts.
Rates of forgetting for the sequentially Markov coalescent
This paper analyzes the forgetting rates of the sequentially Markov coalescent (SMC), showing how quickly genetic correlations decay across a chromosome.
Centering Ecological Goals in Automated Identification of Individual Animals
This paper argues that automated animal identification systems must prioritize ecological context and data collection methods to be truly useful in conservation.
Emergence biases in molecular evolution
This paper formalizes 'emergence bias,' a molecular predisposition influencing the acquisition of new genetic functions, crucial for evolutionary innovation.
Indirect Prey-taxis VS a Shortwave External Signal in Multiple Dimensions
This paper develops a short-wave asymptotic expansion for predator-prey models where predators respond to a prey-generated signal influenced by an external field.
Meeting times on graphs in near-cubic time
A new algorithm drastically speeds up calculating meeting times for random walkers on graphs, reducing complexity from O(N^6) to near O(N^3).
Analysis of persistence thresholds for a nonlocal PDE--ODE model of bacterial persister cells
This paper analyzes a PDE-ODE model to identify a sharp parameter threshold for bacterial persister cell persistence, independent of internal structure.
IDOBE: Infectious Disease Outbreak forecasting Benchmark Ecosystem
IDOBE is a new benchmark ecosystem with over 10,000 curated outbreaks for evaluating and standardizing infectious disease forecasting models.
Effect of antibiotic spectrum on the abundance of resistant bacteria in multispecies communities
This paper develops a mathematical measure to predict how antibiotic spectrum influences resistant bacteria abundance in multispecies communities.
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