Populations & Evolution
Population dynamics, evolutionary biology, and epidemiological modeling.
q-bio.PE · 101 papersInformation on hidden birth events restores identifiability in phylodynamic inference
This paper shows that information on hidden birth events, especially mutations at birth, restores parameter identifiability in phylodynamic inference.
Evolution as fitness landscape navigation: Concepts, Measures, and Emerging Questions
This review clarifies concepts, measures, and open questions in fitness landscape navigation, proposing a new navigability metric.
Phase transitions in microbial lineage trees
This paper demonstrates how phase transitions arise in microbial populations, linking them to genealogies and setting a lower bound for stable plasmid maintenance.
From Physical Difference to Meaning: A Constructor-Theoretic Framework for Prebiotic Information in Casimir-Lifshitz-Coupled Protocell Clusters
This paper uses Constructor Theory to model how information and meaning could emerge prebiotically in Casimir-Lifshitz-coupled protocell clusters.
Synchronized disease and behavioural dynamics in weakly coupled populations
This paper shows that weak social coupling between populations can synchronize disease and vaccination dynamics, with payoff sensitivity determining synchronization type.
A generative model for bipartite gene-sharing networks
This paper proposes a two-parameter generative model for bipartite gene-sharing networks, explaining observed gene and genome degree distributions.
What good is modeling? Introducing biology students to theory
This paper details a graduate course designed to help biology students with limited math backgrounds understand theoretical papers using modern teaching methods.
An abstract model of nonrandom, non-Lamarckian mutation in evolution using a multivariate estimation-of-distribution algorithm
This paper introduces a simulation model demonstrating nonrandom, non-Lamarckian mutation, aligning with Interaction-based Evolution (IBE).
Predicting success of cooperators across arbitrary heterogeneous environmental landscapes
A new framework and Spatial Correlation Index (SCI) predict how environmental heterogeneity and spatial organization determine the success of cooperation.
Phylogenetic Inference under the Balanced Minimum Evolution Criterion via Semidefinite Programming
This paper applies Semidefinite Programming (SDP) to solve the Balanced Minimum Evolution (BME) problem for accurate phylogenetic inference.
Modeling of Pneumococcal and Respiratory Syncytial Virus Pneumonia: An Epidemiological Review, with Statistical Inference
This review synthesizes recent epidemiological models for vaccine-preventable pneumococcal and RSV pneumonia, aiding public health strategies.
Fixation probabilities for multi-allele Moran dynamics with weak selection
A new perturbative framework computes fixation probabilities for multi-allele Moran dynamics under weak selection, extending analytical understanding.
Can AI Detect Life? Lessons from Artificial Life
AI methods for detecting extraterrestrial life are easily fooled by out-of-distribution samples, leading to high false positives.
The origin of the genetic code is encrypted in the structure of present-day transfer RNAs
Present-day tRNA structures from Bacillus subtilis provide a genealogical tree that encrypts the evolutionary timeline of the genetic code.
Will a Large Complex System be Stable? Revisited
This paper re-examines Robert May's complexity-stability debate using a new mathematical approach, challenging his original conclusion.
Neutralization titers reveal the structure of polyclonal antibody responses
A new method uses neutralization titers to quantitatively predict polyclonal antibody response structure, avoiding complex experimental measurements.
Strategy evolution on networks under payoff uncertainty and risk preference
This paper explores how individual risk preferences and network structure influence the evolution of cooperation under uncertain social interactions.
How complex behavioural contagion can prevent infectious diseases from becoming endemic
This paper shows that complex behavioral contagion, where behavior uptake is nonlinear, can lead to disease elimination, even for high R0.
A molecular clock for writing systems reveals the quantitative impact of imperial power on cultural evolution
This paper reveals a molecular clock for writing systems, showing how imperial power significantly alters their evolution and leads to extinctions.
Kinetic models of opinion-driven epidemic dynamics modulated by graphons
This paper introduces kinetic models to simulate opinion-driven epidemic dynamics on social networks represented by graphons, showing how opinions and leaders affect disease spread.
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