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Every paper Pith has read. Search by title, abstract, or pith.
94 papers in q-bio.PE · page 1
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Costly signals sustain cooperation by the responses they trigger
The Co-evolution of Costly Signaling and Cooperation in Social Dilemmas
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Time discard rule orders population behavior for free
Conditioning as a route to stereotyped behavior in growing populations
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Analytical reproduction numbers from correlated traits on networks
The interplay of network structure and correlated infectious traits in epidemic models
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Mitigation inverts epidemic trend on scale-free networks
Susceptible-Infected-Susceptible Model with Mitigation on Scale-Free Networks
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Log scaling turns sweeps into tents or houses
Logarithmic scaling of selective sweep curves: from tents to houses
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Persistence speeds one bacterial invasion wave but not the reverse
Travelling waves of invasion in microbial communities with phenotypic switching
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Two fear channels trigger state switches in stochastic Allee populations
Dual Fear Mechanisms Shaping Stochastic Population Dynamics under the Allee Effect
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Model estimates R0 of 2.76 for cruise ship hantavirus
Modeling the Impact of Exposed Cases in a Hantavirus Outbreak on a Cruise Ship
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Papal names follow random copying rule across 2000 years
Quo nomine vis vocari? A random-copying model explains the temporal sequence of papal names
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Extrinsic noise required to explain E
Essential Role of Extrinsic Noise in Models of E. coli Division Control
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Pairwise models can mask higher-order interactions in ecology
Higher-order interactions in ecology can be hidden in plain sight
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New edge-based μ-representation yields distance for orchard networks
A $\mu$-distance for semidirected orchard phylogenetic networks
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Positive feedbacks create multiple stable states in ecosystems
Towards a unified framework for multiple stable states in ecological systems
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LUCA was already complex and adapted long before modern life
The Origin of Life in the Light of Evolution
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Origin of life requires evolution before LUCA
The Origin of Life in the Light of Evolution
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Replicator trajectories miss fitness maxima without symmetry conditions
Chapter 2: Geometry of the Fitness Surface and Trajectory Dynamics of Replicator Systems
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Optimizers like SGD derive from Darwinian evolution with added noise
Direct From Darwin: Deriving Advanced Optimizers From Evolutionary First Principles
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Optimizers simulate Darwinian evolution with added drift noise
Direct From Darwin: Deriving Advanced Optimizers From Evolutionary First Principles
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Dispersal model separates habitat from connectivity in range shifts
A process-based dynamic occupancy model to study range dynamics under non-equilibrium conditions
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Two coding thresholds explain the Great Filter
Algorithmic bottlenecks in evolution: Genetic code, symbolic language, and the Great Filter hypothesis
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Genotype decides if heterogeneity amplifies or suppresses selection
Genotype specificity and spatial arrangement govern the direction and magnitude of selection in variable environments
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Log-mean process alone decides survival in varying branching models
Catastrophe-dispersion models in random and varying environments across generations
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One log-mean criterion settles four dispersal rules at once
Catastrophe-dispersion models in random and varying environments across generations
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Algorithms build networks from required and forbidden LCA rules
Inferring Phylogenetic Networks from Required and Forbidden LCA-Constraints
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Algorithms decide if required and forbidden LCA constraints fit a phylogenetic network
Inferring Phylogenetic Networks from Required and Forbidden LCA-Constraints
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Edit-flow model localizes changes more accurately on indel-rich sequences
Tree-Conditioned Edit Flows for Ancestral Sequence Reconstruction
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Infection model reduces to Fokker-Planck for resistance analysis
From Individual-Based Models to Macroscopic Dynamics of Antimicrobial Resistance
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Coalescent model unifies IBD tracts with ROH lengths
Connecting IBD tracts and runs of homozygosity: A coalescent framework for inferring effective population size
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Temperature model captures Usutu virus clockwise spread
A temperature-driven diffusion model of Usutu virus spread in Germany with spillover into neighbouring countries
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Correlation of fitness effects sets number of peaks in random landscapes
Epistatic strength, modularity, and locus heterogeneity shape the number of local optima in fitness landscapes
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Frankenstein ancestry yields counting dual for interactive Moran model
Genealogical structures under interactive neutral reproduction: factorial moment duality via a Frankenstein process
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Higher-order reproduction eliminates invasion fronts
Emergent population dynamics of random walkers with cooperative reproduction and spatial selection
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Decision computation constrains social scale and structure
Computational foundations of the human world
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Polymer equilibria form only above a resource threshold
Equilibrium and Competition in Evolutionary Dynamics
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Tool embeds editable phylogenetic trees in notebooks and websites
Heat-tree: Cross-platform software for interactive and embeddable phylogenetic tree visualization and editing
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Framework keeps epidemic simulations positive and bounded at any step size
EPITIME: A Computational Framework for Integral Epidemic Models with Structure-Preserving Discretizations
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Overuse and underuse both emerge as evolutionary outcomes
Incorporating the underuse problem in the tragedy of the commons
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Continuous models let epidemics persist past one infected person
Epidemic Extinction in a Continuous SIRS Model with Vaccination
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Shortening preferred-host infection time curbs disease spread
Modeling the impact of host diversity on the evolution of vector feeding preferences and implications for disease control
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Degree and distance contact rules slow epidemic growth
Degree-dependent and distance-dependent contact rates interpolate between explosive, exponential and polynomial epidemic growth
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Dispersal diversity buffers rare species against vulnerability
Rare but Resilient: Dispersal diversity buffers species vulnerability
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Noise selects for aligned gene-regulatory networks
How is gene-regulatory evolution affected by cell-to-cell variability?
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Black Sigatoka lingers below the reproduction threshold
The Curse of Black Sigatoka: A Backward Bifurcation Perspective
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Lab incubation times flatten dengue epidemic peaks
From lab to outbreak: experimental mosquito extrinsic incubation period distributions shape dengue epidemic dynamics
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Models allowing exit from mosquito transmitting state fit data better in 7 of 10 cases
A modelling perspective on mosquito infectiousness: time-varying transmission competence in arbovirus vector
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Bayesian method infers nucleic acid motif rates from ligation data
Bayesian Rate Inference for Sequence Motif Dynamics in Systems of Reactive Nucleic Acids
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Learned ODEs link within-host TB models to population dynamics
Equation Learning for multiscale models of infectious diseases
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Diffusion models match ensembles on flu forecasts
Generative diffusion models for spatiotemporal influenza forecasting
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Clustering cuts bias in sampled Fisher information for dynamics
Fisher Information and Dynamical Sampling I
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Polynomial-time method completes overlapping phylogenetic trees
Polynomial-time completion of phylogenetic tree sets