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Every paper Pith has read. Search by title, abstract, or pith.
238 papers in q-bio.PE · page 2
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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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Algorithms build networks from required and forbidden LCA rules
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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Method adds socio-demographic layers to epidemic contact matrices
A method for including socio-demographic factors in social contact matrices for compartment-based epidemic models
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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 reproduction orders erase invasion fronts in walker models
Emergent population dynamics of random walkers with cooperative reproduction and spatial selection
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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
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SIRI on Poisson networks matches mean-field ODEs when transmission is weak
Mean-Field and Pairwise Approaches for the SIRI Model on Poisson Networks
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Simple sign epistasis forces detours with back-mutations to peaks
Simple sign epistasis and evolutionary detours in fitness landscapes
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Noise reverses which strain wins in epidemic competition
Stochastic reversal of deterministic selection in epidemic strain competition
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Vegetation patterns reveal if drylands are drying or recovering
Global remote sensing reveals vegetation clustering as a physical footprint of shifting aridity trends in drylands
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Three parameters generate nearly all mollusk shell shapes
Local growth laws determine global shape of molluscan shells
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Combining mutational opportunities
Integrating opportunities and parametrized signatures for improved mutational processes estimation in extended sequence contexts
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SMC jump chain ergodic geometrically
Rates of forgetting for the sequentially Markov coalescent
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Workflow mismatch limits automated animal ID in ecology
Centering Ecological Goals in Automated Identification of Individual Animals
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Sequences carry bias toward new functions
Emergence biases in molecular evolution
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Short-wave external signals stabilize or destabilize prey-taxis equilibria
Short-wave signal versus indirect prey-taxis
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Random walker meeting times on graphs solved in O(N^4) time
Meeting times on graphs in near-cubic time
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Bacterial persistence decided by one parameter independent of structure
Analysis of persistence thresholds for a nonlocal PDE--ODE model of bacterial persister cells
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MLP models lead in tests across 10,000 disease outbreaks
IDOBE: Infectious Disease Outbreak forecasting Benchmark Ecosystem
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Net-effect measure from microbe networks forecasts resistant bacteria under different drug
Effect of antibiotic spectrum on the abundance of resistant bacteria in multispecies communities
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Hidden birth data identifies all parameters in time-varying birth-death models
Information on hidden birth events restores identifiability in phylodynamic inference
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Outcome-based metric measures fitness landscape navigability
Evolution as fitness landscape navigation: Concepts, Measures, and Emerging Questions
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Phase transition sets strict lower bound on stable plasmid numbers
Phase transitions in microbial lineage trees
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Physical differences become meaningful states in protocell clusters
From Physical Difference to Meaning: A Constructor-Theoretic Framework for Prebiotic Information in Casimir-Lifshitz-Coupled Protocell Clusters
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Weak social ties sync disease cycles across groups
Synchronized disease and behavioural dynamics in weakly coupled populations
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Two-parameter model reproduces power-law gene and exponential genome degrees
A generative model for bipartite gene-sharing networks
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Course teaches biology students to read theory papers
What good is modeling? Introducing biology students to theory