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A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
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Optimal point process filtering and estimation of the coalescent process.

Kris V Parag1, Oliver G Pybus1

  • 1Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.

Journal of Theoretical Biology
|April 8, 2017
PubMed
Summary

The Bayesian Snyder filter offers a new, accessible method for estimating population history from genetic data. This tool accurately reconstructs demographic models and performs well on real-world viral sequence data.

Keywords:
Bayesian inferenceCoalescent theoryNon-linear filtersParametric estimationSnyder filters

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Area of Science:

  • Population genetics
  • Computational biology
  • Statistical inference

Background:

  • The coalescent process is fundamental for inferring population demographic history from genetic diversity.
  • Existing coalescent inference methods (e.g., MCMC, Gaussian processes) can be complex to implement.
  • There is a need for more accessible and flexible estimation methodologies.

Purpose of the Study:

  • Introduce the Bayesian Snyder filter as a novel, user-friendly minimum mean square error estimator.
  • Adapt coalescent inference for both isochronous and heterochronous sampling.
  • Provide an alternative tool for parametric demographic function estimation.

Main Methods:

  • Reinterpreting the coalescent as a self-exciting Markov process.
  • Applying the Snyder filter to parametric demographic functions on fixed genealogies.
  • Analytically and numerically solving filter equations for different population size models.

Main Results:

  • The Snyder filter accurately recovers demographic history in tested models.
  • Demonstrated robustness to prior distribution specification for constant population size models.
  • The filter shows comparable performance to existing phylodynamic methods on Hepatitis C virus data.

Conclusions:

  • The Bayesian Snyder filter is an exact and direct Bayesian estimation method.
  • It offers a flexible and easily implementable alternative for coalescent inference.
  • This method has the potential to become a valuable tool in population genetics research.