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Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster
Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome.
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks
- Jeffrey Chan, Valerio Perrone, J. P. Spence, P. Jenkins, Sara Mathieson, Yun S. Song
- Computer ScienceNeurIPS
- 16 February 2018
This work develops an exchangeable neural network that performs summary statistic-free, likelihood-free inference, and demonstrates the power of the approach on the recombination hotspot testing problem, outperforming the state-of-the-art.
Exact simulation of the Wright-Fisher diffusion
This article demonstrates that it is in fact possible to simulate exactly from a broad class of Wright-Fisher diffusion processes and their bridges and develops an exact rejection algorithm for processes with more general drift functions, including those modelling natural selection, using ideas from retrospective simulation.
Importance sampling and the two-locus model with subdivided population structure
The diffusion-generator approximation technique developed by De Iorio and Griffiths is extended to the neutral coalescent model with recombination, thus obtaining novel sampling distributions for the two-locus model, and these are shown to be generally closer to the true distributions than are Fearnhead and Donnelly's.
Poisson Random Fields for Dynamic Feature Models
- Valerio Perrone, P. Jenkins, Dario Spanò, Y. Teh
- Computer ScienceJ. Mach. Learn. Res.
- 22 November 2016
A new framework for generating dependent Indian buffet processes is established, where the Poisson random field model from population genetics is used as a way of constructing dependent beta processes.
The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele.
General Triallelic Frequency Spectrum Under Demographic Models with Variable Population Size
The predicted frequency spectrum of a site that has experienced at most two mutation events is obtained, under very general assumptions about the distribution of branch lengths in the underlying coalescent tree, and it is shown that triallelic sites will have use if they can be incorporated into demographic inference.
PADÉ APPROXIMANTS AND EXACT TWO-LOCUS SAMPLING DISTRIBUTIONS.
It is proved here that only a finite number of terms in the asymptotic expansion is needed to recover the exact two-locus sampling distribution as an analytic function of ρ; this function is exact for all values of ς ∈ [0, ∞).
Sub-Doppler mid-infrared spectroscopy of molecular ions
High-precision and high-accuracy rovibrational spectroscopy of molecular ions.
- J. N. Hodges, A. Perry, P. Jenkins, Brian M. Siller, B. McCall
- PhysicsThe Journal of chemical physics
- 29 October 2013
A versatile new instrument capable of measuring rovibrational transition frequencies of molecular ions with sub-MHz accuracy and precision is presented, expected to open up many new possibilities for state-of-the-art ab initio calculations and astronomical observations.