Supervised machine learning for population genetics: a new paradigm

DR Schrider, AD Kern - Trends in Genetics, 2018 - cell.com
As population genomic datasets grow in size, researchers are faced with the daunting task
of making sense of a flood of information. To keep pace with this explosion of data …

Fundamentals and recent developments in approximate Bayesian computation

J Lintusaari, MU Gutmann, R Dutta, S Kaski… - Systematic …, 2017 - academic.oup.com
Bayesian inference plays an important role in phylogenetics, evolutionary biology, and in
many other branches of science. It provides a principled framework for dealing with …

Robust demographic inference from genomic and SNP data

L Excoffier, I Dupanloup, E Huerta-Sánchez… - PLoS …, 2013 - journals.plos.org
We introduce a flexible and robust simulation-based framework to infer demographic
parameters from the site frequency spectrum (SFS) computed on large genomic datasets …

Viral phylodynamics

EM Volz, K Koelle, T Bedford - PLoS computational biology, 2013 - journals.plos.org
Viral phylodynamics is defined as the study of how epidemiological, immunological, and
evolutionary processes act and potentially interact to shape viral phylogenies. Since the …

Reliable ABC model choice via random forests

P Pudlo, JM Marin, A Estoup, JM Cornuet… - …, 2016 - academic.oup.com
Abstract Motivation: Approximate Bayesian computation (ABC) methods provide an
elaborate approach to Bayesian inference on complex models, including model choice. Both …

Bayesian optimization for likelihood-free inference of simulator-based statistical models

MU Gutmann, J Cor - Journal of Machine Learning Research, 2016 - jmlr.org
Our paper deals with inferring simulator-based statistical models given some observed data.
A simulator-based model is a parametrized mechanism which specifies how data are …

Deep learning for population genetic inference

S Sheehan, YS Song - PLoS computational biology, 2016 - journals.plos.org
Given genomic variation data from multiple individuals, computing the likelihood of complex
population genetic models is often infeasible. To circumvent this problem, we introduce a …

A comparative review of dimension reduction methods in approximate Bayesian computation

MGB Blum, MA Nunes, D Prangle, SA Sisson - 2013 - projecteuclid.org
Supplement to “A Comparative Review of Dimension Reduction Methods in Approximate
Bayesian Computation”. The supplement contains for each of the three examples a …

[HTML][HTML] The genomic history of the Aegean palatial civilizations

F Clemente, M Unterländer, O Dolgova, CEG Amorim… - Cell, 2021 - cell.com
Summary The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the
Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural …

Genomic signatures of selective pressures and introgression from archaic hominins at human innate immunity genes

M Deschamps, G Laval, M Fagny, Y Itan, L Abel… - The American Journal of …, 2016 - cell.com
Human genes governing innate immunity provide a valuable tool for the study of the
selective pressure imposed by microorganisms on host genomes. A comprehensive …