335 citations · 535 across the 9 of their papers we have counts for
9 papers
Finding high posterior density phylogenies by systematically extending a directed acyclic graph
Chris Jennings-Shaffer, David H Rich, Matthew Macaulay +7
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying…
How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
Andrew F. Magee, Michael D. Karcher, Frederick A. Matsen +1
Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judg…
Variational Bayesian Supertrees
Michael Karcher, Cheng Zhang, Frederick A Matsen
Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior di…
Estimating effective population size changes from preferentially sampled genetic sequences
Michael D. Karcher, Marc A. Suchard, Gytis Dudas +1
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population…
phylodyn: an R package for phylodynamic simulation and inference
Michael D. Karcher, Julia A. Palacios, Shiwei Lan +1
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population…
The Romulus Cosmological Simulations: A Physical Approach to the Formation, Dynamics and Accretion Models of SMBHs
Michael Tremmel, Michael Karcher, Fabio Governato +5
We present a novel implementation of supermassive black hole (SMBH) formation, dynamics, and accretion in the massively parallel tree+SPH code, ChaNGa. This approach improves the m…
The Little Galaxies that Could (Reionize the Universe): Predicting Faint End Slopes & Escape Fractions at z > 4
Lauren Anderson, Fabio Governato, Michael Karcher +2
The sources that reionized the universe are still unknown, but likely candidates are faint but numerous galaxies. In this paper we present results from running a high resolution, u…
Quantifying and mitigating the effect of preferential sampling on phylodynamic inference
Michael D. Karcher, Julia A. Palacios, Trevor Bedford +2
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this tas…
An Efficient Bayesian Inference Framework for Coalescent-Based Nonparametric Phylodynamics
Shiwei Lan, Julia A. Palacios, Michael Karcher +2
Phylodynamics focuses on the problem of reconstructing past population size dynamics from current genetic samples taken from the population of interest. This technique has been ext…