4 citations · 5 across the 2 of their papers we have counts for
6 papers
Shrinkage-based random local clocks with scalable inference
Alexander A. Fisher, Xiang Ji, Akihiko Nishimura +2
Local clock models propose that the rate of molecular evolution is constant within phylogenetic sub-trees. Current local clock inference procedures scale poorly to large taxa probl…
From viral evolution to spatial contagion: a biologically modulated Hawkes model
Andrew J. Holbrook, Xiang Ji, Marc A. Suchard
Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this his…
Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models
Zhenyu Zhang, Akihiko Nishimura, Paul Bastide +5
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced f…
A phylogenetic approach disentangles interlocus gene conversion tract length and initiation rate
Xiang Ji, Jeffrey L. Thorne
Interlocus gene conversion (IGC) homogenizes paralogs. Little is known regarding the mutation events that cause IGC and even less is known about the IGC mutations that experience f…
Relaxed random walks at scale
Alexander A. Fisher, Xiang Ji, Philippe Lemey +1
Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny a…
Gradients do grow on trees: a linear-time -dimensional gradient for statistical phylogenetics
Xiang Ji, Zhenyu Zhang, Andrew Holbrook +5
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target r…