79 citations · 164 across the 20 of their papers we have counts for
23 papers
Phylodynamic inference with the bounded coalescent: a point process perspective
Bingjing Tang, Shuangping Li, Julia A. Palacios
The coalescent is a central framework in population genetics for modelling the ancestral relationships among sampled individuals through a genealogy, represented as a rooted and ra…
Matrix representations and distance metrics for unlabeled ranked phylogenetic networks
Jiayang Wang, Julia A. Palacios, Claudia Solís-Lemus
Phylogenetic networks are graphs inferred from molecular sequence data that represent ancestral histories shaped by reticulate processes such as recombination, hybridization, and h…
Coalescent Inference for Epidemics with Latent Periods
Isaac H. Goldstein, Julia A. Palacios
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent para…
Generalizing matrix representations to fully heterochronous ranked tree shapes
Chris Jennings-Shaffer, Ziyue, Chen +2
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible wit…
The space of multifurcating ranked tree shapes: enumeration, lattice structure, and Markov chains
Julie Zhang, Noah A. Rosenberg, Julia A. Palacios
Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not…
Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling
Catalina M. Medina, Julia A. Palacios, Volodymyr M. Minin
The COVID-19 pandemic demonstrated that fast and accurate analysis of continually collected infectious disease surveillance data is crucial for situational awareness and policy mak…
Multiple merger coalescent inference of effective population size
Julie Zhang, Julia A. Palacios
Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard…
Exact Bayesian Gaussian Cox Processes Using Random Integral
Bingjing Tang, Julia Palacios
A Gaussian Cox process is a popular model for point process data, in which the intensity function is a transformation of a Gaussian process. Posterior inference of this intensity f…
CRP-Tree: A phylogenetic association test for binary traits
Julie Zhang, Gabriel A. Preising, Molly Schumer +1
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tr…
Statistical Challenges in Tracking the Evolution of SARS-CoV-2
Lorenzo Cappello, Jaehee Kim, Sifan Liu +1
Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular sequences i…
Enumeration of binary trees compatible with a perfect phylogeny
Julia A. Palacios, Anand Bhaskar, Filippo Disanto +1
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a geneal…
Scalable Bayesian change point detection with spike and slab priors
Lorenzo Cappello, Oscar Hernan Madrid Padilla, Julia A. Palacios
We study the use of spike and slab priors for consistent estimation of the number of change points and their locations. Leveraging recent results in the variable selection literatu…
Statistical summaries of unlabelled evolutionary trees and ranked hierarchical clustering trees
Samyak Rajanala, Julia A. Palacios
Rooted and ranked binary trees are mathematical objects of great importance used to model hierarchical data and evolutionary relationships with applications in many fields includin…
An adjacent-swap Markov chain on coalescent trees
Mackenzie Simper, Julia A. Palacios
The standard coalescent is widely used in evolutionary biology and population genetics to model the ancestral history of a sample of molecular sequences as a rooted and ranked bina…
Adaptive preferential sampling in phylodynamics
Lorenzo Cappello, Julia A. Palacios
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case coun…
The Tajima heterochronous n-coalescent: inference from heterochronously sampled molecular data
Lorenzo Cappello, Amandine Veber, Julia A. Palacios
The observed sequence variation at a locus informs about the evolutionary history of the sample and past population size dynamics. The Kingman coalescent is used in a generative mo…
Sequential importance sampling for multi-resolution Kingman-Tajima coalescent counting
Lorenzo Cappello, Julia A. Palacios
Statistical inference of evolutionary parameters from molecular sequence data relies on coalescent models to account for the shared genealogical ancestry of the samples. However, i…
Exact Limits of Inference in Coalescent Models
James E. Johndrow, Julia A. Palacios
Recovery of population size history from molecular sequence data is an important problem in population genetics. Inference commonly relies on a coalescent model linking the populat…
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…
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…
Integrated Nested Laplace Approximation for Bayesian Nonparametric Phylodynamics
Julia A. Palacios, Vladimir N. Minin
The goal of phylodynamics, an area on the intersection of phylogenetics and population genetics, is to reconstruct population size dynamics from genetic data. Recently, a series of…
Gaussian Process-Based Bayesian Nonparametric Inference of Population Trajectories from Gene Genealogies
Julia A. Palacios, Vladimir N. Minin
Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are intere…