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03/08/2023
Many-core algorithms for high-dimensional gradients on phylogenetic trees
The rapid growth in genomic pathogen data spurs the need for efficient i...
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11/09/2022
TreeFlow: probabilistic programming and automatic differentiation for phylogenetics
Probabilistic programming frameworks are powerful tools for statistical ...
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09/16/2021
How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
Bayesian inference is a popular and widely-used approach to infer phylog...
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07/02/2020
Lack of evidence for a substantial rate of templated mutagenesis in B cell diversification
B cell receptor sequences diversify through mutations introduced by purp...
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06/27/2019
A Bayesian Phylogenetic Hidden Markov Model for B Cell Receptor Sequence Analysis
The human body is able to generate a diverse set of high affinity antibo...
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03/29/2019
Estimation of cell lineage trees by maximum-likelihood phylogenetics
CRISPR technology has enabled large-scale cell lineage tracing for compl...
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03/10/2019
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
Maximum likelihood estimators are used extensively to estimate unknown p...
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11/28/2018
19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
The marginal likelihood of a model is a key quantity for assessing the e...
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11/27/2018
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Bayesian Markov chain Monte Carlo explores tree space slowly, in part be...
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05/28/2018
Non-bifurcating phylogenetic tree inference via the adaptive LASSO
Phylogenetic tree inference using deep DNA sequencing is reshaping our u...
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05/20/2018
Generalizing Tree Probability Estimation via Bayesian Networks
Probability estimation is one of the fundamental tasks in statistics and...
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11/11/2017