Exact and efficient phylodynamic simulation from arbitrarily large populations

no code implementations • 27 Feb 2024 • Michael Celentano, William S. DeWitt, Sebastian Prillo, Yun S. Song

Consequently, the computational cost is determined not by the size of the final simulated tree, but by the size of the population tree in which it is embedded.

Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph

1 code implementation • 11 Oct 2023 • Will Dumm, Mary Barker, William Howard-Snyder, William S. DeWitt, Frederick A. Matsen IV

In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees.

Uncertainty Quantification

Mean-field interacting multi-type birth-death processes with a view to applications in phylodynamics

1 code implementation • 12 Jul 2023 • William S. DeWitt, Steven N. Evans, Ella Hiesmayr, Sebastian Hummel

Here, we introduce a multi-type birth-death process in mean-field interaction with an ensemble of replicas of the focal process.

Probability Populations and Evolution

Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity

1 code implementation • 14 Jul 2020 • Zachary Montague, Huibin Lv, Jakub Otwinowski, William S. DeWitt, Giulio Isacchini, Garrick K. Yip, Wilson W. Ng, Owen Tak-Yin Tsang, Meng Yuan, Hejun Liu, Ian A. Wilson, J. S. Malik Peiris, Nicholas C. Wu, Armita Nourmohammad, Chris Ka Pun Mok

Using single-cell sequencing, we verified reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes.