239 citations · 399 across the 11 of their papers we have counts for
6 papers · 1 filter
Generalised Bayesian distance-based phylogenetics for the genomics era
Matthew J. Penn, Neil Scheidwasser, Mark P. Khurana +3
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conve…
Renewal equations for vector-borne diseases
Cathal Mills, Tarek Alrefae, William S. Hart +5
During infectious disease outbreaks, estimates of time-varying pathogen transmissibility, such as the instantaneous reproduction number R(t) or epidemic growth rate r(t), are used…
Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees
Matthew J Penn, Neil Scheidwasser, Joseph Penn +3
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogen…
Phylo2Vec: a vector representation for binary trees
Matthew J Penn, Neil Scheidwasser, Mark P Khurana +3
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes i…
Intrinsic Randomness in Epidemic Modelling Beyond Statistical Uncertainty
Matthew J. Penn, Daniel J. Laydon, Joseph Penn +7
Uncertainty can be classified as either aleatoric (intrinsic randomness) or epistemic (imperfect knowledge of parameters). The majority of frameworks assessing infectious disease r…
Inference of COVID-19 epidemiological distributions from Brazilian hospital data
Iwona Hawryluk, Thomas A. Mellan, Henrique H. Hoeltgebaum +8
Knowing COVID-19 epidemiological distributions, such as the time from patient admission to death, is directly relevant to effective primary and secondary care planning, and moreove…