60 citations · 117 across the 7 of their papers we have counts for
8 papers
Recoverability of Ancestral Recombination Graph Topologies
Elizabeth Hayman, Anastasia Ignatieva, Jotun Hein
Recombination is a powerful evolutionary process that shapes the genetic diversity observed in the populations of many species. Reconstructing genealogies in the presence of recomb…
Combinatorics of polymer models of early metabolism
Oliver Weller-Davies, Mike Steel, Jotun Hein
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in…
KwARG: Parsimonious reconstruction of ancestral recombination graphs with recurrent mutation
Anastasia Ignatieva, Rune B. Lyngsø, Paul A. Jenkins +1
The reconstruction of possible histories given a sample of genetic data in the presence of recombination and recurrent mutation is a challenging problem, but can provide key insigh…
A characterisation of the reconstructed birth-death process through time rescaling
Anastasia Ignatieva, Jotun Hein, Paul A. Jenkins
The dynamics of a population exhibiting exponential growth can be modelled as a birth-death process, which naturally captures the stochastic variation in population size over time.…
Combinatorial results for network-based models of metabolic origins
Oliver Weller-Davies, Mike Steel, Jotun Hein
A key step in the origin of life is the emergence of a primitive metabolism. This requires the formation of a subset of chemical reactions that is both self-sustaining and collecti…
Toroidal diffusions and protein structure evolution
Eduardo García-Portugués, Michael Golden, Michael Sørensen +3
This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction…
A generative angular model of protein structure evolution
Michael Golden, Eduardo García-Portugués, Michael Sørensen +3
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliabl…
Approximate statistical alignment by iterative sampling of substitution matrices
Joseph L. Herman, Adrienn Szabó, Instván Miklós +1
We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorith…