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Article
Open AccessEvolutionary shift detection with ensemble variable selection
Abrupt environmental changes can lead to evolutionary shifts in trait evolution. Identifying these shifts is an important step in understanding the evolutionary history of phenotypes. The detection performance...
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Article
Open AccessApplication of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes
The vast majority of microbiome research so far has focused on the structure of the microbiome at a single time-point. There have been several studies that measure the microbiome from a particular environment ...
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Article
Open AccessDiscrepant gut microbiota markers for the classification of obesity-related metabolic abnormalities
The gut microbiota (GM) is related to obesity and other metabolic diseases. To detect GM markers for obesity in patients with different metabolic abnormalities and investigate their relationships with clinical...
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Article
Open AccessTesting adequacy for DNA substitution models
Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum like...
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Article
Open AccessImproved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates
An excess of nonsynonymous substitutions, over neutrality, is considered evidence of positive Darwinian selection. Inference for proteins often relies on estimation of the nonsynonymous to synonymous ratio (ω = d
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Article
Open AccessLearning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization
Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of...
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Article
Coxeter groups, Coxeter monoids and the Bruhat order
Associated with any Coxeter group is a Coxeter monoid, which has the same elements, and the same identity, but a different multiplication. (Some authors call these Coxeter monoids 0-Hecke monoids, because of t...
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Article
Graphical algebras — a new approach to congruence lattices
In 1970, H. Werner considered the question of which sublattices of partition lattices are congruence lattices for an algebra on the underlying set of the partition lattices. He showed that a complete sublattic...
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Article
The General Theory of Diads
A diad is a generalisation of a monad and a comonad. The idea is that we ignore the unit or counit, and consider only the natural transformations between T and T 2. It turns out that almos...
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Article
Diads and their Application to Topoi
It is well known that the category of coalgebras for a finite-limit preserving comonad on a topos is again a topos, and the category of algebras for a finite-limit preserving monad is a topos if the monad is i...
