5 papers
Fitness Inference in Presence of Migrations between Coupled Evolving Populations
Yu-Han Huang, Bastien Dumont, Hong-Li Zeng +2
The phase of Quasi-Linkage Equilibrium (QLE) in evolutionary populations is analogous to the thermal equilibrium state in statistical mechanics, a concept pioneered by Kimura in 19…
Classification of SARS-CoV-2 Variants through The Epistatical Circos Plots with Convolutional Neural Networks
Bo Jing, Kai-Rui Zhang, Hong-Li Zeng +1
The COVID-19 pandemic has profoundly affected global health, driven by the remarkable transmissibility and mutational adaptability of the SARS-CoV-2 virus. Although five variants o…
Fitness inference tested by in silico population genetics
Hong-Li Zeng, Yu-Han Huang, John Barton +1
We consider populations evolving according to natural selection, mutation, and recombination, and assume that the genomes of all or a representative selection of individuals are kn…
Two fitness inference schemes compared using allele frequencies from 1,068,391 sequences sampled in the UK during the COVID-19 pandemic
Hong-Li Zeng, Cheng-Long Yang, Bo Jing +2
Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV…
Mutation frequency time series reveal complex mixtures of clones in the world-wide SARS-CoV-2 viral population
Hong-Li Zeng, Yue Liu, Vito Dichio +3
We compute the allele frequencies of the alpha (B.1.1.7), beta (B.1.351) and delta (B.167.2) variants of SARS-CoV-2 from almost two million genome sequences on the GISAID repositor…