Biology subjects

He, Y.-H.

Publications and source records attributed to He, Y.-H..

2 recordsLinked to original sources

bioRxiv2019

Dynamics of genetic code evolution: The emergence of universality

AO_SCPLOWBSTRACTC_SCPLOWWe study the dynamics of genetic code evolution. The algorithm of Vetsigian et al. [1] provides a solution that is both optimal and universal. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on achieving universality. We show that by allowing specific parameters to vary with time, the algorithm converges much faster to a universal solution. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions in order to understand the origin of universality and find that there is a direct link to mutation rate.

genomics↗

bioRxiv2019

Machine-learning a virus assembly fitness landscape

Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via computationally expensive stochastic assembly models, giving a fitness landscape in terms of the assembly efficiency. Using latest machine-learning techniques by establishing a neural network, we show that the intensive computation can be short-circuited in a matter of minutes to astounding accuracy.

bioinformatics↗