Artificial neural networks have shown great potential when applied to breeding programs. In this study, we propose the use of artificial neural networks as a viable alternative to conventional prediction methods. We conduct a thorough evaluation of t...
A central challenge in human genomics is to understand the cellular, evolutionary, and clinical significance of genetic variants. Here, we introduce a unified population-genetic and machine-learning model, called inear llele-pecific election nferenc ...
Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited....
Quantifying the pathogenicity of protein variants in human disease-related genes would have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences. In principle, computational...
A neutral network connects all genotypes with equivalent phenotypes in a fitness landscape and plays an important role in the mutational robustness and evolvability of biomolecules. In contrast to earlier theoretical works, evidence of large neutral ...
The design of proteins with specific tasks is a major challenge in molecular biology with important diagnostic and therapeutic applications. High-throughput screening methods have been developed to systematically evaluate protein activity, but only a...
The relationship between genotype and fitness is fundamental to evolution, but quantitatively mapping genotypes to fitness has remained challenging. We propose the Phenotypic-Embedding theorem (P-E theorem) that bridges genotype-phenotype through an ...
MOTIVATION: Experimental characterization of fitness landscapes, which map genotypes onto fitness, is important for both evolutionary biology and protein engineering. It faces a fundamental obstacle in the astronomical number of genotypes whose fitne...
Evolution by natural selection occurs at its most basic through the change in frequencies of alleles; connecting those genomic targets to phenotypic selection is an important goal for evolutionary biology in the genomics era. The relative abundance o...
Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon ...