Natalya S. Bogatyreva

This paper introduces a Gene Space framework to characterize genome organization by analyzing nucleotide token frequencies, enabling species-specific gene classification and evolutionary pathway constraints.

This study introduces two new methods to predict protein expression levels from gene sequences, achieving high correlation with experimental data in E. coli.

The paper investigates the optimal number of Psi-BLAST iterations to maintain query sequence relevance in homolog detection, finding that query sequences are less frequently retained after 2 iterations in the 2021 nr database.

The paper experimentally assays a fitness landscape on a macroevolutionary scale by analyzing the effects of amino acid substitutions in yeast His3 orthologs.