Dariya K. Sydykova

Theory of measurement for site-specific evolutionary rates in amino-acid sequences

The paper develops a theory for measuring site-specific evolutionary rates in amino-acid sequences using maximum likelihood under a mutation-selection model, showing that rates measured relative to a naive exchangeability matrix recover true expected rates.

The E. coli molecular phenotype under different growth conditions

This study presents a comprehensive transcriptomics and proteomics dataset of E. coli under 34 growth conditions, revealing differences between exponential and stationary phases and differential gene expression under specific stresses.

Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design

The paper evaluates how structural properties predict evolutionary sequence variation in viral proteins and finds that buriedness and packing density are better predictors than flexibility or design-based measures.