Igor M. Rouzine

Estimating fitness effects of mutations in the presence of genetic linkage

The paper develops a method to estimate mutation fitness effects under genetic linkage and applies it to E. coli genomic data to infer adaptive landscapes.

Epistasis detection and fitness valleys in viral evolution

This paper detects epistatic interactions in viral evolution using synthetic data and applies the method to SARS-CoV-2 sequences, finding evidence of fitness valleys connecting viral variants.

Long-range Hill-Robertson effect in adapting populations with recombination and standing variation

The paper shows that in populations with pre-existing variation, linkage effects persist even with recombination, leading to strong genetic background and clonal interference effects.

The evolutionary origin of the universal distribution of mutation fitness effect

The paper shows that the exponential distribution of beneficial mutation fitness effects emerges naturally in evolutionary processes and introduces a new method to measure selection coefficients from DNA sequences.

An evolution-based high-fidelity method of epistasis measurement: theory and application to influenza

The paper develops a method to measure epistasis from sequence data by filtering out false interactions, applying it to influenza virus sequences to infer an epistatic network between pre-pandemic and pandemic strains.

Epistasis detectably alters correlations between genomic sites in a narrow parameter window

The paper shows that epistasis can be detected in genomic data within a narrow parameter window, but is masked by linkage outside this range unless recombination is strong.