Iakov I. Davydov

This paper introduces a regression-based approach for gene-set enrichment analysis that identifies sparse, interpretable gene-sets for genes of interest.

The paper compares codon models that account for substitution rate variation and finds that ignoring rate variation leads to many false positives in positive selection detection.

The paper analyzes genome rearrangements and selection in Burkholderia species, finding non-random inversion patterns and potential phase variation mechanisms.