Iakov I. Davydov

This study develops a transcriptome-based classifier to predict CD8+ T cell spatial infiltration patterns in the tumor microenvironment and shows its prognostic and predictive value across clinical trials.

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.