Alisa Yurovsky

Improving Differential Expression and Survival Analyses with Sample Specific Compartment Deconvolution.

This paper introduces SSCD, a method to improve differential expression and survival analyses by deconvolving tumor samples into their component tissues on a per-sample basis.

No Ramp Needed: Spandrels, Statistics, and a Slippery Slope

The paper re-examines the slow translation ramp at gene 5 ends in yeast, finding it is a spandrel rather than an adaptive feature, as slow translation correlates with poor gene expression.

Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria

The paper shows that synonymous mutations in mycobacteria can create new transcription start sites within genes, leading to smaller protein isoforms.

A Statistical Detector for Ribosomal Frameshifts and Dual Encodings based on Ribosome Profiling

The paper develops a statistical method to detect programmed ribosomal frameshifts using ribosome profiling data, identifying potential frameshifts in yeast and demonstrating high sensitivity.