Stefka Tyanova

scRM is a single-cell foundation model trained on raw scRNA-seq reads, showing that raw data pretraining is feasible and cost-effective compared to count-based models.

This study identifies ARMC1 as a regulator of mitochondrial fatty acid oxidation through its interaction with MTCH2, showing that this interaction suppresses FAO during starvation.

The paper identifies a third mode of IRE1 activation called TRES, triggered by reduced protein influx into the ER, leading to a distinct gene expression program to rebalance ER load.

The paper develops a theoretical model of the ISR using time-resolved proteomics data to show molecular timers and a translational cliff limit ISR activation.

This study tracks the fate of monocyte-derived macrophages (MDMs) after traumatic brain injury (TBI) and finds they persist in the brain for up to 8 months, maintaining a distinct transcriptomic profile and phagocytic activity.

The paper generates a single-cell ISR atlas in a mouse model of persistent ISR activation, identifying cell-type-specific ISR programs and their roles in cognitive decline.