Angela H. DePace

This study uses biophysical models to show that transcription factors can act as activators, repressors, or both, with their effects influenced by binding affinity and regulatory context.

The paper shows that Hill functions are the universal limit for sharpness of input-output responses in thermodynamic equilibrium models.

The paper integrates modeling and synthetic biology to show that transcriptional synergy depends on both kinetic regulation of the transcription cycle and TF binding.

The paper defines the kinetic roles of three transcription factors in the Drosophila embryo by analyzing their effects on transcriptional output through live imaging.

The paper shows that a mutation in a minimal enhancer of Drosophila eve stripe 2 is buffered by flanking sequences in extended enhancer constructs, but not in the endogenous context.

The paper investigates the HbP2 enhancer in Drosophila, showing that cooperative binding of Bcd is insufficient to explain its sharp expression pattern, and identifies other factors like pioneer factors and histone modifiers as key contributors.

The paper compares anterior-posterior patterning gene expression across five Drosophila species to identify evolutionary changes in developmental programs.

The paper quantifies how shadow enhancers and their duplications combine transcriptional output in Drosophila embryos, showing variation in their computational behavior across expression patterns.

The paper shows that Caudal counter-represses Hunchback to enable even-skipped stripe 2 expression in Drosophila embryos, challenging the traditional view of Hunchback as a direct activator.

This study develops a quantitative framework to explore how transcription factors regulate gene expression through different kinetic steps of the transcription cycle, showing that combinatorial control can generate diverse computational outcomes without requiring co-localization.

This study shows that rearranging enhancers in the even-skipped locus of Drosophila embryos affects gene expression levels but not their position.