Miles A. Pufall

Biomarkers indicate altered outer retinal fluid homeostasis in the absence of Kv2.1/Kv8.2 channels.

The paper investigates the role of Kv2.1/Kv8.2 channels in outer retinal fluid homeostasis using mouse models and finds altered fluid dynamics and upregulated osmosensitive genes in their absence.

De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding

The paper introduces Affinity Distillation (AD), a method to extract thermodynamic affinities from deep learning models of in vivo TF binding, showing it outperforms motif-based methods in predicting sequence variation impacts.

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

The paper uses GRO-seq to show glucocorticoids rapidly repress transcription without local GR occupancy and induce anti-inflammatory effects through GR-NF-kB cooperation.

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

This study identifies differences in DNA-binding preferences between androgen and glucocorticoid receptors using SELEX-seq and SelexGLM, revealing AR's greater sequence sensitivity and enthalpy-driven binding.

The effect of sequence mismatches on binding affinity and endonuclease activity are decoupled throughout the Cas9 binding site

The paper investigates how sequence mismatches affect Cas9 binding affinity and endonuclease activity, finding that these effects are sometimes decoupled and depend on the PAM region.