Ryan M. Sheridan

AI discovery of sequence rules for RNA polymerase II pausing revises the pause-release model of gene activation

The paper uses AI to discover sequence rules for RNA polymerase II pausing, challenging the pause-release model of gene activation by showing pausing is not required for certain activation responses.

Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint

The paper identifies a direct interaction between Integrator and NELF that regulates transcriptional pausing and premature termination.

A specific and portable gene expression program underlies antigen archiving by lymphatic endothelial cells

The paper identifies a unique transcriptional program in lymphatic endothelial cells that predicts antigen archiving capacity and validates it across datasets and in vivo.

The Unkempt RNA binding protein reveals a local translation program in centriole overduplication

The paper identifies Unkempt as a key RNA-binding protein promoting local translation at centrosomes during Plk4-induced centriole overduplication.

PP1 PNUTS binds the restrictor and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination

The paper identifies PP1 phosphatase activity in the PPWZ complex as essential for antisense transcription termination by dephosphorylating RNA pol II CTD Ser5.

scraps: an end-to-end pipeline for measuring alternative polyadenylation at high resolution using single-cell RNA-seq

The paper introduces scraps, a pipeline for high-resolution APA detection in scRNA-seq, showing it outperforms existing methods and enables assessment of internal priming events.

Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia

The paper uses long-read sequencing to analyze poly(A) signals in Giardia lamblia, revealing a unique AGURAA signal and alternative polyadenylation events.

clustifyr: An R package for automated single-cell RNA sequencing cluster classification

clustifyr assigns cell types to scRNA-seq clusters using diverse reference data and provides tools for exploratory analysis.