Joseph Azofeifa
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View article: Enhancer RNA profiling predicts transcription factor activity
Enhancer RNA profiling predicts transcription factor activity Open
Transcription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in coordination of gene expression programs. Active enhancers are often characterized by the presence of short, unstable transcripts t…
View article: Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers
Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers Open
Histone deacetylase inhibitors (HDACIs) are known to alter gene expression by both up- and down-regulation of protein-coding genes in normal and cancer cells. However, the exact regulatory mechanisms of action remain uncharacterized. Here …
View article: Stochastic Modeling of RNA Polymerase Predicts Transcription Factor Activity
Stochastic Modeling of RNA Polymerase Predicts Transcription Factor Activity Open
Seventy-six percent of disease associated variants occur in non-genic sites of open chromatin suggesting that the regulation of gene expression plays a crucial role in human health. Nucleosome- free with flanking chromatin modifications, t…
View article: A generative model for the behavior of RNA polymerase
A generative model for the behavior of RNA polymerase Open
Motivation Transcription by RNA polymerase is a highly dynamic process involving multiple distinct points of regulation. Nascent transcription assays are a relatively new set of high throughput techniques that measure the location of activ…
View article: An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq
An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq Open
We present a fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol that captures nascent transcripts from actively engaged polymerase, providing a …