Long non-coding RNAs (lncRNAs) are over 200 nucleotides in length and are transcribed
from the mammalian genome in a tissue-specific and developmentally regulated pattern …

Background Enhancers are distal cis-regulatory elements that control gene expression.
Despite an increasing appreciation of the importance of enhancers in cellular function and …

Affinity and dose of T cell receptor (TCR) interaction with antigens govern the magnitude of
CD4+ T cell responses, but questions remain regarding the quantitative translation of TCR …

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 …

Background Global run-on coupled with deep sequencing (GRO-seq) provides extensive
information on the location and function of coding and non-coding transcripts, including …

Nascent RNA profiling is growing in popularity; however, there is no standard analysis
pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a …

The roles of miRNAs as important post-transcriptional regulators in the circadian clock have
been suggested in several studies. But the search for circadian miRNAs has led to disparate …

TF profiler is a method of inferring transcription factor regulatory activity, ie when a TF is
present and actively regulating transcription, directly directly from nascent sequencing …

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 …

Although nascent RNA profiling data are widely used in transcriptional regulation studies,
the development and standardization of data processing pipeline lags far behind RNA-seq …