Despite gene expression programs being notoriously complex, RNA abundance is usually
assumed as a proxy for transcriptional activity. Recently developed approaches, able to …

Global quantification of total RNA is used to investigate steady state levels of gene
expression. However, being able to differentiate pre-existing RNA (that has been …

Metabolic labeling of newly transcribed RNAs coupled with RNA-seq is being increasingly
used for genome-wide analysis of RNA dynamics. Methods including standard biochemical …

Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of
gene expression. Nucleotide conversion approaches greatly facilitate the generation of data …

Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in
cellular RNA levels, but provides limited information about the kinetic mechanisms …

The quantification of the kinetic rates of RNA synthesis, processing, and degradation are
largely based on the integrative analysis of total and nascent transcription, the latter being …

Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has
become the de facto standard approach to study alterations in RNA transcription, processing …

Computational experiments have been important since the 70s to find solutions to problems
using computers, and even more now with the advancement of technology, especially …

The abundance of RNA species and their response to perturbations are set by the kinetics
rates of RNA synthesis, processing, and degradation. However, the visualization …

In the context of transcriptional dynamics modeled by ordinary differential equations (ODEs),
the RNA level in a single cell is controlled by specific RNA kinetics parameters, which …