Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response

S Aitken, S Magi, AMN Alhendi, M Itoh… - PLoS computational …, 2015 - journals.plos.org
The immediate-early response mediates cell fate in response to a variety of extracellular
stimuli and is dysregulated in many cancers. However, the specificity of the response across …

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

A Vacca, M Itoh, H Kawaji, E Arner… - Open …, 2018 - royalsocietypublishing.org
The promoters of immediate early genes (IEGs) are rapidly activated in response to an
external stimulus. These genes, also known as primary response genes, have been …

Modeling gene expression cascades during cell state transitions

D Rosebrock, M Vingron, PF Arndt - Iscience, 2024 - cell.com
During cellular processes such as differentiation or response to external stimuli, cells exhibit
dynamic changes in their gene expression profiles. Single-cell RNA sequencing (scRNA …

Open Library of Bioscience

C Trapnell, D Cacchiarelli, J Grimsby, P Pokharel, S Li… - dynamics, 2014 - ngdc.cncb.ac.cn
Defining the transcriptional dynamics of a temporal process such as cell differentiation is
challenging owing to the high variability in gene expression between individual cells. Time …

Characterizing the temporal dynamics of gene expression in single cells with sci-fate

J Cao, W Zhou, F Steemers, C Trapnell, J Shendure - bioRxiv, 2019 - biorxiv.org
Gene expression programs are dynamic, eg the cell cycle, response to stimuli, normal
differentiation and development, etc. However, nearly all techniques for profiling gene …

Computational challenges, tools, and resources for analyzing co‐and post‐transcriptional events in high throughput

E Bahrami‐Samani, DT Vo… - Wiley …, 2015 - Wiley Online Library
Co‐and post‐transcriptional regulation of gene expression is complex and multifaceted,
spanning the complete RNA lifecycle from genesis to decay. High‐throughput profiling of the …

chronODE: A framework to integrate time-series multi-omics data based on ordinary differential equations combined with machine learning

B Borsari, M Frank, ES Wattenberg, K Xu, SX Liu, X Yu… - bioRxiv, 2023 - biorxiv.org
Most functional genomic studies are conducted in steady-state conditions, therefore
providing a description of molecular processes at a particular moment of cell differentiation …

Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data

Y Wu, L Xue, W Huang, M Deng… - PLOS Computational …, 2022 - journals.plos.org
Activities of transcription factors (TFs) are temporally modulated to regulate dynamic cellular
processes, including development, homeostasis, and disease. Recent developments of …

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data

C wa Maina, A Honkela, F Matarese… - PLoS computational …, 2014 - journals.plos.org
Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression.
The dynamics of pol-II moving along the transcribed region influence the rate and timing of …

Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism

JW Wragg, PL White, Y Hadzhiev… - Nature Structural & …, 2023 - nature.com
Global changes in transcriptional regulation and RNA metabolism are crucial features of
cancer development. However, little is known about the role of the core promoter in defining …