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 …
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
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 …
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 …
dynamic changes in their gene expression profiles. Single-cell RNA sequencing (scRNA …
Open Library of Bioscience
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 …
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
Gene expression programs are dynamic, eg the cell cycle, response to stimuli, normal
differentiation and development, etc. However, nearly all techniques for profiling gene …
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 …
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
Most functional genomic studies are conducted in steady-state conditions, therefore
providing a description of molecular processes at a particular moment of cell differentiation …
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 …
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 …
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 …
cancer development. However, little is known about the role of the core promoter in defining …