Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules
Deciphering how the regulatory DNA sequence of a gene dictates its expression in
response to intra and extracellular cues is one of the leading challenges in modern …
response to intra and extracellular cues is one of the leading challenges in modern …
Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications
The genomic revolution has indubitably brought about a paradigm shift in the field of
molecular biology, wherein we can sequence, write and re-write genomes. In spite of …
molecular biology, wherein we can sequence, write and re-write genomes. In spite of …
A stochastic model of bacterial infection associated with neutrophils
J Xu, T Zhang, K Song - Applied Mathematics and Computation, 2020 - Elsevier
We study stochastic phenomena for a model of bacterial infection and neutrophils defense.
Sufficient conditions of stochastic permanence and extinction for the random model are …
Sufficient conditions of stochastic permanence and extinction for the random model are …
Transition Yet Energy Consuming for Tumor Growth Regulated by the Colored Microenvironment
L Chen, Y Wang, Q Li, H Wang - Complexity, 2023 - Wiley Online Library
Transition or metastasis is a main characteristic of tumor developmental processes.
However, the mechanism behind the transition and what costs involved are obscure when …
However, the mechanism behind the transition and what costs involved are obscure when …
First passage time in post-transcriptional regulation by multiple small RNAs
The post-transcriptional regulation of a protein by multiple small RNA molecules has been
formulated as a stochastic process. An approximate solution of the master equation shows …
formulated as a stochastic process. An approximate solution of the master equation shows …
Nascent RNA kinetics: Transient and steady state behavior of models of transcription
S Choubey - Physical Review E, 2018 - APS
Regulation of transcription is a vital process in cells, but mechanistic details of this regulation
still remain elusive. The dominant approach to unravel the dynamics of transcriptional …
still remain elusive. The dominant approach to unravel the dynamics of transcriptional …
Mathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for …
D Nyayanit, CJ Gadgil - Rna, 2015 - rnajournal.cshlp.org
MicroRNAs bind to and regulate the abundance and activity of target messenger RNA
through sequestration, enhanced degradation, and suppression of translation. Although …
through sequestration, enhanced degradation, and suppression of translation. Although …
Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis
MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding
and degrading target eukaryotic mRNAs. We use a quantitative model to study gene …
and degrading target eukaryotic mRNAs. We use a quantitative model to study gene …
Stochastic models of regulation of transcription in biological cells
V Fromion, P Robert, J Zaherddine - Journal of Mathematical Biology, 2023 - Springer
In this paper we study an important global regulation mechanism of transcription of
biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S …
biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S …
Distribution of initiation times reveals mechanisms of transcriptional regulation in single cells
Transcription is the dominant point of control of gene expression. Biochemical studies have
revealed key molecular components of transcription and their interactions, but the dynamics …
revealed key molecular components of transcription and their interactions, but the dynamics …