Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules

S Choubey, J Kondev, A Sanchez - PLoS computational biology, 2015 - journals.plos.org
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 …

Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications

MZ Ali, S Choubey - Physical Biology, 2019 - iopscience.iop.org
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 …

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 …

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 …

First passage time in post-transcriptional regulation by multiple small RNAs

K Biswas, A Ghosh - The European Physical Journal E, 2021 - Springer
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 …

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 …

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 …

Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis

J Noorbakhsh, AH Lang, P Mehta - PLoS One, 2013 - journals.plos.org
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 …

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 …

Distribution of initiation times reveals mechanisms of transcriptional regulation in single cells

S Choubey, J Kondev, A Sanchez - Biophysical journal, 2018 - cell.com
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 …