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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 …
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 …
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 …
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 …
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 …
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 …
Exact distributions of threshold crossing times of proteins under post-transcriptional regulation by small RNAs
The timings of several cellular events like cell lysis, cell division, or pore formation in
endosomes are regulated by the time taken for the relevant proteins to cross a threshold in …
endosomes are regulated by the time taken for the relevant proteins to cross a threshold in …
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 …
Proteolytic crosstalk in multi-protease networks
CT Ogle, WH Mather - Physical biology, 2016 - iopscience.iop.org
Processive proteases, such as ClpXP in E. coli, are conserved enzyme assemblies that can
recognize and rapidly degrade proteins. These proteases are used for a number of …
recognize and rapidly degrade proteins. These proteases are used for a number of …