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Bayesian inference of polymerase dynamics over the exclusion process
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Cavallaro, Massimo, Wang, Yuexuan, Hebenstreit, Daniel and Dutta, Ritabrata (2023) Bayesian inference of polymerase dynamics over the exclusion process. Royal Society Open Science , 10 (8). 221469. doi:10.1098/rsos.221469 ISSN 2054-5703.
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Official URL: https://doi.org/10.1098/rsos.221469
Abstract
Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non- equilibrium statistical physics, i.e., the asymmetric exclusion processes in the hydrodynamic limit, assuming a Gaussian process prior for the polymerase progression rate as a latent variable. Our framework allows us to infer the speed of polymerases during transcription given their spatial dis- tribution, whilst avoiding the explicit inversion of the system’s dynamics. The results, which show processing rates strongly varying with genomic position and minor role of traffic-like congestion, may have strong implications for the understanding of gene expression.
Item Type: | Journal Article | ||||||||||||||||||||||||||||||||||||||||||
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Subjects: | Q Science > QA Mathematics Q Science > QH Natural history > QH426 Genetics |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Science > Mathematics Faculty of Science, Engineering and Medicine > Science > Statistics |
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Library of Congress Subject Headings (LCSH): | Genetic transcription -- Mathematical models, Gaussian processes, Bayesian statistical decision theory, Mathematical statistics, Enzymatic analysis, Gene expression -- Statistical methods | ||||||||||||||||||||||||||||||||||||||||||
Journal or Publication Title: | Royal Society Open Science | ||||||||||||||||||||||||||||||||||||||||||
Publisher: | The Royal Society Publishing | ||||||||||||||||||||||||||||||||||||||||||
ISSN: | 2054-5703 | ||||||||||||||||||||||||||||||||||||||||||
Official Date: | 2 August 2023 | ||||||||||||||||||||||||||||||||||||||||||
Dates: |
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Volume: | 10 | ||||||||||||||||||||||||||||||||||||||||||
Number: | 8 | ||||||||||||||||||||||||||||||||||||||||||
Article Number: | 221469 | ||||||||||||||||||||||||||||||||||||||||||
DOI: | 10.1098/rsos.221469 | ||||||||||||||||||||||||||||||||||||||||||
Status: | Peer Reviewed | ||||||||||||||||||||||||||||||||||||||||||
Publication Status: | Published | ||||||||||||||||||||||||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||||||||||||||||||||||||||||||||
Date of first compliant deposit: | 12 July 2023 | ||||||||||||||||||||||||||||||||||||||||||
Date of first compliant Open Access: | 12 July 2023 | ||||||||||||||||||||||||||||||||||||||||||
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