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Analytical solutions of the chemical master equation with bursty production and isomerization reactions

Gorin, Gennady and Pachter, Lior (2021) Analytical solutions of the chemical master equation with bursty production and isomerization reactions. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210325-075042340

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Abstract

Splicing cascades that alter gene products post-transcriptionally also affect expression dynamics. We study a class of processes and associated distributions which emerge from a bursty promoter coupled to a path graph of downstream mRNA splicing, and more generally the behavior of finite-activity jump distributions coupled to rooted directed acyclic graphs of splicing. These solutions provide full time-dependent joint distributions for an arbitrary number of species, offering qualitative and quantitative insights about how splicing can regulate expression dynamics.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.03.24.436847DOIDiscussion Paper
https://github.com/pachterlab/GP_2021_2Related ItemCode
https://ipyparallel.readthedocs.io/en/latest/dag_dependencies.htmlRelated ItemIPython Parallel reference documentation
ORCID:
AuthorORCID
Gorin, Gennady0000-0001-6097-2029
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. This version posted March 24, 2021. The DNA illustration used in Figures 1 and 4, modified from [23], is a derivative of the DNA Twemoji by Twitter, Inc., used under CC-BY 4.0. The directed acyclic graph generation code was adapted from the IPython Parallel reference documentation: https://ipyparallel.readthedocs. io/en/latest/dag_dependencies.html. The yellow and gray colors used in Figures 1, 3, and 4 are the Pantone Colors of the Year 2021, PANTONE 17-5104 Ultimate Gray and PANTONE 13-0647 Illuminating. G.G. and L.P. were partially funded by NIH U19MH114830. Code availability: Python code that can be used to reproduce Figure 5, including the graph generation, simulation, and plotting routines, is available at https://github.com/pachterlab/GP_2021_2.
Funders:
Funding AgencyGrant Number
NIHU19MH114830
Record Number:CaltechAUTHORS:20210325-075042340
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210325-075042340
Official Citation:Analytical solutions of the chemical master equation with bursty production and isomerization reactions. Gennady Gorin, Lior Pachter. bioRxiv 2021.03.24.436847; doi: https://doi.org/10.1101/2021.03.24.436847
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108549
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:25 Mar 2021 23:07
Last Modified:19 Apr 2021 22:04

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