Title: Tutorial — Totally Asymmetric Simple Exclusion Process models for single-mRNA Translation
Lecturer: Will Raymond
Lecturer Website: https://www.engr.colostate.edu/~munsky/
Lecturer Email: firstname.lastname@example.org
Examine simple TASEP processes.
Produce a flow density diagram and describe each canonical flow regime.
- See how TASEP process naturally extends to mRNA translation (and other biological processes).
- Test out the rSNAPsim package and examine some of its TASEP trajectories.
- Learn how to read Kymographs.
Will Raymond graduated in May 2017 from Colorado State University with a Bachelors in Biomedical Engineering and a Bachelors in Chemical and Biological Engineering.
Will has been a PhD student in Dr. Munsky’s lab since 2019 working on a myriad of projects. He is currently the lead developer on the rSNAPsim, an open source Python TASEP mRNA simulation package. In addition to that, he also works on implementing machine learning for nascent chain tracking fluorescent spot identification. Additionally, a recent area of focus has been modeling tRNA abundances and their effect on translation dynamics.
His primary area of interest is the intersection of machine learning, bioinformatics, and RNA biology. He is most excited about novel ncRNA discovery and advancements in RNA structural identification and disease classification.
Title: Totally Asymmetric Simple Exclusion Process models for single-mRNA Translation
Abstract: In this tutorial we will work through the TASEP notebook and provide hands on instruction to the students. We will start with a very simple canonical tasep and work through adding different features and processes, concluding with simulating mRNA translation with the rSNAPsim.
Suggested Reading or Key Publications:
- Zia, R. K. P., J. J. Dong, and B. Schmittmann. “Modeling translation in protein synthesis with TASEP: A tutorial and recent developments.” Journal of Statistical Physics 144.2 (2011): 405-428. https://link.springer.com/article/10.1007/s10955-011-0183-1#citeas (A good in-depth paper on applications of the TASEP specifically for protein synthesis.)
- Aguilera, Luis U., et al. “Computational design and interpretation of single-RNA translation experiments.” PLoS computational biology 15.10 (2019): e1007425, https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007425&rev=2 (A specific formulation of TASEP models for Nascent Chain Tracking experiments.)
- Koch et al, Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells. https://www.nature.com/articles/s41594-020-0504-7/ (An example of TASEP models being used to model Internal Ribosome Entry Sites using single mRNA nascent chain tracking experiments.)
- Lyon et al, Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting. https://www.cell.com/molecular-cell/pdfExtended/S1097-2765(19)30355-7 (An example of TASEP models being used to model viral frameshift dynamics using single mRNA nascent chain tracking experiments.)
Links to Relevant Software:
- Question 1
- Question 2