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Stochastic Foundations for Single-Cell RNA Sequencing

Citation

Gorin, Gennady (2023) Stochastic Foundations for Single-Cell RNA Sequencing. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/jn6n-x368. https://resolver.caltech.edu/CaltechTHESIS:06022023-194724728

Abstract

Single-cell RNA sequencing, which quantifies cell transcriptomes, has seen widespread adoption, accompanied by proliferation of analysis methods. However, there has been relatively little systematic investigation of its best practices and their underlying assumptions, leading to challenges and discrepancies in interpretation. I present a set of generic, principled strategies for modeling the biological and technical components of sequencing experiments and use case studies to motivate their application to sequencing data.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Chemical master equations; Fokker-Planck equations; Stochastic differential equations; Stochastic processes; Markov chains; Single-cell RNA sequencing; Single-cell genomics; Single-cell transcriptomics; Transcriptomics; Genomics; Bioinformatics
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemical Engineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Pachter, Lior S.
Thesis Committee:
  • Shapiro, Mikhail G. (chair)
  • Wang, Zhen-Gang
  • Chong, Shasha
  • Ismagilov, Rustem F.
  • Pachter, Lior S.
Defense Date:19 May 2023
Non-Caltech Author Email:gennady.gorin (AT) gmail.com
Funders:
Funding AgencyGrant Number
NIH5UM1HG012077-02
NIHU19MH114830
Record Number:CaltechTHESIS:06022023-194724728
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:06022023-194724728
DOI:10.7907/jn6n-x368
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2023.01.13.523995DOIPreprint adapted for 10.3
https://doi.org/10.1101/2020.09.25.312868DOIPreprint adapted for 7.1
https://doi.org/10.1103/PhysRevE.102.022409DOIPublication adapted for 5.2
https://doi.org/10.1016/j.bpj.2022.02.004DOIPublication adapted for 10.2
https://doi.org/10.1101/2022.06.11.495771DOIPreprint adapted for 5.4, 7.1, 8.3, 8.4, and 9
https://doi.org/10.1016/j.bpr.2022.100097DOIPublication adapted for 5.4, 7.1, 8.2, 8.3, and 9.2
https://doi.org/10.1101/2023.01.17.524309DOIPreprint adapted for A.8
https://doi.org/10.1186/s13059-020-1945-3DOIPublication adapted for 11.1
https://doi.org/10.1101/2022.06.16.496448DOIPreprint adapted for 5.3
https://doi.org/10.1371/journal.pcbi.1010492DOIPublication adapted for 6 and B
https://doi.org/10.1038/s41467-022-34857-7DOIPublication adapted for 5.5 and 7.2
https://doi.org/10.1101/2022.10.17.512599DOIPreprint adapted for 4.3, 5.5, and 7.3
https://doi.org/10.1101/2023.05.17.541250DOIPreprint adapted for 2, 4, 6.2, 7.1, 8.1, A, and B.2
ORCID:
AuthorORCID
Gorin, Gennady0000-0001-6097-2029
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16062
Collection:CaltechTHESIS
Deposited By: Gennady Gorin
Deposited On:03 Jun 2023 01:58
Last Modified:08 Nov 2023 00:31

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