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 Agency	Grant Number
NIH	5UM1HG012077-02
NIH	U19MH114830

Record Number:

CaltechTHESIS:06022023-194724728

Persistent URL:

https://resolver.caltech.edu/CaltechTHESIS:06022023-194724728

DOI:

10.7907/jn6n-x368

Related URLs:

URL	URL Type	Description
https://doi.org/10.1101/2023.01.13.523995	DOI	Preprint adapted for 10.3
https://doi.org/10.1101/2020.09.25.312868	DOI	Preprint adapted for 7.1
https://doi.org/10.1103/PhysRevE.102.022409	DOI	Publication adapted for 5.2
https://doi.org/10.1016/j.bpj.2022.02.004	DOI	Publication adapted for 10.2
https://doi.org/10.1101/2022.06.11.495771	DOI	Preprint adapted for 5.4, 7.1, 8.3, 8.4, and 9
https://doi.org/10.1016/j.bpr.2022.100097	DOI	Publication adapted for 5.4, 7.1, 8.2, 8.3, and 9.2
https://doi.org/10.1101/2023.01.17.524309	DOI	Preprint adapted for A.8
https://doi.org/10.1186/s13059-020-1945-3	DOI	Publication adapted for 11.1
https://doi.org/10.1101/2022.06.16.496448	DOI	Preprint adapted for 5.3
https://doi.org/10.1371/journal.pcbi.1010492	DOI	Publication adapted for 6 and B
https://doi.org/10.1038/s41467-022-34857-7	DOI	Publication adapted for 5.5 and 7.2
https://doi.org/10.1101/2022.10.17.512599	DOI	Preprint adapted for 4.3, 5.5, and 7.3
https://doi.org/10.1101/2023.05.17.541250	DOI	Preprint adapted for 2, 4, 6.2, 7.1, 8.1, A, and B.2

ORCID:

Author	ORCID
Gorin, Gennady	0000-0001-6097-2029

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

Thesis Files

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