A Caltech Library Service

Stochastic Foundations for Single-Cell RNA Sequencing


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


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)
Funding AgencyGrant Number
Record Number:CaltechTHESIS:06022023-194724728
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for 10.3 adapted for 7.1 adapted for 5.2 adapted for 10.2 adapted for 5.4, 7.1, 8.3, 8.4, and 9 adapted for 5.4, 7.1, 8.2, 8.3, and 9.2 adapted for A.8 adapted for 11.1 adapted for 5.3 adapted for 6 and B adapted for 5.5 and 7.2 adapted for 4.3, 5.5, and 7.3 adapted for 2, 4, 6.2, 7.1, 8.1, A, and B.2
Gorin, Gennady0000-0001-6097-2029
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16062
Deposited By: Gennady Gorin
Deposited On:03 Jun 2023 01:58
Last Modified:08 Nov 2023 00:31

Thesis Files

[img] PDF - Final Version
Creative Commons Attribution Non-commercial No Derivatives.


Repository Staff Only: item control page