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Dynamics and Correlated Noise in Gene Regulation


Dunlop, Mary Julia (2008) Dynamics and Correlated Noise in Gene Regulation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/AC8V-6S05.


Gene regulatory interactions are context dependent, active in some cell types or cellular states but not in others. In this thesis we present a method for determining when a regulatory link is active given temporal measurements of gene expression. Correlations in time-series data are used to determine how genes influence each other and their causal relationships. Natural stochastic noise is shown to aid in the process of network identification by perturbing the expression of genes; the speed and direction at which the noisy signal propagates shows how the network is connected. Cross correlation functions are used to reveal time-delayed correlations.

We develop a stochastic model of gene expression and show that by measuring correlations in cellular noise, it is possible to infer network activity and temporal properties of gene regulation. Using a linearized version of the model, we introduce a method for analytically deriving cross correlation functions for arbitrary networks. These results are validated experimentally using a synthetic gene circuit in E. coli bacteria. Single-cell time-lapse microscopy is used to measure noisy expression of multiple genes over time. Extending this work to natural systems, we study feed-forward loops and determine that certain classes of feed-forward loops are more robust to noise and parameter variations that others. Noise in two naturally occurring feed-forward loops involved in galactose utilization is measured experimentally and it is shown that neither is actively regulating its target in the conditions tested.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:biological control systems; cell-cell variability; gene regulatory networks; noise; synthetic biology
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Mechanical Engineering
Awards:Graduate Deans’ Award for Outstanding Community Service, 2008.
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Murray, Richard M.
Thesis Committee:
  • Murray, Richard M. (chair)
  • Winfree, Erik
  • Elowitz, Michael B.
  • Phillips, Robert B.
Defense Date:21 May 2008
Non-Caltech Author Email:mjdunlop (AT)
Record Number:CaltechETD:etd-05302008-141602
Persistent URL:
Dunlop, Mary Julia0000-0002-9261-8216
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:2320
Deposited By: Imported from ETD-db
Deposited On:02 Jun 2008
Last Modified:17 Jan 2020 00:14

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PDF (Full thesis) - Final Version
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PDF (01_intro_mjdunlop.pdf) - Final Version
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PDF (02_chapter2_mjdunlop.pdf) - Final Version
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PDF (03_chapter3_mjdunlop.pdf) - Final Version
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PDF (04_chapter4_mjdunlop.pdf) - Final Version
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PDF (05_chapter5_mjdunlop.pdf) - Final Version
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PDF (06_conclusion_mjdunlop.pdf) - Final Version
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