PhD Theses


Prof. Mjolsness has supervised the following PhD theses (except his own at the end):


  • (2012) David Orendorff, “Exact and Hierarchical Reaction Leaping: Asymptotic Improvements to the
    Stochastic Simulation Algorithm”. PhD thesis, UC Irvine, June 2012.
    [ Thesis web site. Links to software: ERleap, hierleap.]
  • (2012)  Behnam Compani-Tabrizi, “Schematic Representation and Database Population Strategies for
    Sigmoid, a Biochemical Network Modeling System”. PhD thesis, UC Irvine, May 2012. [Thesis web site.]
  • (2012) Gary Todd Johnson, “Dependency Diagrams and Graph-Constrained Correlation Dynamics:
    New Systems for Probabilistic Graphical Modeling”, UC Irvine, March 2012. 
    [Thesis web site . Links to thesis and to software: dependency diagrams and graph-constrained correlation dynamics.]
  • (2009) Guy Yosiphon, Stochastic Parameterized Grammars: Formalization, Inference, and Modeling Applications ,
    June 2009. [ Guy Yosiphon Thesis web site ]
  • (2008)  Li Zhang, Dynamic Biological Signal Pathway Modeling and Parameter Estimation through Optimization ,
    June 2008.
  • (2005)  Tarek Najdi, Biological Analysis and Mathematical Modeling of Glucose Metabolism and the
    Aspartate and Pyruvate Family Amino Acid Biosyntheses in Escherichia coli K12 ,
    jointly supervised with Prof. Wesley Hatfield, UC Irvine, March 2008.
  • (2005)  Christopher Hart, Inferring genetic regulatory network structure: Integrative analysis of genome-scale data ,
    jointly supervised with Prof. Barbara Wold, California Institute of Technology, March 2005.
  • (1997)  Dimitris Tsioutsias, Multiscale attention as a globally convergent framework for
    large-scale nonlinear optimization, Yale University, May 1997.
  • (1997)  Georgios Marnellos, Gene network models applied development and evolution, Yale University, May 1997.
  • (1996)  Steven Gold, Matching and learning structural and spatial representations with neural networks,
    Yale University, May 1996 .
  • (1996)  Chien-Ping Lu, Online pose estimation and model matching, Yale University, May 1996.
  • (1985)  Eric Mjolsness, Neural Networks, Pattern Recognition, and Fingerprint Hallucination.
    Thesis advisor: John J. Hopfield, September 1985. [Mjolsness Thesis]