Independent Study

  • Boolean Modeling projects.  Building on each other’s IS projects, a subset of my students  model life, death, damage and other interesting behaviors of mammalian cells (dots mark the modules a student developed, extended or analyzed):

  • Other IS projects:
    • Epigenetics: modeling the dynamics of epigenetic marks at the Oct4 promoter
    • Viral communication: modeling the benefits of molecular communication between viruses as they influence the lysis-lysogeny switch of their neighbors
    • OARDC projects co-advised by faculty at the OARDC.


  • Caroline Obermeier (Biology) – Modeling the Effect of p16 on Two Types of Senescence
  • Elizabeth Obi (BCMB) – Modeling the Effects of p14 and p53 on Common Oncogenic Pathways
  • Emma Schroeter (Neuroscience) – A Boolean Model of Neuronal Death upon Cell Cycle Re-entry
  • Campbell Elliott (BCMB) – Using a Boolean Model to Identify Requirements for Successful Yamanaka Reprogramming
  • Brendan Kelley-Bukovac (Biology) – Should You Lyse your Neighbors’ Houses? This Model Says ‘No’: An In Silico Examination of the Interactions between Bacterial and Viral Populations in the Presence of the Arbitrium System for Viral Communications


  • Micah Auerbach (BCMB) – A Boolean Model of Early Stem Cell Fate Decisions
  • Laura Cremer (Biology) – Modeling the Dynamics of Epigenetic Changes on Key Pluripotency Genes in Response to Reprogramming
  • Herbert Sizek (BCMB) – Modeling the Commitment to Senescence Through Mitochondrial Fusion and Chromosomal Restructuring
  • Nathan Sundheimer (Neuroscience) – A Boolean Modeling Approach to Understanding Synergies Between Cell Phenotypes in Early Neurogenesis
  • Andrea Wade (BCMB) – Insecticide Fungicide Interaction and Synergistic Toxicity in Honey Bees (work @ OARDC, Reed Johnson’s Lab)


  • Andrew Hamel (BCMB) – A Dynamical Systems Approach to Understanding Synergies Between Thyroid Cancer Mutations
  • Heather Skinner (BCMB) – The Putative Regulatory Role of Hydrogen Cyanide in Ethylene Signaling and Biosynthesis in Arabidopsis seedlings and tomato fruit (work @ OARDC, Christopher Taylor’s Lab)