Independent Study

  • Boolean Modeling projects.  Building on each other’s IS projects, a subset of my students  model life, death, damage, epithelial to mesenchymal transition, 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.
    • Bioinformaticsprojects: identification of transcriptional switches from single-cell time series data during development, mapping the functional impact of Phytophthora sojae effector proteins (with W. Morgan, Wooster)

2021

  • Hikmet Sherief (BCMB) – Modeling mechano-sensitive differentiation and reprogramming of embryonic stem cells
  • Marlayna Harris (BCMB) – Modeling the relationship between epithelial to mesenchymal transition and cellular senescence 
  • Stuart Ball (BCMB) – Quantifying epithelial tissue fitness with a two-scale agent-based / Boolean model 
  • Brieanna Jarell & Alyssa Ramirez (BCMB ; joint project co-advised by Stephanie Strand) – Experimental and computational study of the flocking phenotype of yeast and its parallels with EMT
  • Paige Sogandares (Biology) – Meta-Analysis of Antibiotic Resistance of Helicobacter pylori in Developing Countries (co-advised by the University of Arkansas for Medical Sciences)

2020

  • Bao Nguyen (Neuro-BIO) – Modeling neuroinflammation by microglial activation, resolution of inflammation and return to a resting state 
  • Emma Sullivan (Biology) – The senescence associated secretory phenotype promotes epithelial mesenchymal transition in neighboring cells
  • Qaiser Zaidi (BCMB) – Computational prediction of developmental switches from single-cell time-series RNA-seq data
  • Vi Huynh (BCMB & Math) – Computational Analysis of PsAvh172 Data to Investigate the Targets of Phytophthora sojae in Soybean Host — A Hierarchical Clustering Evaluation of Yeast RNA-Seq Data

2019

  • Afton Widdershins (BCMB) – Investigating the Development and Behavior of Heterogeneous Tumors
  • Carolina Shams (Neuro-BCMB) – Defying the System: A Boolean Model of Neuronal Fate Decision and Aberrant Cell Cycle Re-entry in Alzheimer’s Disease
  • Eric Guberman (BCMB) – A Boolean Model of Contact Inhibition of Proliferation

Afton and Eric presenting their IS work at NetSci’19 in Burlington, Vermont

2018

  • 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

Left: Emma, Caroline and Cam presenting their IS work at Recomb’18 (Paris); Right: Elizabeth, Emma and Caroline after an amazing joint IS Symposium talk where they tied their very different IS projects into a single story.

2017

  • 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)

2016

  • 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)

Andrew presenting his IS work at Winter Q-Bio’16, Waikiki, Hawaii