Independent Study

  • Boolean Modeling projects in mammalian cells.  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):
Modular mammalian cell regulatory network model.
Module-level view with students who contributed to each module during their IS.
  • Boolean Modeling in baker’s yeast. During the summer of 2o2o we embarked on a new project to model some of the conserved single-cell functions such as programmed cell death, or apoptosis, in yeast cells. This involved modules related to mitochondrial dynamics, MOMP, and DNA fragmentation, followed by a modular cell cycle model. Stay tuned for its growth as more students take up the challenge.
Modular yeast regulatory network model.
Module-level view with students who contributed to each module during their IS.
  • 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.
    • Bioinformatics projects: 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)

2024

  • Fareeda Abu-Juam (BCMB) – Probing The Relationship Between Partial Epithelial-to-Mesenchymal-Transition and Cell Shape in Epithelial Cells
  • Grant Greene (BCMB) – Boolean Modeling of the Molecular Dynamics Governing the Epithelial and Endothelial Hypoxic Response
  • Rue Ressler (BCMB) –
  • Nina Reddy (Neurobiology) – Boolean Modeling and Microglial Matters: Replicating Microglial Behavior in Inflammation and Testing Model Validity

2023

  • Caitlin Strassburg (BCMB / Mathematics) – Conservation of Dynamic Modularity in the Regulation of Cell Cycle and Apoptosis control in Saccharomyces cerevisiae
  • Katie Fleig (Neurobiology) – An Overworked Powerhouse: a Boolean Model of Mitochondrial Dysfunction Associated Senescence in the Context of Aging Microglia

2022

  • Andrea Brown (BCMB) – The Seven Deadly Pathways: A Boolean Model of Yeast Apoptosis in Response to Reactive Oxygen Species, DNA damage, and Salt
  • Emma Davidson (Neurobiology) – Time Flies: An analysis of Circadian impact upon cell cycle regulation using Boolean modeling and a developmental Drosophila model
  • Aelon Ketema Samuel (Neurobiology) – A Knock-out Experiment on a Neuronal Boolean Model
  • Ian Zonfa (BCMB) – Boolean Modeling of the Interactions Between Inflammation, Hypoxia, and the Epithelial-Mesenchymal Transition (EMT)
  • Thinh Huynh (BCMB) – Characterization of a Potential Novel Redox Partner in S. Cerevisiae Mitochondrial Disulfide Relay System and in silico Elucidating Its Essentiality
  • Arnav Bhatnagar (BCMB) – Boolean Model of Mesenchymal Cell’s Resistance to Chromosomal Senescence
The 2021-2022 Regan IS lab at Winter Q-Bio’22, enjoying the sunshine and getting ready to present! #ISoutofPandemic

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
  • Haoyu Jiang (Biology) – Investigation of Autophagy: Modeling the Cellular Responds to the Undernutrition Condition
  • Paige Sogandares (Biology) – Meta-Analysis of Antibiotic Resistance of Helicobacter pylori in Developing Countries (co-advised by the University of Arkansas for Medical Sciences)
The 2020-2021 Regan IS lab, meeting as we almost always did – on Teams. #ISinaPandemic

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