- 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)
- Publications with IS students:
- Eric Guberman, Hikmet Sherief, E. Ravasz Regan, Boolean model of anchorage dependence and contact inhibition points to coordinated inhibition but semi-independent induction of proliferation and migration, Computational and Structural Biotechnology Journal, 2020 (in press).
- Herbert Sizek, Andew Hamel, D. Deritei, S. Campbell, E. Ravasz Regan, Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K. PLoS Computational Biology 15(3): e1006402, 2019.
- Andrea Wade, CH Lin, C Kurkul, E Ravasz Regan, RM Johnson RM, Combined toxicity of insecticides and fungicides applied to California almond orchards to honey bee larvae and adults. Insects, 10(1), 20, 2019.
- 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)
- Bao Nguyen (Neuro-BIO) – Modeling neuroinflammation by microglial activation, resolution of inflammation and return to a resting state
- VIDEO summary for non-experts (in Vietnamese with subtitles & live action!)
- 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
- 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
- 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.
- 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)
Andrew presenting his IS work at Winter Q-Bio’16, Waikiki, Hawaii