Computation of three-dimensional Brinkman flows using regularized methods. - Ricardo Cortez; Bree Cummins; Karin Leiderman; Douglas Varela (J. Comput. Phys., 2010)

A Spatial Model of Mosquito Host-Seeking Behavior. - Bree Cummins; Ricardo Cortez; Ivo M. Foppa; Justin Walbeck; James Mac Hyman (PLoS Comput. Biol., 2012)

On the Efficacy of State Space Reconstruction Methods in Determining Causality. - Bree Cummins; Tomás Gedeon; Kelly Spendlove (SIAM J. Appl. Dyn. Syst., 2015)

Combinatorial Representation of Parameter Space for Switching Networks. - Bree Cummins; Tomás Gedeon; Shaun Harker; Konstantin Mischaikow; Kafung Mok (SIAM J. Appl. Dyn. Syst., 2016)

Database of Dynamic Signatures Generated by Regulatory Networks (DSGRN). - Bree Cummins; Tomás Gedeon; Shaun Harker; Konstantin Mischaikow (CMSB, 2017)

Combinatorial Dynamics for Regulatory Networks. - Zane Huttinga; Bree Cummins; Tomas Geadon (MLCSB, 2018)

Identifying robust hysteresis in networks. - Tomás Gedeon; Bree Cummins; Shaun Harker; Konstantin Mischaikow (PLoS Comput. Biol., 2018)

Model Rejection and Parameter Reduction via Time Series. - Bree Cummins; Tomás Gedeon; Shaun Harker; Konstantin Mischaikow (SIAM J. Appl. Dyn. Syst., 2018)

A poset metric from the directed maximum common edge subgraph. - Robert Nerem; Peter Crawford-Kahrl; Bree Cummins; Tomás Gedeon (CoRR, 2019)

Comparison of Combinatorial Signatures of Global Network Dynamics Generated by Two Classes of ODE Models. - Peter Crawford-Kahrl; Bree Cummins; Tomás Gedeon (SIAM J. Appl. Dyn. Syst., 2019)

Multistability in the epithelial-mesenchymal transition network. - Ying Xin; Bree Cummins; Tomás Gedeon (BMC Bioinform., 2020)

Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. - Francis C. Motta; Robert C. Moseley; Bree Cummins; Anastasia Deckard; Steven B. Haase (BMC Bioinform., 2022)

Extremal Event Graphs: A (Stable) Tool for Analyzing Noisy Time Series Data. - Robin Belton; Bree Cummins; Brittany Terese Fasy; Tomás Gedeon (CoRR, 2022)

Joint realizability of monotone Boolean functions. - Peter Crawford-Kahrl; Bree Cummins; Tomás Gedeon (Theor. Comput. Sci., 2022)

Extending Combinatorial Regulatory Network Modeling to Include Activity Control and Decay Modulation. - Bree Cummins; Marcio Gameiro; Tomás Gedeon; Shane Kepley; Konstantin Mischaikow; Lun Zhang (SIAM J. Appl. Dyn. Syst., 2022)

Experimental guidance for discovering genetic networks through hypothesis reduction on time series. - Breschine Cummins; Francis C. Motta; Robert C. Moseley; Anastasia Deckard; Sophia Campione; Marcio Gameiro; Tomás Gedeon; Konstantin Mischaikow; Steven B. Haase (PLoS Comput. Biol., 2022)

Oscillator death in coupled biochemical oscillators. - Tomás Gedeon; Breschine Cummins (Math. Control. Signals Syst., 2023)

Subnetwork inclusion and switching of multilevel Boolean networks preserve parameter graph structure and dynamics. - William Duncan; Breschine Cummins; Tomás Gedeon (Frontiers Appl. Math. Stat., 2024)

An introduction to collaborative filtering through the lens of the Netflix Prize. - Jacob Munson; Breschine Cummins; Dominique Zosso (Knowl. Inf. Syst., 2025)