Bree Cummins

Expanded stoichiometric model of chondrocyte metabolism: response to cyclical shear and compressive loading

This study develops a stoichiometric model of chondrocyte metabolism to examine how cyclical shear and compressive loading affect matrix protein synthesis, revealing sex-dependent differences and nitrogen limitations.

Multistability and predominant double-positive states in a four node mutually repressive network: a case study of Th1/Th2/Th17/T-reg differentiation

The paper studies a four-node mutually repressive network, showing it allows for six stable double-positive states and applies this to explain Th1/Th2/Th17/Treg differentiation.

Assessing biological network dynamics: Comparing numerical simulations with analytical decomposition of parameter space

The paper compares two methods for analyzing gene regulatory network dynamics, finding strong agreement between parameter sampling and combinatorial analysis despite differing assumptions about model parameters.

Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop

This paper introduces DART, a DBTL loop for synthetic genetic circuit design, showing that complex circuits can be more robust and reproducible than simpler ones in budding yeast.

Computational Prediction of Synthetic Circuit Function Across Growth Conditions

The paper develops a computational method to predict synthetic circuit robustness across growth conditions and validates it with experimental results in budding yeast.

Experimental Guidance for Discovering Genetic Networks through Iterative Hypothesis Reduction on Time Series

The paper introduces a computational pipeline to identify core genetic networks from time-series data by iteratively reducing hypotheses, validated on synthetic and yeast cell-cycle data.

Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes

The paper identifies core gene regulatory network components across species by analyzing transcriptome dynamics, revealing shared features in GRNs controlling periodic biological processes.

Highly-Automated, High-Throughput Replication of Yeast-based Logic Circuit Design Assessments

The paper replicates yeast-based logic circuit design assessments using a high-throughput robotic framework, generating more flow cytometry data than the original study.