Timothy J. Rudge

Self-generated environmental feedback drives traveling waves of gene expression in bacterial colonies

The paper shows that bacterial colonies generate traveling waves of gene expression driven by self-generated environmental feedback during growth and development.

Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories

The paper introduces XDC, a tool that connects digital repositories for experimental data and metadata using standard formats, enabling reproducible and exchangeable datasets.

Phase-based genetic logic circuits

The paper designs and models phase-based genetic logic gates and circuits, demonstrating their feasibility and robustness to molecular noise.

LOICA: Logical Operators for Integrated Cell Algorithms

LOICA is a Python package for modeling genetic circuits using object-oriented design, linking high-level designs to experimental data via SynBioHub and Flapjack.

Accurate reconstruction of dynamic gene expression and growth rate profiles from noisy measurements

The paper introduces a method to accurately reconstruct dynamic gene expression and growth rate profiles from noisy measurements, showing it is more accurate than existing approaches.

Flapjack: a data management and analysis tool for genetic circuit characterization

Flapjack is a tool for managing and analyzing genetic circuit data to support the DBTL cycle by organizing measurements and metadata for model parameterization and prediction.

Phase space characterization for gene circuit design

The paper introduces a method to characterize gene circuit dynamics using phase space and shows that expression rates are context-dependent but follow piecewise linear dynamics.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

The paper describes a low-cost, open-source multi-fluorescence imaging system for teaching and research, capable of imaging from single colonies to entire plates.