John P. Marken

This paper introduces flux-species sampling (FSS) to explore biocircuit behavior by directly sampling steady-state species and fluxes, improving the identification of regulatory modes and behavior-realizing regimes.

The paper measures repression curves of genetic NOT gates in E. coli under growth and arrest conditions, finding growth arrest reduces unrepressed expression by >100-fold.

This study identifies a novel mechanism by which E. coli Nissle 1917 colonizes the nematode Steinernema hermaphroditum through immune cell interactions and cuticle persistence.

This study develops engineered sentinel plants that detect belowground microbial activity through an aboveground signal, enabling noninvasive monitoring of soil microbial processes.

This paper develops a framework for addressable and adaptable DNA messaging in engineered consortia, enabling targeted message transfer and dynamic recipient list updates.

The paper evaluates three OD calibration protocols for bacterial cell count estimation and recommends serial dilution of silica microspheres for its precision and compatibility with flow cytometry.

The paper introduces a theoretical framework for analyzing genetic circuit dynamics, focusing on structural properties to predict bistability and oscillations in biological systems.

The paper develops a system for packet-based intercellular communication in bacteria using plasmid conjugation with gRNA-based addressing and integrase-mediated message editing.

The paper introduces a modular genetic system that controls gene expression response time by adjusting protein degradation rates using tags with varying protease affinities.

This study quantifies how the genetic insulator RiboJ increases expression of downstream genes, showing twofold to tenfold increases in protein abundance and twofold increases in transcript abundance depending on promoter strength.