Jeffrey J. Czajka

ChatGEM: An Agentic Architecture Enabling Interactive Simulation of Genome-Scale Metabolic Models

ChatGEM enables interactive simulation of genome-scale metabolic models via natural language, improving performance and reducing execution time for complex tasks.

CRISPR-Cas9/Cas12a Systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger

This paper compares CRISPR-Cas9 and Cas12a systems for genome editing and large fragment deletions in Aspergillus niger, showing Cas12a's higher efficiency with single gRNA and both systems achieving 100% efficiency with two gRNAs.

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

BayFlux quantifies metabolic fluxes and their uncertainty using Bayesian inference, showing genome-scale models reduce flux uncertainty compared to core models and improve knockout predictions.

Optimizing a High Performing Multiplex-CRISPRi P. putida strain with Integrated Metabolomics and 13C-Metabolic Flux Analyses

The paper optimizes a P. putida strain for indigoidine production using 13C-MFA and metabolomics, identifying key metabolic bottlenecks and engineering improvements.