Michael Lynch

This study improves ethylene glycol production from xylose in E. coli using two-stage dynamic control, achieving 140 g/L in 70 hours with 92% theoretical yield.

This paper introduces a Gluconate-Bypass in E. coli to decouple central metabolism from catabolite repression, enabling robust co-consumption of multiple lignocellulosic sugars.

This paper introduces a gluconate-bypass platform to enhance stationary-phase biomanufacturing in E. coli by decoupling glucose uptake from pyruvate inhibition and co-generating NADPH, achieving high product titers.

This paper develops a foundation model for microbial growth dynamics using self-supervised learning on diverse datasets, enabling accurate reconstruction and prediction of growth patterns and antibiotic responses.

This paper describes a systems engineering approach to improve the scalable and robust production of nanobodies in E. coli through dynamic control of reduction potential and two-stage purification.

The paper develops 2-stage microfermentation protocols for high-throughput evaluation of engineered E. coli strains for producing various products.

This paper describes an improved bioprocess for producing Q-Griffithsin, a clinical-stage antiviral, using integrated autolysis, DNA hydrolysis, and precipitation to achieve high purity and yield without conventional chromatography.

The paper analyzes CRISPR-Cas9 datasets to identify two inhibitory secondary structures in gRNAs and provides free energy cutoffs to guide future gRNA design.

This paper demonstrates that dynamic deregulation of central metabolism in E. coli improves process robustness and scalability for industrial chemical production.

This paper describes a method for rapidly producing and purifying Taq polymerase using engineered E. coli strains with autoinducible expression and simplified purification steps.

The paper examines how genomic context affects gRNA activity across species and highlights limitations of current gRNA prediction algorithms.

The paper introduces an online tool for techno-economic analysis of bioprocesses, enabling researchers to evaluate commercial competitiveness based on process parameters and strain engineering outcomes.

This paper introduces a multi-agent directed evolution approach that identifies hidden mutations by using multiple substrates, improving enzyme engineering efficiency.

The paper shows that the Cas1/2 endonuclease complex in E. coli causes instability in CRISPR/Cascade guide arrays, and controlled expression of the Cascade operon improves stability.

This paper describes a method to improve protein expression and purification in E. coli by inducing autolysis and DNA/RNA hydrolysis via phage lysozyme and endonuclease, achieving >90% protein release.

This paper describes an improved method for recombinant protein expression in E. coli using phosphate depletion to trigger autoinduction, achieving high protein titers across various scales.

The paper tests the robustness of PhoB-regulated promoters in E. coli across different media and identifies promoters with consistent expression for two-stage autoinduction.