Manish Kushwaha

The paper develops a phagemid toolbox for tunable DNA communication in bacterial consortia by characterizing replication dynamics and optimizing transfer efficiency.

This paper develops a phage-mediated CRISPRi system for intercellular communication in bacterial consortia, enabling multicellular logic gates with up to 7 cells and 3 inputs.

Autoencoder design plus a roughly 24-hour cell-free screen tested 500 candidates over five rounds, finding 30 functional AMPs; six were broad-spectrum with no resistance emerging in E. coli.

Galaxy-SynBioCAD provides an automated pipeline for synthetic biology design and engineering, achieving an 83% success rate in retrieving validated pathways.

PeroxiHUB is a cell-free biosensing platform that detects metabolites by converting them into H2O2 using enzymatic transducers, enabling modular and scalable detection.

The paper develops a synthetic communication system using phage M13 to study genetic exchange in E. coli and discovers an extracellular immunity factor that reduces infection rates by 70%.

This paper develops exonuclease-deficient cell-free extracts and optimized buffers to enable robust expression from unprotected linear DNA without additional protection strategies.

The paper introduces metabolic perceptrons for binary classification of metabolite combinations using computational models and experimental validation in synthetic biological circuits.