The paper introduces TMSE-BioCRNpyler, a library for mechanistic modeling of toehold-mediated strand exchange circuits, validated against existing models and supporting interoperability with standard formats.

bioRxiv · Jul 23, 2026 · PreprintBioengineering

High-throughput DNA engineering by mating bacteria

Takeshi Matsui, Po-Hsiang Hung, Mei Han, Xianan Liu, Fangfei Li, John Collins, Weiyi Li, Darach Miller, Neil Wilson, Esteban Toro, Geoffrey J. Taghon, Gavin J. Sherlock, Sasha F. Levy

This paper introduces SCRIVENER, a bacterial mating-based DNA assembly platform that enables high-throughput, low-error DNA construction of up to 23 kb constructs.

Cell Systems · Jul 1, 2026Peer-reviewedSynthetic Biology

SimpleFold-Turbo: Adaptive Inference Caching Yields 14-fold Acceleration of Flow-Matching Protein Structure Prediction

Geoffrey J. Taghon

SimpleFold-Turbo accelerates protein structure prediction by 9-14x using adaptive caching with minimal quality loss.

bioRxiv · Apr 10, 2026 · PreprintBioinformatics

Experimental evaluation of AI-driven protein design risks using safe biological proxies

Svetlana P. Ikonomova, Bruce J. Wittmann, Fernanda Piorino, David J. Ross, Samuel W. Schaffter, Olga B Vasilyeva, Eric Horvitz, James Diggans, Elizabeth A. Strychalski, Sheng Lin‐Gibson, Geoffrey J. Taghon

This study evaluates the risks of AI-driven protein design by testing synthetic homologs against biosecurity screening software.

bioRxiv · May 15, 2025 · PreprintSynthetic Biology