Samuel W. Schaffter

Towards interoperable modeling of toehold-mediated strand exchange circuits across DNA nanotechnology and engineering biology

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.

Comparative Transcriptomic Analysis of Perfluoroalkyl Substances-Induced Responses of Exponential and Stationary Phase Escherichia coli

This study uses RNA sequencing to compare the transcriptional responses of Escherichia coli to PFAS and non-fluorinated compounds across growth phases, revealing distinct gene expression changes induced by PFAS.

Cell-free systems enable mechanistic characterization of genetically encoded RNA strand exchange circuits for programmable protein expression, logic, and biosensing

This study uses cell-free systems to characterize RNA circuits for programmable protein expression, logic, and biosensing, revealing design principles applicable across different environments.

Genetically encoded RNA strand exchange circuits for programmable protein expression and computation in cells

This study demonstrates genetically encoded RNA strand exchange circuits in living cells, showing that in vitro TMSE design principles apply to E. coli but with cellular-specific caveats.

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

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

Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity

The paper develops an RT-qPCR method to accurately measure context-dependent ribozyme activity by inhibiting cleavage during cDNA synthesis.

Design approaches to expand the toolkit for building cotranscriptionally encoded RNA strand displacement circuits

The paper expands the toolkit for building ctRSD circuits by characterizing 220 gate sequences and identifying design approaches to improve reliability and scalability.

Co-transcriptional RNA strand displacement circuits

This paper introduces co-transcriptional RNA strand displacement circuits that are programmable and scalable for molecular computing in biological systems.