Bryan Bartley

Ontology-driven software engineering using LLMs for knowledge graphs in engineering biology

The paper presents an ontology-driven approach using LLMs to create software libraries for knowledge graphs in engineering biology, demonstrating it with the SBOL3 Ontology and sbol-script library.

Building an Open Representation for Biological Protocols

The paper introduces PAML, an open protocol representation language for biological protocols, enabling precise interpretation, automation, and reuse across different contexts.

Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop

This paper introduces DART, a DBTL loop for synthetic genetic circuit design, showing that complex circuits can be more robust and reproducible than simpler ones in budding yeast.

Computational Prediction of Synthetic Circuit Function Across Growth Conditions

The paper develops a computational method to predict synthetic circuit robustness across growth conditions and validates it with experimental results in budding yeast.

Highly-Automated, High-Throughput Replication of Yeast-based Logic Circuit Design Assessments

The paper replicates yeast-based logic circuit design assessments using a high-throughput robotic framework, generating more flow cytometry data than the original study.

Data Representation in the DARPA SD2 Program

The paper describes challenges in scientific collaboration and presents a flexible data-sharing model to improve information flow and experimentation in multidisciplinary research.

Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)

The paper demonstrates how the SBOL standard can represent multicellular biological systems, enabling better sharing of complex designs across multiple cells.

Verification of genetic engineering in yeasts with nanopore whole genome sequencing

The paper introduces Prymetime, a workflow for accurate whole genome sequencing of engineered yeasts, showing it can assemble and annotate synthetic parts and detect unintended modifications.