Chris John Myers

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.

The paper investigates factors affecting genetic circuit performance and develops a model to predict performance under untested conditions.

SeqImprove helps authors create FAIR sequence data by using ML to extract and annotate sequence information from their work, which they can then review and edit before submission.

The paper introduces XDC, a tool that connects digital repositories for experimental data and metadata using standard formats, enabling reproducible and exchangeable datasets.

The paper introduces an Excel-SBOL Converter that facilitates bidirectional conversion between Excel templates and SBOL, enhancing usability of SBOL standards in synthetic biology workflows.

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.

This paper introduces a method to encode dynamic FBA models in SBML, enabling exchange and simulation of hybrid models across tools.

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

This paper analyzes weighted stochastic simulation methods for rare event estimation in biology and finds they are generally ineffective, suggesting the need for new methods.

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

The paper introduces the SBOL Visual 2 Ontology to standardize the mapping of genetic elements to visual glyphs, facilitating tool development and integration with biological standards.

The paper introduces SBOL-OWL, an ontology that enables machine-readable semantic representation of synthetic genetic circuits, enhancing computational tools' ability to understand and validate designs.