Mark Weston

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.

Prediction of Whole-Cell Transcriptional Response with Machine Learning

The paper introduces a machine learning model to predict whole-cell transcriptional responses to combinations of perturbations using data from single inducers.

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.